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Investigating the determinants of the reproductive biology of fishes is an essential component of fisheries research. Tilapia breeding patterns were investigated to determine the impact of non‐native Oreochromis niloticus on the native congeneric Oreochromis macrochir in the upper Kabompo River in the Northwest of Zambia using the gonadosomatic index and the sex ratios. Oreochromis niloticus was the most abundant fish caught (221, 63.5%) than O. macrochir (127, 36.5%). Results showed that the overall gonadosomatic index means of O. macrochir in both sections were similar. Oreochromis macrochir bred in December and February–March, with no reproduction in June. However, O. niloticus in the invaded section indicated all year reproduction through reduced spawning in May–June, with increased spawning activity in February–March. The sex ratio (females: males) was 1:1.3 and 1:1.7 for O. niloticus and O. macrochir, respectively, and both significantly deviated from the sex ratio of 1:1 (ꭓ2 = 8.42 and 9.37, p

The increasing numbers of infected cases of coronavirus disease 2019 (COVID‐19) caused by severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) poses serious threats to public health and the global economy. Most SARS‐CoV‐2 neutralizing antibodies target the receptor binding domain (RBD) and some the N‐terminal domain (NTD) of the spike protein, which is the major antigen of SARS‐CoV‐2. While the antibody response to RBD has been extensively characterized, the antigenicity and immunogenicity of the NTD protein are less well studied. Using 227 plasma samples from COVID‐19 patients, we showed that SARS‐CoV‐2 NTD‐specific antibodies could be induced during infection. As compared to the results of SARS‐CoV‐2 RBD, the serological response of SARS‐CoV‐2 NTD is less cross‐reactive with SARS‐CoV, a pandemic strain that was identified in 2003. Furthermore, neutralizing antibodies are rarely elicited in a mice model when NTD is used as an immunogen. We subsequently demonstrate that NTD has an altered antigenicity when expressed alone. Overall, our results suggest that while NTD offers a supplementary strategy for serology testing, it may not be suitable as an immunogen for vaccine development., Receptor binding domain (RBD) of the SARS‐CoV‐2 spike protein has been extensively studied in functional antibody screening and COVID‐19 vaccine design. To explore the function of N‐terminal domain (NTD) of spike protein, we reveal that NTD is a supplementary antigen for serology testing, but not a suitable immunogen for vaccine design.

Tooth shape is used to differentiate between morphologically similar species of vertebrates, including fish. This study aimed to quantify tooth shape of three sympatric species: Haplochromis kamiranzovu, H. insidiae, and H. astatodon endemic to Lake Kivu, whose existing identification criteria are currently only qualitative. A quantitative tooth shape analysis was performed based on digitized tooth outline data with a subsequent elliptic Fourier analysis to test for differences among the three species. We looked at crown shape and size differences within H. kamiranzovu and H. insidiae at geographical, habitat, and gender levels. No comparison at habitat level was done for H. astatodon because it is found only in littoral zone. The analysis revealed significant tooth shape differences among the three species. Haplochromis astatodon had a significantly longer major cusp height and a longer and larger minor cusp than that of H. insidiae. It had also a longer major cusp height and a longer and larger minor cusp than that of H. kamiranzovu. Tooth shape differences of H. kamiranzovu and H. insidiae species were not significantly different between littoral and pelagic fish (p > .05) while differences were significant between southern and northern Lake Kivu populations (p .05). Tooth shape was also significantly different with sharp teeth for males compared with females of southern populations versus northern ones. These shape‐ and size‐related differences between sexes suggest differences in the foraging strategies toward available food resources in the lake habitat. Further research should explain the genetic basis of the observed pattern., We quantified tooth shape trait to distinguish the three morphological similar Haplochromis kamiranzovu, H. insidiae, and H. astatodon) endemic to Lake Kivu.

Background and aim We validated a modified risk algorithm based on the Asia-Pacific Colorectal Screening (APCS) score that included body mass index (BMI) for prediction of advanced neoplasia. Methods Among 5744 Chinese asymptomatic screening participants undergoing a colonoscopy in Hong Kong from 2008 to 2012, a random sample of 3829 participants acted as the derivation cohort. The odds ratios for significant risk factors identified by binary logistic regression analysis were used to build a scoring system ranging from 0 to 6, divided into "average risk" (AR): 0; "moderate risk" (MR): 1-2; and "high risk" (HR): 3-6. The other 1915 subjects formed a validation cohort, and the performance of the score was assessed. Results The prevalence of advanced neoplasia in the derivation and validation cohorts was 5.4% and 6.0%, respectively (P = 0.395). Old age, male gender, family history of colorectal cancer, smoking, and BMI were significant predictors in multivariate regression analysis. A BMI cut-off at > 23 kg/m2 had better predictive capability and lower number needed to screen than that of > 25 kg/m2 . Utilizing the score developed, 8.4%, 57.4%, and 34.2% in the validation cohort were categorized as AR, MR, and HR, respectively. The corresponding prevalence of advanced neoplasia was 3.8%, 4.3%, and 9.3%. Subjects in the HR group had 2.48-fold increased prevalence of advanced neoplasia than the AR group. The c-statistics of the modified score had better discriminatory capability than that using predictors of APCS alone (c-statistics = 0.65 vs 0.60). Conclusions Incorporating BMI into the predictors of APCS score was found to improve risk prediction of advanced neoplasia and reduce colonoscopy resources.

Summary This paper presents a careful investigation of the three popular calibration weighting methods: (i) generalised regression; (ii) generalised exponential tilting and (iii) generalised pseudo empirical likelihood, with a major focus on computational aspects of the methods and some empirical evidences on calibrated weights. We also propose a simple weight trimming method for range-restricted calibration. The finite sample behaviour of the weights obtained by the three calibration weighting methods and the effectiveness of the proposed weight trimming method are examined through limited simulation studies.

Site-specific recombinases (SSRs) mediate efficient manipulation of DNA sequences in vitro and in vivo. In particular, serine integrases have been identified as highly effective tools for facilitating DNA inversion, enabling the design of genetic switches that are capable of turning the expression of a gene of interest on or off in the presence of a SSR protein. The functional scope of such circuitry can be extended to biological Boolean logic operations by incorporating two or more distinct integrase inputs. To date, mathematical modelling investigations have captured the dynamical properties of integrase logic gate systems in a purely qualitative manner, and thus such models are of limited utility as tools in the design of novel circuitry. Here, the authors develop a detailed mechanistic model of a two-input temporal logic gate circuit that can detect and encode sequences of input events. Their model demonstrates quantitative agreement with time-course data on the dynamics of the temporal logic gate, and is shown to subsequently predict dynamical responses relating to a series of induction separation intervals. The model can also be used to infer functional variations between distinct integrase inputs, and to examine the effect of reversing the roles of each integrase on logic gate output.

Ectopic pancreas located in the mediastium is an extremely rare anomaly. We present a case of an ectopic pancreas located in a giant mediastinal cyst in an 18-year-old man. He presented with symptoms of dyspnea due to external compression of the cyst on the left main bronchus. Complete surgical resection was performed through median sternotomy, with relief of the bronchial compression postoperatively. Literature review showed 20 previously reported cases. These masses were usually large (>10 cm), almost exclusively located in the anterior mediastinum, predominately cystic in nature and generally benign. Surgical resection was performed in all reported cases with a favorable prognosis. Due to the size of these masses, operative treatment can be challenging and should be carefully planned, with specific considerations regarding anesthetic and surgical management.

Background Bardet‐Biedl syndrome (BBS) is an autosomal recessive pleiotropic disorder of the primary cilia that leads to severe visual loss in the teenage years. Approximately 80% of BBS cases are explained by mutations in one of the 21 identified genes. Documented causative mutation types include missense, nonsense, copy number variation (CNV), frameshift deletions or insertions, and splicing variants. Methods Whole genome sequencing was performed on a patient affected with BBS for whom no mutations were identified using clinically approved genetic testing of the known genes. Analysis of the WGS was done using internal protocols and publicly available algorithms. The phenotype was defined by retrospective chart review. Results We document a female affected with BBS carrying the most common BBS1 mutation (BBS1: Met390Arg) on the maternal allele and an insertion of a ~1.7‐kb retrotransposon in exon 13 on the paternal allele. This retrotransposon insertion was not automatically annotated by the standard variant calling protocols used. This novel variant was identified by visual inspection of the alignment file followed by specific genome analysis with an available algorithm for transposable elements. Conclusion This report documents a novel mutation type associated with BBS and highlights the importance of systematically performing transposon detection analysis on WGS data of unsolved cases.

Replication-based variance estimation methods including the bootstrap, balanced repeated replication, and the Jackknife have been studied extensively. They have been applicable primarily to stratified multistage sampling designs in which the clusters within strata are sampled with replacement or the first-stage sampling fraction is negligible with a notable exception of a two-stage cluster sampling with equal probability and without replacement in Rao & Wu (1988). It is common practice, however, that the first-stage sampling fraction may not be negligible, resulting in overestimation. To alleviate this practical issue, we derive the balanced repeated replication methods and the bootstrap methods for one- and two-stage stratified unequal probability sampling, where the sampling fractions are not negligible. The asymptotic property of the proposed methods is studied. In addition, the methodologies are applied to a simulated population with characteristics of a real sample survey. The Canadian Journal of Statistics 41: 696-716; 2013 © 2013 Statistical Society of Canada Resume Les methodes d'estimation de la variance fondees sur le reechantillonnage ont ete largement etudiees, y compris les methodes du bootstrap, du reechantillonnage a repliques equilibrees et du Jackknife. Celles-ci sont generalement applicables a des plans d’echantillonnage stratifies a plusieurs degres dans lesquels soit les grappes sont tirees avec remise au sein des strates, soit la fraction d’echantillonnage du premier degre est negligeable, mais avec l'exception notable d'un echantillonnage en grappes a deux degres equiprobable et sans remise presente par Rao et Wu (1988). Cependant, il est courant que la fraction d’echantillonnage du premier degre ne soit pas negligeable, ce qui induit une surestimation. Pour contourner ce probleme, les auteurs derivent les methodes de reechantillonnage a repliques equilibrees et de bootstrap pour un echantillonnage stratifie a probabilites d'inclusion inegales et a un et deux degres, ou les fractions d’echantillonnage ne sont pas negligeables. Les auteurs examinent les proprietes asymptotiques des methodes proposees et appliquent cette methodologie a une population simulee possedant les caracteristiques d'un sondage reel. La revue canadienne de statistique 41: 696-716; 2013 © 2013 Societe statistique du Canada

BACKGROUND: By using genome-wide methylation screening, the authors identified ring finger protein 180 (RNF180) as preferentially methylated in cancer. This study was undertaken to clarify its structure and functional role in gastric cancer. METHODS: The transcription start site and core functional promoter region of RNF180 were revealed by 5′ rapid amplification of cDNA ends and luciferase activity assays. Promoter methylation was detected by combined bisulfite restriction analysis and bisulfite genomic sequencing. Cell growth was detected by colony formation assay, apoptosis by annexin V assay, and RNF180 target genes by cDNA microarray. RESULTS: The authors revealed the transcription start site of RNF180 gene and identified the functional core promoter region (−202/+372) in the CpG island, which could be silenced by in vitro methylation assay. RNF180 was silenced in 6 of 7 gastric cancer cell lines and significantly down-regulated in primary gastric cancers compared with adjacent normal tissues (P = .001). Loss of gene expression was associated with promoter methylation. Re-expression of RNF180 suppressed cell growth (P < .001) and induced apoptosis (P < .05), which were mediated by up-regulating the antiproliferation regulators MTSS1 and CDKN2A and the proapoptotic mediator TIMP3. Promoter methylation of RNF180 was detected in 76% (150 of 198) of primary gastric cancers and 55% (11 of 20) of intestinal metaplasia, but in none of 23 normal gastric tissues. Methylated RNF180 DNA was detected in the plasma of 56% of gastric cancer patients, but not in healthy controls (P = .003). Patients with low or loss of RNF180 expression had significantly poorer overall survival. CONCLUSIONS: RNF180 is a novel potential tumor suppressor in gastric carcinogenesis and has potential clinical utility as a biomarker for gastric cancer patients. Cancer 2012;. © 2011 American Cancer Society.

Disseminated peritoneal leiomyomatosis (DPL) is a rare condition characterized by scattered smooth muscle nodules over the peritoneal surfaces. The pathogenesis of DPL remains unclear. Herein, we report a case of DPL occurring 7 years after laparoscopic supracervical hysterectomy with morcellation for uterine leiomyomata (UL). We analyzed both the original UL and the subsequent DPL by molecular cytogenetics to assess the role of chromosomal abnormalities in DPL pathobiology. Interestingly, all of the chromosomal aberrations detected in this case of DPL, including r(1)(p34.3q41), del(3)(q23q26.33), and t(12;14)(q14.3;q24.1), are characteristic chromosomal abnormalities detected in UL. Fluorescence in situ hybridization analysis of the initial UL confirmed an interstitial deletion spanning at least 3q24 and 3q25.1, suggesting that functional alteration of a potential gene in this chromosomal region may play a role in DPL development from UL. With the increasing rate of hysterectomy through laparoscopic approach to UL, the unique complications of laparoscopy with morcellation, especially seeding and proliferation of tumor cells over abdominal organs and peritoneum, are becoming more significant and may necessitate review of current surgical protocols to prevent future seeding of the pelvic region with tumor particles.

To evaluate the effect of SMN2 copy number on disease severity in spinal muscular atrophy (SMA), we stratified 45 adult SMA patients based on SMN2 copy number (3 vs. 4 copies). Patients with 3 copies had an earlier age of onset and lower spinal muscular atrophy functional rating scale (SMAFRS) scores and were more likely to be non-ambulatory. There was, however, no difference between the groups in quantitative muscle strength or pulmonary function testing. Functional scale may be a more discriminating outcome measure for SMA clinical trials.