Pashto poetry generation: deep learning with pre-trained transformers for low-resource languages.

Generating poetry using machine and deep learning techniques has been a challenging and exciting topic of research in recent years. It has significance in natural language processing and computational linguistics. This study introduces an innovative approach to generate high-quality Pashto poetry by leveraging two pre-trained transformer models, LaMini-Cerebras-590M and bloomz-560m. The models were trained on an extensive new and quality Pashto poetry dataset to learn the underlying complex patterns and structures. The trained models are then used to generate new Pashto poetry by providing them with a seed text or prompt. To evaluate the quality of the generated poetry, we conducted both subjective and objective evaluations, including human evaluation. The experimental results demonstrate that the proposed approach can generate Pashto poetry that is comparable in quality to human-generated poetry. The study provides a valuable contribution to the field of Pashto language and poetry generation and has potential applications in natural language processing and computational linguistics.

Sequence variants underlying severe combined immunodeficiency and leukocyte adhesion deficiency type 1 in six consanguineous families.

Inborn errors of immunity (IEI) are defined as genetic disorders affecting the immune system and resulting in diverse clinical signs and symptoms. Despite the lack of diagnosis and unavailability of IEI estimation in the Pakistani population, consanguinity is exacerbating its prevalence. The current study focuses on severe combined immunodeficiency (SCID) and leukocyte adhesion deficiency type 1 (LAD1). SCID is associated with the life-threatening symptoms developing at post-birth. LAD1 is clinically characterized by recurrent bacterial infections related to the skin, mouth, and respiratory tract owing to impaired leukocytes. Herein, in six consanguineous families, flow cytometry was used to evaluate the patient's immune status. Whole-exome sequencing (WES) was then conducted to search for the causative variations in immunodeficiency genes. Sanger sequencing was used to assess the segregation of the variants with the disorder within the families. Sequence analysis revealed five homozygous variants in four different causative genes. This included four novel nonsense variants in CD70 p.(Thr126Profs*33), CD3e p.(Trp151*), IL7R p.(Val138Ilefs*10), and ITGB2 p.(Ser627Valfs*61), and one previously reported in ITGB2 p.(Cys62*). In one of the families, two variants in two different genes, including DNAH6 p.(Tyr2653His) and NIPAL4 p.(Gly121Ser), were detected in an unclassified patient. All the identified variants were found in a homozygous state in the patient but in a heterozygous state in the available parents. The study will facilitate the diagnosis and management of IEI patients.

Novel pathogenic variants in HR underlie atrichia with papular lesions in a cohort of 10 families.

Atrichia with papular lesions (APL) is a hair abnormality characterized by loss of hair on the scalp and rest of the body. In a few cases, hair loss is accompanied by the appearance of keratotic papules on the body. It is inherited in an autosomal recessive manner. Sequence variants in the HR (hairless) gene are responsible for this hair abnormality. Here, we present nine consanguineous families and one nonconsanguineous family with clinical manifestations of APL. Whole exome followed by Sanger sequencing and/or direct Sanger sequencing was performed to identify pathogenic variants. The study revealed seven novel pathogenic variants c.794del;p.(Pro265Argfs*98), c.2921-2936del;p.(Tyr974Leufs*16), c.2889C>A;p.(Cys963*), c.2689C>T;p.(Gln897*), c.3186_3187dup;p.(Gln1063Profs*43), c.560dup;p.(Tyr188Ilefs*131), c.2203+5G>C, c.2776+5G>A, and the previously reported variant c.1837C>T;p.(Arg613*) in HR in these families. The study not only expands the mutational spectrum in the HR gene but also highlights the unusual phenotypic findings and will facilitate genetic counseling of families with members showing various types of hair loss disorders in the local population.

Clinical and genetic investigation of 14 families with various forms of short stature syndromes.

Skeletal dysplasias are a heterogeneous group of disorders presenting mild to lethal defects. Several factors, such as genetic, prenatal, and postnatal environmental may contribute to reduced growth. Fourteen families of Pakistani origin, presenting the syndromic form of short stature either in the autosomal recessive or autosomal dominant manner were clinically and genetically investigated to uncover the underlying genetic etiology. Homozygosity mapping, whole exome sequencing, and Sanger sequencing were used to search for the disease-causing gene variants. In total, we have identified 13 sequence variants in 10 different genes. The variants in the HSPG2 and XRCC4 genes were not reported previously in the Pakistani population. This study will expand the mutation spectrum of the identified genes and will help in improved diagnosis of the syndromic form of short stature in the local population.

Inter-observer and intra-observer agreement of cervical vertebral maturation staging: A systematic review and meta-analysis.

INTRODUCTION: The accurate assessment of active growth is pivotal for the correction of skeletal malocclusion in growing patients. Cervical vertebral maturation (CVM) staging is easy and devoid of unnecessary radiation, but its inter- and intra-observer agreement is still debatable. OBJECTIVE: This study aims to assess inter-observer (reliability) and intra-observer agreement (reproducibility) for CVM staging. METHODS: A comprehensive literature search across five databases up to October 2023 was conducted. Inclusion criteria comprised observational studies that specifically reported intra-rater, inter-rater, or both agreements as their primary objectives for cervical vertebral maturation (CVM) staging. Studies with a sample size exceeding 15 participants were considered for inclusion. After duplicate study selection, data extraction, and risk-of-bias assessment, random-effects meta-analyses of kappa (k)/correlation coefficient (r) and their 95% confidence intervals (CIs) were performed, followed by meta-regressions, sensitivity analyses, and subgroup analyses. RESULTS: Seventeen observational studies (comprising 1437 lateral cephalograms and 110 assessors) were included. The reliability (8 studies; k=0.62 [95% CI: 0.44, 0.78]) and reproducibility (9 studies; k=0.708 [95% CI: 0.59, 0.82]) were substantial. The inter-observer correlation was almost perfect (in 9 studies; r=0.86 [95% CI: 0.82, 0.89]) while intra-observer correlation was substantial (in 2 studies; r=0.75 [95% CI: 0.62, 0.84]). Tracing of lateral cephalograms significantly increased inter-observer reliability (ß=0.29 [0.57, 0.0031]) but cropping and time of assessment (initial vs. follow-up) had no significant impact. The reliability (P<0.001) and reproducibility (P=0.049) of high-quality studies were superior to those observed in low-quality studies. CONCLUSION: Assessment of the CVM staging is accurate and reproducible to a satisfactory level. The accuracy and reproducibility of CVM are higher in studies utilizing traced cephalograms and those with a low-risk of bias. REGISTRATION: PROSPERO registration (CRD42023468521). Data is openly available at https://doi.org/10.5281/zenodo.10599129.

Mutational analysis in different genes underlying severe combined immunodeficiency in seven consanguineous Pakistani families.

BACKGROUND: Severe Combined Immunodeficiency (SCID) is an autosomal recessive inborn error of immunity (IEI) characterized by recurrent chest and gastrointestinal (GI) infections and in some cases associated with life-threatening disorders. METHODOLOGY AND RESULTS: This current study aims to unwind the molecular etiology of SCID and also extended the patients' phenotype associated with identified particular variants. Herein, we present 06 disease-causing variants identified in 07 SCID-patients in three different SCID related genes. Whole Exome Sequencing (WES) followed by Sanger Sequencing was employed to explore genetic variations. The results included identification of two previously reported heterozygous variants in homozygous form for the first time in RAG1gene [(p.Arg410Gln);(p.Arg737His)], followed by a recurrent variant (p.Trp959*) in RAG1, a novel variant in IL2RG (p.Asp48Lfs*24), a recurrent variant in IL2RG (p.Gly271Glu) and a recurrent variant in DCLRE1C (p.Arg191*) gene. CONCLUSION: To conclude, the immune-profiling and WES revealed two novel, two as homozygous state for the first time, and two recurrent disease causing variants contributing valuably to our existing knowledge of SCID.

Utilizing the drug repurposing strategy on current drugs: new leads for peptic ulcers via biochemical and biomolecular dynamics studies.

The hyperactivity of urease enzymes plays a crucial role in the development of hepatic coma, hepatic encephalopathy, urolithiasis, gastric and peptic ulcers. Additionally, these enzymes adversely impact the soil's nitrogen efficiency for crop production. In the current study 100 known drugs were tested against Jack Bean urease and Proteus mirabilis urease and identified three inhibitors i.e. terbutaline (compound 1), Ketoprofen (compound 2) and norepinephrine bitartrate (compound 3). As a result, these compounds showed excellent inhibition against Jack Bean urease i.e. (IC50 = 2.1-11.3 µM), and Proteus mirabilis urease (4.8-11.9 µM). Moreover, in silico studies demonstrate maximum interactions of compounds in the enzyme's active site. Furthermore, intermolecular interactions between compounds and enzyme atoms were examined using STD-NMR spectrophotometry. In parallel, molecular dynamics simulation was carried out to study compounds dynamic behavior within the urease binding region. Urease remained stable during most of the simulation time and ligands were bound in the protein active pocket as observed from the Root mean square deviation (RMSD) and ligand RMSD analyses. Furthermore, these compounds display interactions with the crucial residues, including His492 and Asp633, in 100 ns simulations. In the binding energy analysis, norepinephrine bitartrate exhibited the highest binding energy (-76.32 kcal/mol) followed by Ketoprofen (-65.56 kcal/mol) and terbutaline (-62.15 kcal/mol), as compared to acetohydroxamic acid (-52.86 kcal/mol). The current findings highlight the potential of drug repurposing as an effective approach for identifying novel anti-urease compounds.Communicated by Ramaswamy H. Sarma.

Artemisinin resistance mutations in Pfcoronin impede hemoglobin uptake.

Artemisinin (ART) combination therapies have been critical in reducing malaria morbidity and mortality, but these important drugs are threatened by growing resistance associated with mutations in Pfcoronin and Pfkelch13 . Here, we describe the mechanism of Pfcoronin -mediated ART resistance. Pf Coronin interacts with Pf Actin and localizes to the parasite plasma membrane (PPM), the digestive vacuole (DV) membrane, and membrane of a newly identified preDV compartment-all structures involved in the trafficking of hemoglobin from the RBC for degradation in the DV. Pfcoronin mutations alter Pf Actin homeostasis and impair the development and morphology of the preDV. Ultimately, these changes are associated with decreased uptake of red blood cell cytosolic contents by ring-stage Plasmodium falciparum . Previous work has identified decreased hemoglobin uptake as the mechanism of Pfkelch 13-mediated ART resistance. This work demonstrates that Pf Coronin appears to act via a parallel pathway. For both Pfkelch13 -mediated and Pfcoronin -mediated ART resistance, we hypothesize that the decreased hemoglobin uptake in ring stage parasites results in less heme-based activation of the artemisinin endoperoxide ring and reduced cytocidal activity. This study deepens our understanding of ART resistance, as well as hemoglobin uptake and development of the DV in early-stage parasites.

A variant in sperm-specific glycolytic enzyme enolase 4 (ENO4) causes human male infertility.

BACKGROUND: Although defects in sperm morphology and physiology lead to male infertility, in many instances, the exact disruption of molecular pathways in a given patient is often unknown. The glycolytic pathway is an essential process to supply energy in sperm cell motility. Enolase 4 (ENO4) is crucial for the glycolytic process, which provides the energy for sperm cells in motility. ENO4 is located in the sperm principal piece and is essential for the motility and organization of the sperm flagellum. In the present study, we characterized a family with asthenozoospermia and abnormal sperm morphology as a result of a variant in the enolase 4 (ENO4) gene. METHODS: Computer-assisted semen analysis, papanicolaou smear staining and scanning electron microscopy were used to examine sperm motility and morphology for semen analysis in patients. For genetic analysis, whole-exome sequencing followed by Sanger sequencing was performed. RESULTS: Two brothers in a consanguineous family were being clinically investigated for sperm motility and morphology issues. Genetic analysis by whole-exome sequencing revealed a homozygous variant [c.293A>G, p.(Lys98Arg)] in the ENO4 gene that segregated with infertility in the family, shared by affected but not controls. CONCLUSIONS: In view of the association of asthenozoospermia and abnormal sperm morphology in Eno4 knockout mice, we consider this to be the first report describing the involvement of ENO4 gene in human male infertility. We also explore the possible involvement of another variant in explaining other phenotypic features in this family.

Sequence variants in different genes underlying Bardet-Biedl syndrome in four consanguineous families.

BACKGROUND: Bardet-Biedl Syndrome (BBS) is a rare (1:13,500-1-160,000) heterogeneous congenital disorder, characterized by postaxial polydactyly, obesity, hypogonadism, rod-cone dystrophy, cognitive impairment, and renal abnormalities (renal cystic dysplasia, anatomical malformation). To date about twenty-five genes have been identified to cause BBS, which accounts for about 80% of BBS diagnosis. METHODS: In the current study, we have performed mutational screening of four Pakistani consanguineous families (A-D) with clinical manifestation of BBS by microsatellite-based genotyping and whole exome sequencing. RESULTS: Analysis of the data revealed four variants, including a novel/unique inheritance pattern of compound heterozygous variants, p.(Ser40*) and p.(Thr259Leufs*21), in MKKS gene, novel homozygous variant, p.(Gly251Val)] in BBS7 gene and two previously reported p.(Thr259Leufs*21) in MKKS and p.(Met1Lys) in BBS5 gene. The variants were found segregated with the disorder within the families. CONCLUSION: The study not only expanded mutations spectrum in the BBS genes, but this will facilitate diagnosis and genetic counselling of families carrying BBS related phenotypes in Pakistani population.

A variant in the LDL receptor-related protein encoding gene LRP4 underlying polydactyly and phalangeal synostosis in a family of Pakistani origin.

A family of Pakistani origin, segregating polydactyly, and phalangeal synostosis in an autosomal dominant manner, has been investigated and presented in the present report. Whole-exome sequencing (WES), followed by segregation analysis using Sanger sequencing, revealed a heterozygous missense variant [c.G1696A, p.(Gly566Ser)] in the LRP4 gene located on human chromosome 11p11.2. Homology protein modeling revealed the mutant Ser566 generated new interactions with at least four other amino acids and disrupted protein folding and function. Our findings demonstrated the first direct evidence of involvement of LRP4 in causing polydactyly and phalangeal synostosis in the same family. This study highlighted the importance of inclusion of LRP4 gene in screening individuals presenting polydactyly in hands and feet, and phalangeal synostosis in the same family.

Src- and Abl-family kinases activate spleen tyrosine kinase to maximize phagocytosis and Leishmania infection.

Leishmania spp. are obligate intracellular parasites that must be internalized by phagocytic cells to evade immune responses and cause disease. The uptake of both Leishmania promastigotes (insect-stage parasites) and amastigotes (proliferative-stage parasites in humans and mice) by phagocytes is thought to be mainly host cell driven, not parasite driven. Our previous work indicates that host Src- and Abl-family kinases facilitate Leishmania entry into macrophages and pathogenesis in murine cutaneous leishmaniasis. Here, we demonstrate that host spleen tyrosine kinase (SYK) is required for efficient uptake of Leishmania promastigotes and amastigotes. A Src-family kinase-Abl-family kinase-SYK signaling cascade induces Leishmania amastigote internalization. Finally, lesion size and parasite burden during Leishmania infection is significantly decreased in mice lacking SYK in monocytes or by treatment with the SYK inhibitor entospletinib. In summary, SYK is required for maximal Leishmania uptake by macrophages and disease in mice. Our results suggest potential for treating leishmaniasis using host cell-directed agents.

Thiourea derivatives inhibit key diabetes-associated enzymes and advanced glycation end-product formation as a treatment for diabetes mellitus.

This study was designed to screen novel thiourea derivatives against different enzymes, such as α-amylase, α-glucosidase, protein tyrosine phosphatase 1 B, and advanced glycated end product (AGEs). A cytotoxicity analysis was performed using rat L6 myotubes and molecular docking analysis was performed to map the binding interactions between the active compounds and α-amylase and α-glucosidase. The data revealed the potency of five compounds, including E (1-(2,4-difluorophenyl)-3-(3,4-dimethyl phenyl) thiourea), AG (1-(2-methoxy-5-(trifluoromethyl) phenyl)-3-(3-methoxy phenyl) thiourea), AF (1-(2,4-dichlorophenyl)-3-(4-ethylphenyl) thiourea), AD (1-(2,4-dichlorophenyl)-3-(4-ethylphenyl) thiourea), and AH (1-(2,4-difluorophenyl)-3-(2-iodophenyl) thiourea), showed activity against α-amylase. The corresponding percentage inhibitions were found to be 85 ± 1.9, 82 ± 0.7, 75 ± 1.2, 72 ± 0.4, and 65 ± 1.1%, respectively. These compounds were then screened using in vitro assays. Among them, AH showed the highest activity against α-glucosidase, AGEs, and PTP1B, with percentage inhibitions of 86 ± 0.4% (IC50  = 47.9 µM), 85 ± 0.7% (IC50  = 49.51 µM), and 85 ± 0.5% (IC50  = 79.74 µM), respectively. Compound AH showed an increased glucose uptake at a concentration of 100 µM. Finally, an in vivo study was conducted using a streptozotocin-induced diabetic mouse model and PTP1B expression was assessed using real-time PCR. Additionally, we examined the hypoglycemic effect of compound AH in diabetic rats compared to the standard drug glibenclamide.

Compliance To Colonoscopy In Patients Visiting The Department Of Gastroenterology At Lady Reading Hospital, Peshawar.

Background: Colorectal cancer is the largest cause of mortality in patients admitted to any Gastroenterology units. Diagnostic colonoscopy is a valuable tool for the disease's diagnosis and proper treatment but its compliance has been historically low. Our main objective was to find out social, cultural, and psychological barriers among those patients who finally did not show up for their colonoscopy appointment and, make a comparative analysis with those who did. Methods: A cross-sectional study was conducted in the Lady Reading Hospital, Peshawar from October 2021 to March 2022, selecting 224 patients through consecutive sampling. Results: Out of the 224 patients included, males (48.2%) were more likely to show up for the procedure than females (51.8%) (p<0.05). Overall, the most recurring barrier was a lack of knowledge with 116 (51.7%) for both the groups, but especially more for the non-compliant patients (p<0.05). Fear of results, fear of complications of the procedure, and affordability issues stood out as important differences between the compliant and non-compliant patients. Conclusion: For the country's healthcare to be able to overcome these problems, and enter an era where screening colonoscopy is a norm, mass education regarding the issue is imperative.

Partial differential equations modeling of thermal transportation in Casson nanofluid flow with arrhenius activation energy and irreversibility processes.

The formation of entropy in a mixed convection Casson nanofluid model with Arhenius activation energy is examined in this paper using magnetohydrodynamics (MHD). The expanding sheet, whose function of sheet velocity is nonlinear, confines the Casson nanofluid. The final equations, which are obtained from the first mathematical formulations, are solved using the MATLAB built-in solver bvp4c. Utilizing similarity conversion, ODEs are converted in their ultimate form. A number of graphs and tabulations are also provided to show the effects of important flow parameters on the results distribution. Slip parameter was shown to increase fluid temperature and decrease entropy formation. On the production of entropy, the Brinkman number and concentration gradient have opposing effects. In the presence of nanoparticles, the Eckert number effect's augmentation of fluid temperature is more significant. Furthermore, a satisfactory agreement is reached when the findings of the current study are compared to those of studies that have been published in the past.

Finite Element Methodology of Hybridity Nanofluid Flowing in Diverse Wavy Sides of Penetrable Cylindrical Chamber under a Parallel Magnetic Field with Entropy Generation Analysis.

In a cylindrical cavity, the convection and entropy of the hybrid nanofluid were studied. We have introduced a rectangular fin inside the cylinder; the fin temperature is at Th. The right waving wall is cooled to Tc. The upper and lower walls are insulated. This study contains the induction of a constant magnetic field. The Galerkin finite element method (GFEM) is utilized to treat the controlling equations obtained by giving Rayleigh number values between Ra (103-106) and Hartmann number ratio Ha (0, 25, 50, 100) and Darcy ranging between Da (10-2-10-5) and the porosity ratio is ε (0.2, 0.4, 0.6, 0.8), and the size of the nanoparticles is ϕ (0.02, 0.04, 0.06, 0.08). The range is essential for controlling both fluid flow and the heat transport rate for normal convection. The outcomes show how Da affects entropy and leads to a decline in entropy development. The dynamic and Nusselt mean diverge in a straight line. The domain acts in opposition to the magnetic force while flowing. Highest entropy-forming situations were found in higher amounts of Ra, Da, and initial values of Ha. Parameters like additive nanoparticles (ϕ) and porosity (ε) exert diagonal dominant trends with their improving values.

A novel homozygous variant in homologous recombination repair gene ZSWIM7 causes azoospermia in males and primary ovarian insufficiency in females.

Infertility is a common, clinically heterogeneous reproductive disorder worldwide with a prevalence of about 15%. To date about eighty genes have been discovered to cause non-syndromic infertility, affecting males and females equally, though traditionally the genetic analysis of each group has been conducted separately. Here, we report the clinical and genetic characterization of a consanguineous family of Pakistani origin with multiple individuals, including male and female, affected with infertility. Males exhibited non-obstructive azoospermia whereas females had primary ovarian insufficiency. Whole exome sequencing revealed a missense variant [c.176C > T, p. (Ser59Leu)] in the ZSWIM7 gene which functions in homologous recombination repair. The variant was found in a homozygous form in all affected males and females. To our knowledge, this is the first family that has individuals affected with infertility in both sexes. This point to the utility of large consanguineous families with multiple affected siblings to reveal joint mechanisms affecting human reproduction.