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Background: We address the problem of studying recombinational variations in (human) populations. In this paper, our focus is on one computational aspect of the general task: Given two networks G1 and G2, with both mutation and recombination events, defined on overlapping sets of extant units the objective is to compute a consensus network G3 with minimum number of additional recombinations. We describe a polynomial time algorithm with a guarantee that the number of computed new recombination events is within = sz(G1, G2) (function sz is a well-behaved function of the sizes and topologies of G1 and G2) of the optimal number of recombinations. To date, this is the best known result for a network consensus problem. Results: Although the network consensus problem can be applied to a variety of domains, here we focus on structure of human populations. With our preliminary analysis on a segment of the human Chromosome X data we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. These results have been verified independently using traditional manual procedures. To the best of our knowledge, this is the first recombinations-based characterization of human populations. Conclusion: We show that our mathematical model identifies recombination spots in the individual haplotypes; the aggregate of these spots over a set of haplotypes defines a recombinational landscape that has enough signal to detect continental as well as population divide based on a short segment of Chromosome X. In particular, we are able to infer ancient recombinations, population-specific recombinations and more, which also support the widely accepted 'Out of Africa' model. The agreement with mutation-based analysis can be viewed as an indirect validation of our results and the model. Since the model in principle gives us more information embedded in the networks, in our future work, we plan to investigate more non-traditional questions via these structures computed by our methodology. [ABSTRACT FROM AUTHOR]

Pausing of RNA polymerase II (Pol II) at transcription start sites (TSSs) primes target genes for productive elongation. Coincidentally, DNA double-strand breaks (DSBs) enrich at highly transcribed and Pol II-paused genes, although their interplay remains undefined. Using androgen receptor (AR) signaling as a model, we have uncovered AR-interacting protein 4 (ARIP4) helicase as a driver of androgen-dependent transcription induction. Chromatin immunoprecipitation sequencing analysis revealed that ARIP4 preferentially co-occupies TSSs with paused Pol II. Moreover, we found that ARIP4 complexes with topoisomerase II beta and mediates transient DSB formation upon hormone stimulation. Accordingly, ARIP4 deficiency compromised release of paused Pol II and resulted in R-loop accumulation at a panel of highly transcribed AR target genes. Last, we showed that ARIP4 binds and unwinds R-loops in vitro and that its expression positively correlates with prostate cancer progression. We propose that androgen stimulation triggers ARIP4-mediated unwinding of R-loops at TSSs, enforcing Pol II pause release to effectively drive an androgen-dependent expression program. [ABSTRACT FROM AUTHOR]

RNA-binding proteins (RBPs) regulate key aspects of RNA processing including alternative splicing, mRNA degradation and localization by physically binding RNA molecules. Current methods to map these interactions, such as CLIP, rely on purifying single proteins at a time. Our new method, ePRINT, maps RBP-RNA interaction networks on a global scale without purifying individual RBPs. ePRINT uses exoribonuclease XRN1 to precisely map the 5' end of the RBP binding site and uncovers direct and indirect targets of an RBP of interest. Importantly, ePRINT can also uncover RBPs that are differentially activated between cell fate transitions, including neural progenitor differentiation into neurons., (© 2024. The Author(s).)

Trisomy karyotype occurs in 5%-10% of AML. Its mutational landscape and prognostic significance are not well defined. A cohort of 156 trisomy AML patients was analysed, with reference to 615 cytogenetically normal (CN) AML patients. Trisomy AML showed distinct mutational landscape with more prevalent SMC1A, N/KRAS, ASXL1 and BCOR but fewer CEBPA bZIP and NPM1 mutations in patients ≤60, and fewer NPM1 mutations in those >60. NRAS mutations were associated with poor outcome in trisomy AML, whereas DNMT3A and FLT3-ITD mutations had neutral effect. Trisomy AML appeared biologically distinct from CN-AML., (© 2023 British Society for Haematology and John Wiley & Sons Ltd.)

Background and Aim: While proton pump inhibitor (PPI) therapy has proven to be effective in managing gastroesophageal reflux disease (GERD), a notable portion of patients who experience GERD symptoms may not respond to this treatment. Research suggests that roughly 30% of individuals with a presumed GERD diagnosis may continue to experience symptoms, whether partially or completely, even when receiving PPI therapy. The aim of this study was to assess the treatment of gastrointestinal diseases with a novel potassium-competitive acid blocker (P-CAB), vonoprazan, in terms of its effectiveness and safety in the Pakistani population., Methods: This prospective, multicenter, observational study was conducted in Pakistan. This study included 1,642 patients from January 2023 to August 2023, aged 18 years, with gastrointestinal disorders. All demographic data, medical history, GERD severity assessment questionnaire (GerdQ), and laboratory parameters, including stool assessment for Helicobacter pylori (H. pylori), were observed. Patients were orally treated with vonoprazan at doses of 10 mg or 20 mg, once or twice daily. Statistical analysis was done by one-way ANOVA., Results: Out of 1,642 patients, 840 (51.2%) were males and 802 (48.8%) were females, with a mean age of 39.81±14.61 years. The mean GerdQ score at baseline was 20.37±15.87, 7.24±8.15 at the second week of treatment, and 3.70±6.31 at the fourth week of treatment (p<0.001). 90.74% of patients achieved H. pylori eradication. Most patients were acid regurgitation and heartburn-free for >70% of days. Most of the patients, 1,283 (78.13%), exhibited good treatment compliance. Mild adverse events were reported in 37 (2.3%) patients., Conclusions: The use of vonoprazan significantly reduced the likelihood of GERD by improving symptoms and was also highly effective in the elimination of H. pylori infections. Vonoprazan was generally well tolerated., Competing Interests: The authors have declared financial relationships, which are detailed in the next section., (Copyright © 2023, Abbasi et al.)

Background: Acute graft-versus-host disease (aGvHD) is a life-threatening complication of allogeneic hematopoietic stem cell transplantation (HSCT). Transplantation of immunosuppressive human mesenchymal stromal cells (hMSCs) can protect against aGvHD post-HSCT; however, their efficacy is limited by poor engraftment and survival. Moreover, infused MSCs can be damaged by activated complement, yet strategies to minimise complement injury of hMSCs and improve their survival are limited., Methods: Human MSCs were derived from bone marrow (BM), adipose tissue (AT) and umbilical cord (UC). In vitro immunomodulatory potential was determined by co-culture experiments between hMSCs and immune cells implicated in aGvHD disease progression. BM-, AT- and UC-hMSCs were tested for their abilities to protect aGvHD in a mouse model of this disease. Survival and clinical symptoms were monitored, and target tissues of aGvHD were examined by histopathology and qPCR. Transplanted cell survival was evaluated by cell tracing and by qPCR. The transcriptome of BM-, AT- and UC-hMSCs was profiled by RNA-sequencing. Focused experiments were performed to compare the expression of complement inhibitors and the abilities of hMSCs to resist complement lysis., Results: Human MSCs derived from three tissues divergently protected against aGvHD in vivo. AT-hMSCs preferentially suppressed complement in vitro and in vivo, resisted complement lysis and survived better after transplantation when compared to BM- and UC-hMSCs. AT-hMSCs also prolonged survival and improved the symptoms and pathological features of aGvHD. We found that complement-decay accelerating factor (CD55), an inhibitor of complement, is elevated in AT-hMSCs and contributed to reduced complement activation. We further report that atorvastatin and erlotinib could upregulate CD55 and suppress complement in all three types of hMSCs., Conclusion: CD55, by suppressing complement, contributes to the improved protection of AT-hMSCs against aGvHD. The use of AT-hMSCs or the upregulation of CD55 by small molecules thus represents promising new strategies to promote hMSC survival to improve the efficacy of transplantation therapy. As complement injury is a barrier to all types of hMSC therapy, our findings are of broad significance to enhance the use of hMSCs for the treatment of a wide range of disorders., (© 2023. The Author(s).)

Collagen VI-related myopathies are a group of disorders that cause muscle weakness and joint contractures with significant variability in disease severity among patients. Here we report the clinical and genetic characteristics of 13 Chinese patients. Detailed histological, radiological and muscle transcriptomic evaluations were also conducted for selected representative patients. Across the cohort, fifteen putative disease causal variants were identified in three genes encoding collagen VI subunits, COL6A1 (n=6), COL6A2 (n=5), and COL6A3 (n=4). Most of these variants (12/15, 80%) were dominant negative and occurred at the triple helical domain. The rest (3/15, 20%) were located at the C-terminus. Two previously unreported variants, an in-frame mutation (COL6A1:c.1084&#95;1092del) and a missense mutation (COL6A2:c.811G>C), were also noted. The transcriptome data from the muscle biopsies of two patients in the study with dominant negative mutations [COL6A2:c.811G>C and COL6A1:c.930+189C>T] supports the accepted aetiology of Collagen VI myopathy as dysfunction of the extracellular matrix. It also suggests there are perturbations to skeletal muscle differentiation and skeletal system development. It should be noted that although the phenotypes of patients can be mostly explained by the position and dominant-negative effect of the variants, exceptions and variability still exist and have to be reckoned with. This study provides valuable data explaining the varying severity of phenotypes among ethnically Chinese patients., Competing Interests: Declaration of Competing Interest The authors declare that they have no competing interests., (Copyright © 2023 The Author(s). Published by Elsevier B.V. All rights reserved.)

Identifying signals that govern the differentiation of tumor-infiltrating CD8 + T cells (CD8 + TILs) toward exhaustion can improve current therapeutic approaches for cancer. Here, we show that type I interferons (IFN-Is) act as environmental cues, enhancing terminal CD8 + T cell exhaustion in tumors. We find enrichment of IFN-I-stimulated genes (ISGs) within exhausted CD8 + T cells (Tex cells) in patients across various cancer types, with heightened ISG levels correlating with poor response to immune checkpoint blockade (ICB) therapy. In preclinical models, CD8 + TILs devoid of IFN-I signaling develop less exhaustion features, provide better tumor control, and show greater response to ICB-mediated rejuvenation. Mechanistically, chronic IFN-I stimulation perturbs lipid metabolism and redox balance in Tex cells, leading to aberrant lipid accumulation and elevated oxidative stress. Collectively, these defects promote lipid peroxidation, which potentiates metabolic and functional exhaustion of Tex cells. Thus, cell-intrinsic IFN-I signaling regulates the extent of CD8 + TIL exhaustion and has important implications for immunotherapy., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)

The aim of the present research work was to develop halogen and formaldehyde-free, durable flame retardant fabric along with multifunctional properties and to find the optimal conditions and parameters. In this research, zinc oxide nanoparticles (ZnO NPs) were grown onto 100% cotton fabric using the sonochemical method. Zinc acetate dihydrate (Zn(CH 3 COO) 2 ·2H 2 O) and sodium hydroxide (NaOH) were used as precursors. After ZnO NPs growth, N-Methylol dimethylphosphonopropionamide (MDPA) flame retardant was applied in the presence of 1, 2, 3, 4-butanetetracarboxylic acid (BTCA) as cross-linkers using the conventional pad-dry-cure method. Induced coupled plasma atomic emission spectroscopy (ICP-AES) was used to determine the deposited amount of Zn and phosphorous (P) contents. Scanning electron microscopy (SEM), X-ray powder diffraction (XRD), and Fourier-transform infrared spectroscopy (FTIR) were employed to determine the surface morphology and characterization of the developed samples. Furthermore, the thermal degradation of the untreated and treated samples was investigated by thermogravimetric analysis (TGA). Furthermore, the vertical flame retardant test, limiting oxygen index (LOI), ultraviolet protection factor (UPF), and antibacterial activity of samples were examined. The developed samples showed excellent results for flame retardancy (i.e., 39 mm char length, 0 s after flame time, 0 s after glow time), 32.2 LOI, 143.76 UPF, and 100% antibacterial activity.

Zinc oxide nanoparticles (ZnO NPs) have acquired great significance in the textile sector due to their impressive efficiency and multifold utilization, such as antimicrobials, UV protection, photo catalytic activity, and self-cleaning. The aim of this work is in-situ growth of ZnO NPs on 100% cotton fabrics with the one-step hydrothermal method for preparation of multifunctional textile with UV protecting, antibacterial, and photo catalytic properties. Sodium hydroxide (NaOH) and Zinc nitrate hexahydrate [Zn(NO 3 ) 2 ·6H 2 O] were used as reactants for the growth of zinc oxide on the 100% cotton fabrics. The loaded amount of Zn contents on the cotton fabric was determined by using induced coupled plasma atomic emission spectroscopy (ICP-AES). The surface morphological characterization of deposited ZnO NPs was examined, employing scanning electron microscopy (SEM), X-ray powder diffraction (XRD) and, Fourier- transform infrared spectroscopy (FTIR). The characterization results showed the presence of ZnO NPs on cotton fabrics having hexagonal wurtzite crystalline structure. The synthesized ZnO NPs on fabrics exhibited promising results for antibacterial, UV protection, and photo catalytic performance.

Viruses are omnipresent and persistent in wastewater, which poses a risk to human health. In this review, we summarise the different qualitative and quantitative methods for virus analysis in wastewater and systematically discuss the spatial distribution and temporal patterns of various viruses (i.e., enteric viruses, Caliciviridae (Noroviruses (NoVs)), Picornaviridae (Enteroviruses (EVs)), Hepatitis A virus (HAV)), and Adenoviridae (Adenoviruses (AdVs))) in wastewater systems. Then we critically review recent SARS-CoV-2 studies to understand the ongoing COVID-19 pandemic through wastewater surveillance. SARS-CoV-2 genetic material has been detected in wastewater from France, the Netherlands, Australia, Italy, Japan, Spain, Turkey, India, Pakistan, China, and the USA. We then discuss the utility of wastewater-based epidemiology (WBE) to estimate the occurrence, distribution, and genetic diversity of these viruses and generate human health risk assessment. Finally, we not only promote the prevention of viral infectious disease transmission through wastewater but also highlight the potential use of WBE as an early warning system for public health assessment., (Copyright © 2021 Elsevier B.V. All rights reserved.)

One severe weakness of most biopolymers, in terms of their use as packaging materials, is their relatively high solubility in water. The addition of kraft lignin to starch coating formulations has been shown to reduce the water solubility of starch in dry coatings. However, lignin may also migrate into aqueous solutions. For this paper, kraft lignin isolated using the LignoBoost process was used in order to examine the effect of pH level on the solubility of lignin with and without ammonium zirconium carbonate (AZC). Machine-glazed (MG) paper was coated in a pilot coating machine, with the moving substrate at high speed, and laboratory-coated samples were used as a reference when measuring defects (number of pinholes). Kraft lignin became soluble in water at lower pH levels when starch was added to the solution, due to the interactions between starch and lignin. This made it possible to lower the pH of the coating solutions, resulting in increased water stability of the dry samples; that is, the migration of lignin to the model liquids decreased when the pH of the coating solutions was reduced. No significant difference was observed in the water vapor transmission rate (WVTR) between high and low pH for the pilot-coated samples. The addition of AZC to the formulation reduced the migration of lignin from the coatings to the model liquids and led to an increase in the water contact angle, but also increased the number of pinholes in the pilot-coated samples.

Single cell genomics offers an unprecedented resolution to interrogate genetic heterogeneity in a patient's tumour at the intercellular level. However, the DNA yield per cell is insufficient for today's sequencing library preparation protocols. This necessitates DNA amplification which is a key source of experimental noise. We provide an evaluation of two protocols using micro-fluidics based amplification for whole exome sequencing, which is an experimental scenario commonly used in single cell genomics. The results highlight their respective biases and relative strengths in identification of single nucleotide variations. Towards this end, we introduce a workflow SoVaTSiC, which allows for quality evaluation and somatic variant identification of single cell data. As proof of concept, the framework was applied to study a lung adenocarcinoma tumour. The analysis provides insights into tumour phylogeny by identifying key mutational events in lung adenocarcinoma evolution. The consequence of this inference is supported by the histology of the tumour and demonstrates usefulness of the approach., Competing Interests: The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (© 2020 The Authors.)

MITF is a known gene underlying autosomal dominant hearing loss, Waardenburg syndrome (WS). Biallelic MITF mutations have been found associated with a rare hearing loss syndrome consisting eye abnormalities and albinism; and a more severe type of WS whose heterozygous parents were affected with classic WS in both cases. The aims of this study were to identify a new candidate gene causing autosomal recessive nonsyndromic hearing loss (ARNSHL) and confirm its causation by finding additional families affected with the candidate gene and supporting evidences from functional analyses. By using whole exome sequencing, we identified a homozygous c.1022G>A: p.Arg341His variant of MITF, which co-segregated with the hearing loss in five affected children of a consanguineous hearing couple. Targeted exome sequencing in a cohort of 130 NSHL individuals, using our in-house gene panel revealed a second family with c.1021C>T: p.Arg341Cys MITF variant. Functional studies confirmed that the Arg341His and Arg341Cys alleles yielded a normal sized MITF protein, with aberrant cytosolic localization as supported by the molecular model and the reporter assay. In conclusion, we demonstrate MITF as a new cause of ARNSHL, with heterozygous individuals free of symptoms. MITF should be included in clinical testing for NSHL, though it is rare.

Aim: Irrigating rice with groundwater can lead to As accumulation in soil and rice grains. Matched sets of irrigation water, paddy soil, and rice grains were collected to assess the scale of the problem in the Punjab plains of Pakistan., Methods: From a total of 60 sites, irrigation water and rice grains as well as 103 soil samples were collected and analyzed in the laboratory. Irrigation water and 660 soil samples were also analyzed in the field using a field kit., Results: Concentrations of As in irrigation water (65±32 μg/L) are higher in the floodplain of the Ravi River compared to the Chenab (13±9 μg/L) and Jhelum (4±5 μg/L) rivers, as well as the intervening Rechna (6±6 μg/L) and Chaj doabs (0.8±0.2 μg/L). Area-weighted mean soil As concentrations are 12±3 mg/kg along the Ravi, 8.9±2 and 8.1±2 mg/kg along the Chenab and Jhelum, respectively, and 6.2±0.2 mg/kg within the Rachna and 6.1±0.1 mg/kg in Chaj doabs. The As content of polished grains export-quality basmati rice of 0.09±0.05 mg/kg, however, is low across the entire area., Conclusions: Groundwater irrigation leads to elevated As concentrations in paddy soil of some rice-growing regions of Punjab but does not result in increased uptake of As in basmati rice grains., Competing Interests: Competing Interests None

The functional consequences of cancer-associated missense mutations are unclear for the majority of proteins. We have previously demonstrated that the activity of SOX and Pit-Oct-Unc (POU) family factors during pluripotency reprogramming can be switched and enhanced with rationally placed point mutations. Here, we interrogated cancer mutation databases and identified recurrently mutated positions at critical structural interfaces of the DNA-binding domains of paralogous SOX and POU family transcription factors. Using the conversion of mouse embryonic fibroblasts to induced pluripotent stem cells as functional readout, we identified several gain-of-function mutations that enhance pluripotency reprogramming by SOX2 and OCT4. Wild-type SOX17 cannot support reprogramming but the recurrent missense mutation SOX17-V118M is capable of inducing pluripotency. Furthermore, SOX17-V118M promotes oncogenic transformation, enhances thermostability and elevates cellular protein levels of SOX17. We conclude that the mutational profile of SOX and POU family factors in cancer can guide the design of high-performance reprogramming factors. Furthermore, we propose cellular reprogramming as a suitable assay to study the functional impact of cancer-associated mutations., (© 2019 Federation of European Biochemical Societies.)

Purpose: To identify the molecular cause in five unrelated families with a distinct autosomal dominant ocular systemic disorder we called ROSAH syndrome due to clinical features of retinal dystrophy, optic nerve edema, splenomegaly, anhidrosis, and migraine headache., Methods: Independent discovery exome and genome sequencing in families 1, 2, and 3, and confirmation in families 4 and 5. Expression of wild-type messenger RNA and protein in human and mouse tissues and cell lines. Ciliary assays in fibroblasts from affected and unaffected family members., Results: We found the heterozygous missense variant in the ɑ-kinase gene, ALPK1, (c.710C>T, [p.Thr237Met]), segregated with disease in all five families. All patients shared the ROSAH phenotype with additional low-grade ocular inflammation, pancytopenia, recurrent infections, and mild renal impairment in some. ALPK1 was notably expressed in retina, retinal pigment epithelium, and optic nerve, with immunofluorescence indicating localization to the basal body of the connecting cilium of the photoreceptors, and presence in the sweat glands. Immunocytofluorescence revealed expression at the centrioles and spindle poles during metaphase, and at the base of the primary cilium. Affected family member fibroblasts demonstrated defective ciliogenesis., Conclusion: Heterozygosity for ALPK1, p.Thr237Met leads to ROSAH syndrome, an autosomal dominant ocular systemic disorder.

Objective: To compare efficacy of unique antiepileptic drug (AED) polytherapy regimens among patients with focal epilepsy., Methods: From a longitudinal study of AED treatment, we identified patients with active focal epilepsy who had attempted at least two unique AED regimens (mono-, duo-, or tri-therapy). Efficacy was defined as the presence of at least one six-month period of continuous seizure freedom during exposure to a regimen. To control for individual variations in response and epilepsy severity, we used within-patient comparison approaches, in which we: 1) compared head-to-head unique regimens tried within the same patients; 2) compared one regimen versus aggregate of other regimens attempted in that patient; and 3) compared aggregated monotherapy versus polytherapy regimens., Results: 757 patients met our criteria and had collectively attempted 170 unique regimens. In the head-to-head analysis, lamotrigine monotherapy was more effective than phenytoin monotherapy. Two regimens were more effective than the aggregate of other regimens attempted: levetiracetam/lamotrigine duotherapy and lamotrigine monotherapy. Two other regimens exhibited slightly better efficacy but did not reach statistical significance: clobazam/levetiracetam/lamotrigine and levetriacetam/oxcarbazepine. Patients who previously attempted at least four regimens had slightly better outcomes on polytherapy than monotherapy, though this was not significant., Significance: We identified two unique regimens more likely to be associated with ≥6 months of seizure freedom: levetiracetam/lamotrigine duotherapy and lamotrigine monotherapy. Polytherapy may be an effective alternative to monotherapy for patients with focal epilepsy and persistent seizures., (Copyright © 2018 Elsevier B.V. All rights reserved.)

Multiple adult tissues are maintained by stem cells of restricted developmental potential which can only form a subset of lineages within the tissue. For instance, the two adult lung epithelial compartments (airways and alveoli) are separately maintained by distinct lineage-restricted stem cells. A challenge has been to obtain multipotent stem cells and/or progenitors that can generate all epithelial cell types of a given tissue. Here we show that mouse Sox9 + multipotent embryonic lung progenitors can be isolated and expanded long term in 3D culture. Cultured Sox9 + progenitors transcriptionally resemble their in vivo counterparts and generate both airway and alveolar cell types in vitro. Sox9 + progenitors that were transplanted into injured adult mouse lungs differentiated into all major airway and alveolar lineages in vivo in a region-appropriate fashion. We propose that a single expandable embryonic lung progenitor population with broader developmental competence may eventually be used as an alternative for region-restricted adult tissue stem cells in regenerative medicine.

To assess the trace metal pollution in the Siran River, sediments were collected from 12 sites, from the left and right banks of the river in 2013. The concentrations, accumulation, distribution pattern, and pollution status of heavy metals in sediments were investigated using geoaccumulation index (I geo) and enrichment factor (EF). The toxic risk of heavy metals was assessed using interim sediment quality guidelines (ISQGs), portable effect level (PEL), threshold effect level (TEL), and toxic effect threshold (TET). I geo and EF values showed that sediments were loaded with Ni, Cd, Pb, and Co and no obvious variations were found among the left and right banks of the river. The EF and I geo values were found in order of Co > Pb > Ni > As > Cd > Cu > Zn > Fe and Cd > Co > Pb > Ni > As > Fe > Zn > Cu > Mn, respectively. Furthermore, multivariate statistical analysis like inter-metal correlation, cluster analysis (CA), and principal component analysis (PCA) results revealed that geogenic and anthropogenic activities were major sources of sediment contamination in the study area. These results indicated that more attention should be paid to the inner loads of sediment in order to achieve improvements in reservoir water quality after the control of external pollution.

Purpose: Impact of adverse effects of antiepileptic medications (AEDs) such as cognitive side effects (CSEs) on quality of life can be significant. Here we provide an extended follow-up to our earlier study to investigate the predictors of cognitive side effects (CSEs) and relative frequency of CSEs among all commonly used AEDs., Methods: In this retrospective study, medical records of 2860 adult outpatients with epilepsy seen at our center over a 12-year period who had taken one or more AEDs were examined., Results: Of 2860 patients, 15% had intolerable CSEs attributed to at least one AED. On multiple logistic regression analysis, independent predictors of intolerable CSEs were lack of intellectual disability and polytherapy. In polytherapy, we found that intolerable CSEs were most commonly seen with topiramate (22.8% of 281 patients), significantly more than with almost all other AEDs. This was true in monotherapy as well, with significantly more intolerable CSEs occurring with topiramate (18.5% of 54 patients) than with gabapentin, carbamazepine, lamotrigine, and levetiracetam. AEDs with consistently low rates of ICSEs included gabapentin, pregabalin, lamotrigine, levetiracetam and carbamazepine., Conclusion: These data can help facilitate selection of AEDs., (Copyright © 2015. Published by Elsevier Ltd.)

We have analyzed human genetic diversity in 33 Old World populations including 23 populations obtained through Genographic Project studies. A set of 1,536 SNPs in five X chromosome regions were genotyped in 1,288 individuals (mostly males). We use a novel analysis employing subARG network construction with recombining chromosomal segments. Here, a subARG is constructed independently for each of five gene-free regions across the X chromosome, and the results are aggregated across them. For PCA, MDS and ancestry inference with STRUCTURE, the subARG is processed to obtain feature vectors of samples and pairwise distances between samples. The observed population structure, estimated from the five short X chromosomal segments, supports genome-wide frequency-based analyses: African populations show higher genetic diversity, and the general trend of shared variation is seen across the globe from Africa through Middle East, Europe, Central Asia, Southeast Asia, and East Asia in broad patterns. The recombinational analysis was also compared with established methods based on SNPs and haplotypes. For haplotypes, we also employed a fixed-length approach based on information-content optimization. Our recombinational analysis suggested a southern migration route out of Africa, and it also supports a single, rapid human expansion from Africa to East Asia through South Asia.

Recombination is one of the main forces shaping genome diversity, but the information it generates is often overlooked. A recombination event creates a junction between two parental sequences that may be transmitted to the subsequent generations. Just like mutations, these junctions carry evidence of the shared past of the sequences. We present the IRiS algorithm, which detects past recombination events from extant sequences and specifies the place of each recombination and which are the recombinants sequences. We have validated and calibrated IRiS for the human genome using coalescent simulations replicating standard human demographic history and a variable recombination rate model, and we have fine-tuned IRiS parameters to simultaneously optimize for false discovery rate, sensitivity, and accuracy in placing the recombination events in the sequence. Newer recombinations overwrite traces of past ones and our results indicate more recent recombinations are detected by IRiS with greater sensitivity. IRiS analysis of the MS32 region, previously studied using sperm typing, showed good concordance with estimated recombination rates. We also applied IRiS to haplotypes for 18 X-chromosome regions in HapMap Phase 3 populations. Recombination events detected for each individual were recoded as binary allelic states and combined into recotypes. Principal component analysis and multidimensional scaling based on recotypes reproduced the relationships between the eleven HapMap Phase III populations that can be expected from known human population history, thus further validating IRiS. We believe that our new method will contribute to the study of the distribution of recombination events across the genomes and, for the first time, it will allow the use of recombination as genetic marker to study human genetic variation.