Successive observation of fatigue crack initiation process was conducted on six types of thermally simulated HAZ microstructures to clarify the physical significance of fatigue life difference between coarse grain (CG) and fine grain (FG) heat-affected zone (HAZ) microstructures. The results showed the fatigue life-decreasing mechanism in the CGHAZ to be successfully explained by acceleration of the shear mode fatigue crack growth rate provided the crack is smaller than the prior austenite grain size, based on the following experimental results. In other words, the fatigue cracks initiated along the shear stress plane. In addition, the prior austenite grain size of crack initiation life with the FG and CGHAZ were comparable, since the shear mode fatigue crack growth rate of the CGHAZ was faster than that of the FGHAZ. As a result, the remaining fatigue life after the grain size crack initiation of the CGHAZ become shorter than that of the FGHAZ as a function of grain size difference.

The interval $j=[-1,1]$ turns into an Abelian group $\cA(\cJ)$ under the group operation $x+_\cJ y:=(x+y)(1+xy)^{-1},\qquad x,y\in\cJ$. This enables definition of the invariant measure $d_\cJ x=(1-x^2)^{-1}dx$ and the Fourier transform $\cF_\cJ$ on the interval $\cJ$ and, as a consequence, we can consider Fourier convolution operators $W^0_{\cJ,\cA}:=\cF_\cJ^{-1}\cA\cF_\cJ$ on $\cJ$. This class of convolutions includes celebrated Prandtl, Tricomi and Lavrentjev-Bitsadze equations and, also, differential equations of arbitrary order with the natural weighted derivative $\fD_\cJ u(x)=-(1-x^2)u’(x)$, $t\in\cJ$. Equations are solved in the scale of Bessel potential $\bH^s_p(\cJ,d_\cJ x)$, $1\leqslant p\leqslant\infty$, and H\”older-Zygmound $\bZ^\nu(\cJ,(1-x^2)^\mu)$, $0<\mu,\nu<\infty$ spaces, adapted to the group $\cA(\cJ)$. Boundedness of convolution operators (the problem of multipliers) is discussed. The symbol $\cA(\xi)$, $\xi\in\bR$, of a convolution equation $W^0_{\cJ,\cA}u=f$ defines solvability: the equation is uniquely solvable if and only if the symbol $\cA$ is elliptic. The solution is written explicitely with the help of the inverse symbol. We touch shortly the multidimensional analogue-the Abelian group $\cA(\cJ^n)$.

One of the beautiful and very simple inequalities for a convex function is the Hermit-Hadamard inequality [S. Mehmood, et. al. Math. Methods Appl. Sci., 44 (2021) 3746], [S. Dragomir, et. al., Math. Methods Appl. Sci., in press]. The concept of log-convexity is a stronger property of convexity. Recently, the refined Hermit-Hadamard’s inequalities for log-convex functions were introduced by researchers [C. P. Niculescu, Nonlinear Anal. Theor., 75 (2012) 662]. In this paper, by the Hermit-Hadamard inequality, we introduce two parametric Tsallis quantum relative entropy, two parametric Tsallis-Lin quantum relative entropy and two parametric quantum Jensen-Shannon divergence in quantum information theory. Then some properties of quantum Tsallis-Jensen-Shannon divergence for two density matrices are investigated by this inequality. \newline \textbf{Keywords:} \textit{ Hermit-Hadamard’s inequality; log-convexity; Density matrices; Quantum relative entropy; Tsallis quantum relative entropy; quantum Jensen-Shannon divergence divergence.

Background: Coronavirus disease 2019 (COVID-19) is commonly complicated with coagulopathy presented with venous thromboembolism and arterial thromboses. The aim of this study was to evaluate the effect of routine thromboprophylaxis with low molecular weight heparin (LMWH) on clinical outcomes including mortality and need for intensive care unit (ICU) admission in hospitalized COVID-19 patients. Methods: All confirmed patients with COVID-19 hospitalized to COVID-19 dedicated wards, from March 15 to May 15, 2020, were included in this retrospective cohort study. Two groups of patients were established, according to the non-routine and routine application of LMWH with therapeutic, weight-based, anticoagulation dosing. Clinical, laboratory and treatment data were collected, analyzed and compared between the two groups. A logistic regression model was developed to assess the factors related to in-hospital adverse outcomes. Results: A total of 1511 patients (797 men, median age 59.0 years) were retrospectively analyzed (Group non-routine LMWH (n=828); group routine LMWH (n=683)). Multivariate logistic regression analysis showed routine use of LMWH, favipiravir administration, extreme values of WBC count, NLR, and troponin I as factors independently associated with in-hospital adverse outcomes (OR=0.25, 95% CI: 0.83-0.91; p<0.001 for routine use of LMWH). Conclusion: Routine thromboprophylaxis with LMWH reduced mortality and ICU admission in patients admitted with COVID-19 infection.

Background and Purpose: Endothelin-1 (ET-1) and Nucleotide Oligomerization Domain-Like Receptor Family, Pyrin Domain Containing 3 (NLRP3) play an essential role in erectile dysfunction. ET-1 and NLRP3 activate inflammatory processes by increasing calcium (Ca2+) and reactive oxygen species (ROS). In the present study, we hypothesized that endothelin receptors (ETA and ETB) stimulation, through increased calcium and ROS formation, leads to NLRP3 activation. Experimental approach: Intracavernosal pressure (ICP/MAP) was measured in C57BL/6 (WT) mice. Functional and immunoblotting assays were performed in corpora cavernosa (CC) strips from WT, NLRP3-/- and caspase-/- mice after ET-1 (100 nM) stimulation in the presence of vehicle, MCC950, tiron, BAPTA AM, BQ123, or BQ788. Key Results: ET-1 gradually reduced the ICP/MAP in WT mice, and MCC950 administration prevented the effect of ET-1. ET-1 decreased CC relaxation to ACh and sodium nitroprusside (SNP) and increased caspase-1 protein expression, effects reversed by the ETA receptor antagonist BQ123. The ETB receptor antagonist BQ788 also reversed the effect of ET-1 on ACh and SNP relaxation. Additionally, tiron, BAPTA AM, and NLRP3 genetic deletion prevented the ET-1-induced loss of ACh and SNP relaxation. Moreover, BQ123 diminished CC caspase-1 expression, while BQ788 increased caspase-1 and IL-1β levels in a concentration-dependent manner (100 nM to 10 µM). Furthermore, tiron and BAPTA AM prevented ET-1-induced increase in caspase-1. In addition, BAPTA AM blocked ET-1-induced ROS generation. Conclusion and Implications: NLRP3 activation contributes to acute ET-1-induced erectile dysfunction by mechanisms that depend on ETA- and ETB-induced Ca2+ influx and ROS generation.

Objective: Dexmedetomidine (DEX) is a highly selective α2-adrenoceptor agonist that is increasingly used in the daily practice of intensive care units (ICUs) with its sedative, analgesic, anxiolytic, and immunoprotective effects. In this study, we aimed to analyze whether Dexmedetomidine improves the outcomes in patients treated in ICU. Design: A retrospective study Place and Duration of Study: Intensive care units (ICU) of Sakarya University Training and Research Hospital, Sakarya, Turkey, from October 2020 to February 2021 Methodology: The medical records of the patients were analyzed retrospectively. We included 134 patients in the study, in 45 of whom the treatment regimen included dexmedetomidine and 89 of whom were not treated with dexmedetomidine. Patients treated with DEX were defined as the “patient group”, whereas patients not treated with DEX were defined as “control group” and the parameters were compared between these groups. Obtained data were analyzed in the biostatistical program. Results: The median age of all patients was 64 and 62.7% of them were male. No significant difference was found between the groups in terms of median ages (p>0.05). The patients with diabetes mellitus (DM), congestive heart failure (CHF), and undergoing insulin treatment were significantly less treated with DEX (p=0.04, p=0.03, and p=0.016 respectively) whereas intravenous immunoglobulin (IVIG) therapy was found to be more frequently applied to the patient group (p=0.043). The median duration between ICU admission and the time of intubation was 4 days for the control group whereas it was 1 day for the patient group and the difference was strongly significant (p=0.000, p<0.001). The other analyses concerning lab parameters, mortality rates, intubation rates and durations, applied treatments, and comorbidities revealed no significant difference between the groups. Conclusion: Our study revealed that DEX therapy can help us to gain time before intubation however can not reduce mortality rates in severe COVID-19.

Aspirin has known effects beyond inhibiting platelet cyclooxygenase-1 (COX1) that have been incompletely characterized. Transcriptomics can comprehensively characterize the on- and off-target effects of medications. We used a systems pharmacogenomics approach of aspirin exposure in volunteers coupled with serial platelet function and purified platelet mRNA sequencing to test the hypothesis that aspirin’s effects on the platelet transcriptome are associated with platelet function. We prospectively recruited 74 adult volunteers for a randomized cross over study of 81- vs. 325 mg/day, each for 4 weeks. Using mRNA sequencing of purified platelets collected before and after each 4-week exposure, we identified 208 aspirin-responsive genes with no evidence for dosage effects. In independent cohorts of healthy volunteers and patients with diabetes we validated aspirin’s effects on five genes: EIF2S3, CHRNB1, EPAS1, SLC9A3R2, and HLA-DRA. Functional characterization of the effects of aspirin on mRNA as well as platelet ribosomal RNA demonstrated that aspirin may act as an inhibitor of protein synthesis. Database searches for small molecules that mimicked the effects of aspirin on platelet gene expression in vitro identified aspirin but no other molecules that share aspirin’s known mechanisms of action. The effects of aspirin on platelet mRNA were correlated with higher levels of platelet function both at baseline and after aspirin exposure – an effect that counteracts aspirin’s known antiplatelet effect. In summary, this work collectively demonstrates a dose-independent effect of aspirin on the platelet transcriptome that counteracts the well-known antiplatelet effects of aspirin.

For the numerical solution of singularly perturbed second-order parabolic partial differential equation of one dimensional convection-diffusion type with long time delays arising in control theory, a novel class of fitted operator finite difference methods is constructed using non-standard finite difference methods. Since the two parameters; time lag and perturbation parameters are sources for the simultaneous occurrence of time-consuming and high speed phenomena of the physical systems that depends on the present and past history, our study here is to capture the effect of the two parameters on the boundary layer. The spatial derivative is suitably replaced by a difference operator followed by the time derivative is replaced by the Crank-Nicolson based scheme. A second-order parameter-uniform error bounds are established to provide numerical results.

Understanding the soil and water conservation (SWC) impact of steep-slope agricultural practices (e.g. terraces) has arguably never been more relevant than today, in the face of widespread intensifying rainfall conditions. In northern Italy, a diverse mosaic of terraced and non-terraced cultivation systems have historically developed from local traditions and more recently from the introduction of machinery. Previous studies suggested that each vineyard configuration is characterised by a specific set of soil degradation patterns. However, an extensive analysis of SWC impacts by different vineyard configurations is missing, while this is crucial for providing robust guidelines for future-proof viticulture. Here, we provide a unique extensive comparison of SWC in 50 vineyards, consisting of 10 sites of 5 distinct practices: slope-wise cultivation (SC), contour cultivation (CC), contour terracing (CT), broad-base terracing (BT) and diagonal terracing (DT). A big-data analysis of physical erosion modelling based on high-resolution LiDAR data is performed, while four predefined SWC indicators are systematically analysed and statistically quantified. Regular contour terracing (CT) ranked best across all indicators, reflecting a good combination of flow interception and homogeneous distribution of runoff and sediment under intense rainfall conditions. The least SWC-effective practices (SC, CC, and DT) were related to vineyards optimised for trafficability by access roads or uninterrupted inter-row paths, which create high upstream-downstream connectivity and are thus prone to flow accumulation. The novel large-scale approach of this study offers a robust comparison of SWC impacts under intense rainstorms, which is becoming increasingly relevant for sustainable future management of such landscapes.

Hypothyroidism causing rhabdomyolysis is a known but an uncommon entity. Hashimoto's thyroiditis causing rhabdomyolysis in the absence of precipitating factors is even rarer. Here we report a 42- year-old previously healthy male with hypothyroidism due to Hashimotos thyroiditis complicated by severe rhabdomyolysis and acute kidney injury.

To our knowledge,this is the first report of 31 Y F has no family history and usually,patients do not manifest symptoms if they are heterozygous.Individuals heterozygous for C282Y who have a coexisting insult to the liver,associated with the use of medications,may present with overt manifestations of iron overload.

Introduction: Today, whereas hypoxemia and respiratory failure is the major challenging problem in the course of severe COVID-19 pneumonia, to control the disease at a mild-moderate stage or to stop the inflammation by recognizing the cytokine storm early should be the most prominent goal. We aimed to reveal the clinical efficacy and safety of short-term high-dose corticosteroids in severe COVID-19. Material and Methods: This retrospective observational study consisted of 54 patients who were given high-dose steroid (HDS (>250 mg/day methylprednisolone, 3 days.). Low-dose steroid (LDS) therapy (dexamethasone 8 mg ) was applied to all patients. HDS group was reviewed in terms of decreasing hospital mortality and preventing fibrosis development in follow-up. Results: During the observation period, out of 317 severe COVID-19 pneumonia hospitalized, HDS and LDS were administered to 54 and 216 patients, respectively. Higher body mass index, younger age, more oxygen need of patients at admission, and more need for advanced oxygen therapy during hospitalization were found in the HDS group (p<0.001). Furthermore, 18.5% of patients in the HDS group had need transfer to the intensive care unit whereas it was 3.8% in LDS (p<0.001). Additionally, the mortality rate was determined higher in the HDS group (25. 9% vs 9.9%, p<0.001). The HDS group had lower saturated O2 [IQR, 85% (76-89), p <0.001], and higher ferritin at admission. It was found that HDS was given simultaneously with the increased ferritin with deepening lymphopenia on the third and fifth days. There was no difference in fibrosis development between HDS patients receive and not (15.4% vs 26.2%, p=0.11) Conclusion: The use of HDS in hospitalized COVID-19 patients remains unclear. Along with this, our study demonstrated the use of high-dose corticosteroids might not be associated with a lower mortality rate among hospitalized severe COVID-19 patients.

Background: During the current ongoing COVID-19 pandemic, studies had reported that patients with asthma would experience increased asthma-associated morbidity because of the respiratory virus SARS-CoV-2 infection, based on experience with other respiratory viral infections. However, some studies suggested that there was no apparent increase in asthma related morbidity in children with asthma, it is even possible that due to reduced exposures due to confinement, such children may have improved outcomes. In order to understand the impact of Covid-19 on asthma control in children, we performed this systematic review and meta-analysis. Methods: We searched PubMed, Embase, and Cochrane Library to find literature from December 2019 to June 2021 related to Covid-19 and children’s asthma control, among which results such as abstracts, comments, letters, reviews and case reports were excluded. The level of asthma control during the COVID-19 pandemic was synthesized and discussed. Results: A total of 20456 subjects were included in 7 studies. Random effect model is used to account for the data. Compared to the same period before the COVID-19 pandemic, asthma exacerbation, asthma admission, emergency room visit reduced a lot. The outcome of use of inhaled corticosteroids and Beta-2 agonists shows no significant difference. Conclusion: Compared to the same period before the COVID-19 pandemic and the measures in response to it, the level of asthma control has been significantly improved. We need to understand the exact factors leading to these improvements and find methods to sustain it.

INTRODUCTION: The aim of this study was to investigate the important factors affecting the COPD prognosis. MATERIAL AND METHODS: We included 160 hospitalized patients with COPD exacerbation in the study. Hemoglobin-HB, hematocrit-HCT, leukocyte, red cell distribution width- RDW, mean platelet volume, platelet distribution width, plateletcrit, platelet, neutrophil / lymphocyte ratio, platelet / lymphocyte ratio, eosinophil, uric acid, albumin, CRP, procalcitonin, arterial blood gases (PO2, PCO2) pulmonary function test (FEV1, FVC), echocardiography (ejection fraction-EF) GOLD stage, MMRC and BORG scales, Charlson comorbidity index, body mass index-BMI, length of hospital stay were examined on the first day of hospitalization. Admission to the hospital with a new attack, hospitalization in the intensive care unit-ICU, and mortality during the 6 months after discharge were evaluated. RESULTS: High CRP and procalcitonin values were observed in the group with long hospital stay. In mortality group, HB, HCT, BMI and PO2 values were significantly lower than the group without mortality while age and GOLD stage were higher. The age, BORG and MMRC scores, number of exacerbations experienced in the previous 1 year, RDW, eosinophil count, PCO2 were significantly higher in the ICU group than without ICU. HCT, EF values were lower in the ICU group than without ICU. FEV1, FVC values were significantly lower in follow-up attack group than without attack; the duration of COPD and the number of experienced in the previous 1 year were high. CONCLUSION: It has been concluded that the scoring combining selected biomarkers and other factors will be stronger in determining the prognosis.

Background: Various variants of the covid-19 have started to attract attention recently. The clinical course of these variants and possible predictive parameters are being investigated. This study aimed to examine the relationship between thiol levels, which are indicators of oxidative stress, and variant covid-19 types. Methods: In this cross-sectional study, patients with a diagnosis of classic covid-19 and patients with a diagnosis of variant covid-19 with mild and moderate symptoms followed in the clinical observatory of Ankara city hospital were included in the study group. The patients were divided into two groups according to the covid-19 type as variant and classic covid-19, and a healthy control group is added for comparison. A complete blood count and thiol analysis are performed from the venous blood samples. Obtained results were compared between groups, and the ROC analysis is performed. Results: Thiol levels were significantly lower in patients with a diagnosis of Covid-19 compared to the control group. In terms of WBC, lymphocyte, neutrophil, NLR, ferritin and thiol parameters, patients with variant covid-19 differed significantly from patients with a classic covid-19 diagnosis. Thiol levels’ cut-off values to distinguish between variant covid-19 patients and control group from classical covid-19 patients were almost identical (423 and 422 µmol/L, respectively). Conclusions: It seems possible to use thiol as a sensitive, specific and cost-effective marker to suspect variant covid-19 cases. Since this study is probably the first example in this subject, it would form a basis for further studies. Keywords: Covid-19, SARS-CoV-2, variant covid-19, thiol, oxidative stress.

The transcription machinery of archaea can be roughly classified as a simplified version of eukaryotic organisms. The basal transcription factor machinery binds to the TATA-box found around 28 nucleotides upstream of the transcription start site; however, some transcription units lack a clear TATA-box and still have TBP/TFB binding over them. This apparent absence of conserved sequences could be a consequence of sequence divergence associated with the upstream region, operonic and gene organization. Furthermore, earlier studies have found that a structural analysis gains more information compared to a simple sequence inspection. In this work, we evaluated and coded 3630 archaeal promoter sequences of three organisms, Haloferax volcanii, Thermococcus kodakarensis, and Sulfolobus solfataricus into DNA duplex stability, enthalpy, curvature, and bendability parameters. We also split our dataset into conserved TATA and degenerated TATA promoters in order to identify differences among these two classes of promoters. The structural analysis reveals variations in archaeal promoters’ architecture, i.e., a distinctive signal is observed in the TFB, TBP, and TFE binding sites independently of these being TATA-conserved or TATA-degenerated. In addition, the promoter encountering method was validated with upstream regions of 13 other archaea, suggesting that there might be promoter sequences among them. Therefore, we suggest a novel method for locating promoters within the genome of archaea based on energetic/structural features.

The case report by Sicim et al. is the placement of extra-anatomical bypasses in bilateral common carotid arteries. The similar previous reports of the extra-anatomical bypass usually indicate unilateral bypass. Whether or not the Willis' circle is incomplete is difficult to judge during emergency surgery, and the authors' judgment seems to have been correct in the sense that it could maintain cerebral perfusion reliably and quickly. The direct perfusion and extraanatomical bypass of carotid artery is a reasonable strategy in patients with cerebral malperfusion.

Mucopolysaccharidoses (MPSs) are rare, heterogeneous inborn errors of metabolism (IEM) diagnosed through a combination of clinical, biochemical, and genetic investigations. The aim of this study was molecular characterization of the largest cohort of Iranian MPS patients (302 patients from 289 unrelated families), along with tracking their ethnicity and geographical origins. 185/289 patients were studied using an IEM-targeted NGS panel followed by complementary Sanger sequencing, which led to the diagnosis of 154 MPS patients and 5 non-MPS IEMs (diagnostic yield: 85.9%). Furthermore, 106/289 patients who were referred with positive findings went through re-analysis and confirmatory tests which confirmed MPS diagnosis in 104. Among the total of 258 MPS patients, 225 were homozygous, and 9 had copy number variations, and 90 had novel variants. MPS IV was the most common type (34.8%) followed by MPS I (22.7%) and MPS VI (22.5%). Geographical origin analysis unveiled a pattern of distribution for frequent variants in ARSB (c.430G>A, c.962C>T, c.281C>A), GALNS (c.319G>A, c.860C>T, c.1042A>G), and IDUA (c.1A>C, c.1598C>G). Our extensive patient cohort reveals the genetic and geographic landscape of MPS in Iran, which provides insight into the genetic epidemiology of MPS and can facilitate a more cost-effective, time-efficient diagnostic approach based on the region-specific variants.

Hemophagocytic lymphohistiocytosis (HLH) is a potentially fatal syndrome of immune dysregulation that is classified into primary and secondary forms. The standard of care is established with dexamethasone and etoposide, but there are currently no guidelines for refractory HLH or cases triggered by infection or malignancy. [1] We describe here a series of pediatric patients with malignancy-associated HLH (m-HLH) to discuss the complexities in the initial diagnostic considerations, the balance of therapeutic regimens and their toxicities, and the novel use of emapalumab and ruxolitinib in patients with refractory disease.

Essential thrombocythemia is chronic myeloproliferative neoplasia, as defined by WHO in 2016, with the best prognosis. A small percentage of ET cases can be considered Familial ET. In this report we describe 6 cases of Familial ET, evaluating the heterogeneity of the mutational state and the clinical presentation.

Spontaneous pseudoaneurysm of the aortic arch is an exceptionally rare and potentially life-threatening condition.Diagnosis of pseudoaneurysms of the aortic arch mainly depends on imaging examinations.Contrast-enhanced echocardiography, as a non-invasive, bed-side and radiation-free tool, plays an important role in the rapid diagnosis and postoperative follow-up of pseudoaneurysms of the aortic arch.

Protein allergens is a health risk for consumption of soybeans. To understand allerginicity mechanism, T cell epitopes of 7 soybean allergens were predicted and screened by abilities to induce cytokine interleukin 4. The relationships among amino acid composition, properties, allergenicity and pepsin hydrolysis sites were analyzed. Among the 138 T cell epitopes identified, YIKDVFRVIPSEVLS, KDVFRVIPSEVLSNS, DVFRVIPSEVLSNSY of Gly m 6.0501 (P04347), and AKADALFKAIEAYLL, ADALFKAIEAYLLAH of Gly m 4.0101 (P26987) were the most possible epitope candidates. In T cell epitopes pattern, the frequencies of amino acids Q, D, E, P and G decreased, while F, I, N, V, K and H increased. Hydrophobic residues at positions p1 and p2 and positively charged residues in positions p13 might contribute to allergenicity. Most of epitopes could be hydrolyzed by pepsin into small polypeptides within 12 residues length, and the anti-digestive epitope regions contained I, V, S, N, and Q residues. T cell epitopes EEQRQQEGVIVELSK from Gly m 5.03 (P25974) showed resistantence to pepsin hydrolysis and would cause a higher Th2 cell response. This research provides basis for the development of hypoallergenic soybean products in the soybean industry as well as for the immunotherapy design for protein allergy.

Sex-specific ecology has management implications, but rapid sex-chromosome turnover in fishes hinders development of markers to sex monomorphic species. Here, we use annotated genomes and reduced-representation sequencing data for two Australian percichthyids, the Macquarie perch Macquaria australasica and the golden perch M. ambigua, and whole genome resequencing data for 50 Macquarie perch of each sex, to detect sex-linked loci, identify a candidate sex-determining gene and develop an affordable sexing assay. In-silico pool-seq tests of 1,492,004 Macquarie perch SNP loci revealed that a 275-Kb scaffold, containing the transcription factor SOX1b gene, was enriched for gametologous loci. Within this scaffold, 22 loci were sex-linked in a predominantly XY system, with females being homozygous at all 22, and males being heterozygous at two or more. Seven XY-gametologous loci were within a 146-bp region. Being ~38 Kb upstream of SOX1b, it might act as an enhancer controlling SOX1b transcription in the bipotential gonad that drives gonad differentiation. A PCR-RFLP sexing assay, targeting one of the Y-linked SNPs, tested in 66 known-sex Macquarie perch and two individuals of each sex of three confamilial species, and amplicon sequencing of 400 bp encompassing the 146-bp region, revealed that the few sex-linked positions differ between species and between Macquarie perch populations. This indicates sex-chromosome lability in Percichthyidae, also supported by non-homologous scaffolds containing sex-linked loci for Macquarie- and golden perches. The resources developed here will facilitate genomic research in Percichthyidae. Sex-linked markers will be useful for determining genetic sex in some populations and studying sex chromosome turnover.

Predicting the quaternary structure of protein complex is an important problem. Inter-chain residue-residue contact prediction can provide useful information to guide the ab initio reconstruction of quaternary structures. However, few methods have been developed to build quaternary structures from predicted inter-chain contacts. Here, we introduce a gradient descent optimization algorithm (GD) to build quaternary structures of protein dimers utilizing inter-chain contacts as distance restraints. We evaluate GD on several datasets of homodimers and heterodimers using true or predicted contacts. GD consistently performs better than a simulated annealing method and a Markov Chain Monte Carlo simulation method. Using true inter-chain contacts as input, GD can reconstruct high-quality structural models for homodimers and heterodimers with average TM-score ranging from 0.92 to 0.99 and average interface root mean square distance (I-RMSD) from 0.72 Å to 1.64 Å. On a dataset of 115 homodimers, using predicted inter-chain contacts as input, the average TM-score of the structural models built by GD is 0.76. For 46% of the homodimers, high-quality structural models with TM-score >= 0.9 are reconstructed from predicted contacts. There is a strong correlation between the quality of the reconstructed models and the precision and recall of predicted contacts. If the precision or recall of predicted contacts is >20%, GD can reconstruct good models for most homodimers, indicating only a moderate precision or recall of inter-chain contact prediction is needed to build good structural models for most homodimers. Moreover, the accuracy of reconstructed models positively correlates with the contact density in dimers.