Miracle-dz/UniFAR-FTUs huggingface dataset:
COMPARISON OF ELLIPTIC EQUATION – ABC/2 WITH COMPUTERASSISTED SEMIAUTHOMATIC METHODS FOR MEASURING THE VOLUME OF INTRACEREBRAL HEMORRHAGE

Hemorrhage volume, level of consciousness and ventricular extension and expansion of the hematoma are prognostic factors for clinical outcome of intracerebral hemorrhage (ICH). Volumetric measurement of ICH has an important clinical and prognostic meaning. The aim of this study was to compare the methods which are being used to measure ICH volume: the ABC/2 method and semiautomated method with computer volumetric program. Our study represents a retrospective analisys of 54 patients (61.11% male and 38.89% female patients with mean age 67.20±10.30 years) who underwent computed tomography (CT) scan of endocranium. Volumetric measurements were performed by ABC/2 method and computer semiautomated method with volumetric program on Аdvantage Windows 3D Workstation 4.1. Mean value and standard deviation obtained by ABC/2 method were 41.98±35.47, while mean value and standard deviation obtained by computer semiautomated method with volumetric program were 52.12±45.61. There is a statistically significant difference between the values obtained by these two methods (p=0.03). The absolute difference was 10.14 cm. The values acquired by computer method were by 19.46% higher than those acquired by formula. There is a statstically strong positive correlation between these two methods (r=0.852, p<0.05). Both methods are very useful in determining ICH volume. Our results show that values obtained by computer semiauthomatic method were by 19.46% higher than those obtained by the elliptic equation. Elliptic equation-ABC/2 method is better for measuring regular ICH shapes and fast orientation, while semiautomated computer method is more accurate and more selective. Acta Medica Medianae 2015;54(3):34-38.
Multi-drug resistant Staphylococcus aureus isolated from emergency ward of an Iranian hospital

Purpose : To study the prevalence of resistant strains of S. aureus isolated from surfaces, beds and various equipment of an Iranian hospital emergency ward. Methods : Two hundred swab samples were collected from the surfaces, beds, trolleys, surgical equipment and diagnostic medical devices in emergency ward. Samples were cultured and those that were S. aureus -positive were confirmed using polymerase chain reaction (PCR). Antimicrobial resistance pattern was analyzed using disk diffusion method. Results : Nine of 200 samples (4.5 %) collected were positive for S. aureus . Surfaces (8.8 %), beds (5 %) and trolleys (5 %) were the most commonly contaminated. S. aureus isolates exhibited varying levels of resistance against antibiotics with the following being the highest: tetracycline (88.8 %), penicillin (88.8 %) and ampicillin (77.7 %). The prevalence of resistance against methicillin, oxacillin and azithromycin were 44.4, 33.3 and 33.3 %, respectively. There was no pattern of resistance against imipenem. Conclusion : Efficient disinfection of surfaces, beds, trolleys and surgical instruments should be performed periodically to reduce colonization of resistant strains of S. aureus in various areas of emergency health care centers. Keywords : Staphylococcus aureus , Nocosomial infection, Antibiotic resistance, Hospital equipment, Emergency ward
A review of 1125 cases referred for cytogenetic analysis in Syria

Introduction The aim of this review is to evaluate the pattern of referral for cytogenetic analysis and to determine the frequency of chromosomal abnormalities in different groups of referrals, and then to compare these figures with similar studies. Patients and methods This review included 1125 cases referred between 2007 and 2010 to the Cytogenetic Unit, Clinical Laboratories, Assad University Hospital in Damascus, Syria. The referrals fall under two categories: hematological disorders (HD) and constitutional chromosomal aberrations. Subjects and methods All samples were subjected to standard cytogenetic procedures, followed by G-banding using trypsin and giemsa, and some were subjected to fluorescence in-situ hybridization according to the probe manufacturer’s protocol. Results and discussion In HD group there were 847 samples. The chronic myelogenous leukemia group consisted of the largest number of referrals. The next subgroup in number of referrals was acute myelogenous leukemia. The myelodysplastic syndrome group came next, followed by acute lymphoblastic leukemia, and then chronic lymphocytic leukemia. Cytogenetic results were either recurring aberrations with important diagnostic significance (e.g. Philadelphia chromosome) or other aberrations with less clear significance. In the constitutional chromosomal aberrations group, 278 samples were analyzed. Significant statistical differences between the current study and other studies from Turkey, Saudi Arabia, and Jordan were seen in the referring frequencies. The Turner syndrome group had the highest frequency of referrals, followed by the reproductive problems group, which had abnormal results in frequencies similar to previous reports. The Down syndrome suspect group was next in the number of referrals, but it had the highest number of abnormal karyotypes. Then came the chromosomal syndrome suspect group, followed by the Klinefelter group, and the sex determination group with the lowest referral rates. Conclusion This study highlights the importance of considering cytogenetic test during the management of HDs, and demonstrates the importance of incorporating it in evaluation plans for congenital abnormalities, sexual development problems, and reproductive problems.
Engineered gene networks enable non‐genetic drug resistance and enhanced cellular robustness

Drug resistance complicates the treatment of cancer and infectious diseases, and often arises from the elevated expression of a gene that neutralises or reduces drug activity. To investigate this and other expression-based mechanisms of drug resistance, the authors engineered a set of gene regulatory networks in the eukaryotic model organism Saccharomyces cerevisiae to control a homologue of the cancer-related human multidrug resistance gene MDR1. Using this system, they explored experimentally how different gene regulatory network features, also called genetic network motifs, contribute to gene expression dynamics and cellular fitness. They observed that coherent feedforward and positive feedback motifs enable rapid and self-sustained activation of gene expression, and enhance cell survival in the presence of a cytotoxic drug. These observations underscore that genetic network motifs can be critical for drug resistance and that genetic network engineering can be used to enhance cellular tolerance to cytotoxins or other environmental stresses.
Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13)

We describe AlphaFold, the protein structure prediction system that was entered by the group A7D in CASP13. Submissions were made by three free‐modeling (FM) methods which combine the predictions of three neural networks. All three systems were guided by predictions of distances between pairs of residues produced by a neural network. Two systems assembled fragments produced by a generative neural network, one using scores from a network trained to regress GDT_TS. The third system shows that simple gradient descent on a properly constructed potential is able to perform on par with more expensive traditional search techniques and without requiring domain segmentation. In the CASP13 FM assessors' ranking by summed z‐scores, this system scored highest with 68.3 vs 48.2 for the next closest group (an average GDT_TS of 61.4). The system produced high‐accuracy structures (with GDT_TS scores of 70 or higher) for 11 out of 43 FM domains. Despite not explicitly using template information, the results in the template category were comparable to the best performing template‐based methods.
Genomic Characterization and Curation of UCEs Improves Species Tree Reconstruction

Ultraconserved genomic elements (UCEs), are generally treated as independent loci in phylogenetic analyses. The identification pipeline for UCE probes is agnostic to genetic identity, only selecting loci that are highly conserved, single copy, without repeats, and of a particular length. Here we characterized UCEs from 12 phylogenomic studies across the animal tree of life, from birds to marine invertebrates. We found that within vertebrate lineages, UCEs are mostly intronic and intergenic, while in invertebrates, the majority are in exons. We then curated 4 different sets of UCE markers by genomic category from 5 different studies including; birds, mammals, fish, Hymenoptera (ants, wasps and bees) and Coleoptera (beetles). Of genes captured by UCEs, we find that many are represented by 2 or more UCEs, corresponding to non-overlapping segments of a single gene. We considered these UCEs to be non-independent, merged all UCEs that belonged to a particular gene, constructed gene and species trees, and then evaluated the subsequent effect of merging co-genic UCEs on gene and species tree reconstruction. Average bootstrap support for merged UCE gene trees were significantly improved across all datasets. Increased loci length appears to drive this increase in bootstrap support. Additionally, we found that gene trees generated from merged UCEs were more accurate than those generated by unmerged and randomly merged UCEs, based on our simulation study. This modest degree of UCE characterization and curation impacts downstream analyses and demonstrates the advantages of incorporating basic genomic characterizations into phylogenomic analyses.
Characterization of the complete chloroplast genome of an annual halophyte, Chenopodium glaucum (Amaranthaceae)

Abstract The complete chloroplast genome (plastome) of Chenopodium glaucum, an annual halophytic herb, was determined. The plastome was 152,191 bp in size, containing a large single-copy region (83,675 bp), a small single-copy region (18,130 bp), and two inverted repeats regions (25,193 bp). The overall GC content of this plastome was 37.2%. In total, 113 unique genes were annotated including 79 protein-coding genes (PCGs), 30 tRNAs and 4 rRNAs. Phylogenomic analysis showed that C. glaucum was sister to C. album.
Characterization of the complete chloroplast genome of Centaurea maculosa (Asteraceae)

Abstract The complete chloroplast genome of Centaurea maculosa (Asteraceae) was presented in this article. The genome size is 152,518 bp in length, with 43.1% of GC content. It consists of a large single-copy (LSC) region (83,959 bp) and a small single-copy region (SSC) (18,487 bp) which were separated by two inverted repeat (IRs) regions (25,218 bp). The complete chloroplast genome contains 111 unique genes, including 80 coding genes, 4 rRNA genes, and 27 tRNA genes.
EXO70A2 is critical for the exocyst complex function in Arabidopsis pollen

Pollen development, pollen grain germination and pollen tube elongation are crucial biological processes in angiosperm plants that need precise regulation to deliver sperm cells to fertilize ovules. Pollen grains undergo two major developmental switches: dehydration characterized by metabolic quiescent state, and rehydration upon pollination that leads to extraordinary metabolic and membrane trafficking activity, resulting in germination and rapid tip growth of pollen tubes. To sustain these processes, many plant housekeeping genes evolved their pollen-specific paralogs. Highly polarized secretion at a growing pollen tube tip requires the exocyst tethering complex responsible for specific targeting of secretory vesicles to the plasma membrane. Here, we describe that EXO70A2 (At5g52340) is the main exocyst EXO70 isoform in Arabidopsis pollen, which governs the conventional secretory function of the exocyst, analogically to EXO70A1 (At5g03540) in the sporophyte. Our analysis of a CRISPR-generated exo70a2 mutant revealed that EXO70A2 is essential for efficient pollen maturation, pollen grain germination and pollen tube growth. GFP:EXO70A2 was localized similarly to other exocyst subunits to the apical domain in growing pollen tube tips characterized by intensive exocytosis. Moreover, EXO70A2 could substitute for the EXO70A1 function in the sporophyte, indicating functional redundancy of these two closely related isoforms. Phylogenetic analysis revealed that the ancient duplication of EXO70A to two (or more) paralogs, one of which is highly expressed in pollen, occurred independently in monocots and dicots. In summary, EXO70A2 is a crucial component of the exocyst complex in the Arabidopsis pollen required for efficient plant sexual reproduction.
Genetic analysis of osteoblast activity identifies Zbtb40 as a regulator of osteoblast activity and bone mass

Osteoporosis is a genetic disease characterized by progressive reductions in bone mineral density (BMD) leading to an increased risk of fracture. Over the last decade, genome-wide association studies (GWASs) have identified over 1000 associations for BMD. However, as a phenotype BMD is challenging as bone is a multicellular tissue affected by both local and systemic physiology. Here, we focused on a single component of BMD, osteoblast-mediated bone formation in mice, and identified associations influencing osteoblast activity on mouse Chromosomes (Chrs) 1, 4, and 17. The locus on Chr. 4 was in an intergenic region between Wnt4 and Zbtb40, homologous to a locus for BMD in humans. We tested both Wnt4 and Zbtb40 for a role in osteoblast activity and BMD. Knockdown of Zbtb40, but not Wnt4, in osteoblasts drastically reduced mineralization. Additionally, loss-of-function mouse models for both genes exhibited reduced BMD. Our results highlight that investigating the genetic basis of in vitro osteoblast mineralization can be used to identify genes impacting bone formation and BMD.
Genetic divergence among eggplant genotypes under high temperatures

ABSTRACT The aim of this study was to estimate the genetic divergence among eggplant genotypes for agronomic traits in order to gather information for the selection of genotypes in eggplant breeding programs for tolerance to high temperatures. Ten traits recommended by the International Board for Plant Genetic Resources were analyzed in 24 genotypes, arranged in a randomized complete block design with four replicates. Data were submitted to analysis of variance (P<0.01) and later to the UPGMA and Tocher grouping methods, using the generalized Mahalanobis distance (D2) as dissimilarity measure. Three and six groups of similarity were obtained, respectively, for the multivariate techniques used, UPGMA and Tocher, with concordance in the grouping of 87.50% of the genotypes. The characters fruit length (34.71%), fruit width (35.96%) and fruit length/width ratio (14.08%) were the main contributors to genetic divergence, explaining 90.72% of total genetic dissimilarity. The genotypes presented considerable genetic variability for all agronomic traits analyzed and can be used in eggplant genetic breeding programs for high temperatures.
Dependence of bacterial growth rate on dynamic temperature changes

Temperature is an important determinant of bacterial growth. While the dependence of bacterial growth on different temperatures has been well studied for many bacterial species, prediction of bacterial growth rate for dynamic temperature changes is relatively unclear. Here, the authors address this issue using a combination of experimental measurements of the growth, at the resolution of 5 min, of Escherichia coli and mathematical models. They measure growth curves at different temperatures and estimate model parameters to predict bacterial growth profiles subject to dynamic temperature changes. They compared these predicted growth profiles for various step‐like temperature changes with experimental measurements using the coefficient of determination and mean square error and based on this comparison, ranked the different growth models, finding that the generalised logistic growth model gave the smallest error. They note that as the maximum specific growth increases the duration of this growth predominantly decreases. These results provide a basis to compute the dependence of the growth rate parameter in biomolecular circuits on dynamic temperatures and may be useful for designing biomolecular circuits that are robust to temperature.
Identification and Characterization of Macrophomina phaseolina Causing Leaf Blight on White Spider Lilies (Crinum asiaticum and Hymenocallis littoralis) in Malaysia

Abstract Crinum asiaticum and Hymenocallis littoralis, commonly known as spider lilies are bulbous perennial and herbaceous plants that widely planted in Malaysia as ornamental. During 2015–2016, symptom of leaf blight was noticed on the hosts from several locations in Penang. The symptom appeared as irregular brown to reddish lesions surrounded by yellow halos. As the disease progressed, the infected leaves became blighted, dried, and fell off with the presence of black microsclerotia and pycnidia on the lesions parts. The present study was conducted to investigate the causal pathogen of leaf blight on C. asiaticum and H. littoralis. Based on morphological characteristics and DNA sequences of internal transcribed spacer (ITS) region and translation elongation factor 1-alpha (TEF1-α) gene, the causal pathogen was identified as Macrophomina phaseolina. Phylogenetic analysis of combined dataset of ITS and TEF1-α grouped the isolates studied with other isolates of M. phaseolina from GenBank. The grouping of the isolates was supported by 96% bootstrap value. Pathogenicity test proved the role of the fungus in causing leaf blight on both hosts.
Functional role of respiratory supercomplexes in mice: segmentation of the Qpool and SCAF1

Mitochondrial respiratory complexes assemble into different forms of supercomplexes (SC). In particular, SC III2+IV require the SCAF1 protein. However, the structural role of this factor in the formation of the respirasome (I+III2+IV) and the physiological role of SCs are controversial. Here, we study C57BL/6J mice harbouring either non-functional SCAF1, the full knock-out for SCAF1 or the wild-type version of the protein and found a growth and exercise phenotype due to the lack of functional SCAF1. By combining quantitative data-independent proteomics, high resolution 2D Blue Native Gel Electrophoresis and functional analysis of enriched respirasome fractions, we show that SCAF1 confers structural attachment between III2 and IV within the respirasome, increases NADH-dependent respiration and reduces ROS production. Furthermore, through the expression of AOX in cells and mice we confirm that CI-CIII superassembly segments the CoQ in two pools and modulates CI-NADH oxidative capacity. These data demonstrate that SC assembly, regulated by SCAF1, modulates the functionality of the electron transport chain.
Can genetic assignment tests provide insight on the influence of captive egression on the epizootiology of chronic wasting disease?

Identifying the sources of ongoing and novel disease outbreaks is critical for understanding the diffusion of epizootic diseases. Identifying infection sources is difficult when few physical differences separate individuals with different origins. Genetic assignment procedures show great promise for assessing transmission dynamics in such situations. Here, we use genetic assignment tests to determine the source of chronic wasting disease infections in free‐ranging white‐tailed deer (Odocoileus virginianus) populations. Natural dispersal is thought to facilitate the geographic diffusion of chronic wasting disease, but egression from captive cervid populations represents an alternative source of infection that is difficult to detect due to physical similarities with wild deer. Simulated reference populations were created based on allele frequencies from 1,912 empirical microsatellite genotypes collected in four sampling subregions and five captive facilities. These reference populations were used to assess the likelihood of ancestry and assignment of 1,861 free‐ranging deer (1,834 noninfected and 27 infected) and 51 captive individuals to captive or wild populations. The ancestry (Q) and assignment scores (A) for free‐ranging deer to wild populations were high (average Qwild = 0.913 and average Awild = 0.951, respectively), but varied among subregions (Qwild = 0.800–0.947, Awild = 0.857–0.976). These findings suggest that captive egression and admixture are rare, but risk may not be spatially uniform. Ancestry and assignment scores for two free‐ranging deer with chronic wasting disease sampled in an area where chronic wasting disease was previously unobserved in free‐ranging herds indicated a higher likelihood of assignment and proportion of ancestry attributable to captive populations. While we cannot directly assign these individuals to infected facilities, these findings suggest that rare egression events may influence the epizootiology of chronic wasting disease in free‐ranging populations. Continued disease surveillance and genetic analyses may further elucidate the relative disease risk attributable to captive and wild sources.
singleCellHaystack: Finding surprising genes in single-cell transcriptome data

Abstract Summary A typical analysis of single-cell sequencing data includes dimensionality reduction using Principal Component Analysis (PCA) and visualization in 2-dimensional plots, using t-SNE or UMAP. However, identifying differentially expressed genes or extracting biological knowledge remains challenging, even after reducing dimensionality. Here we introduce singleCellHaystack, a methodology that uses Kullback-Leibler Divergence to find genes that are expressed in subsets of cells that are non-randomly positioned in a multi-dimensional space. Critically, singleCellHaystack does not rely on arbitrary clustering of cells. We illustrate the usage of singleCellHaystack through applications on several single-cell datasets. Genes with highly biased expression profiles often include known cell type marker genes. singleCellHaystack is implemented as an R package, and includes additional functions for clustering and visualization of genes with interesting expression patterns. Availability and implementation https://github.com/alexisvdb/singleCellHaystack
Design to Data for mutants of β-glucosidase B from Paenibacillus polymyxa: M319C, T431I, and K337D

The use of computational tools has become an increasingly popular tool for engineering protein function. While there are numerous examples of computational tools enabling the design of novel protein functions, there remains room for improvement in both prediction accuracy and success. To improve algorithms for functional and stability predictions, we have initiated the development of a data set designed to be used for training new computational algorithms for enzyme design. To date our dataset is composed of over 129 mutants with associated expression levels, kinetic data, and thermal stability for the enzyme β-glucosidase B (BglB) from Paenibacillus polymyxa. In this study, we introduced three new variants (M319C, T431I, and K337D) to our existing dataset with the goal of cultivating a larger dataset to train new design algorithms and more broadly explore structure-function relationships in BglB.