Miracle-dz/UniFAR-FTUs huggingface dataset:
Initial Sequencing and Characterization of Gastrointestinal and Oral Microbiota in Urban Pakistani Adults Reveals Abnormally High Levels of Potentially Starch Metabolizing Bacteria in the General Population

We describe the characterization of the gastrointestinal tract (gut) and oral microbiota (bacteria) in 32 urban Pakistani adults representing seven major geographies and six ethnicities in the country. Study participants were between ages 18 and 40, had body mass index between 18 and 25 Kg/m2, and were early-career students or professionals belonging to 25 major cities of the country. These individuals donated a total of 61 samples (32 gut and 29 oral) that were subjected to 16S ribosomal RNA (rRNA) gene sequencing. Microbiome composition of Pakistani individuals was compared against the uBiome database of selected individuals who self-reported to be in excellent health. Using the crude measure of percentage overlap or similarity between the gut microbiota profile of Pakistani and uBiome dataset as proxy for health, our sequencing indicated that the Pakistani gut microbiota was moderately healthy relative to the uBiome dataset and Pakistani women appeared healthier relative to men. The Pakistani gut microbiome seemed susceptible to obesity and weight gain, levels of probiotics was very high likely due to the popularity of milk-based and fermented foods in the Pakistani diet, and bacteria that metabolize starch and carbohydrates (typically seen in the gut microbiota of honey bee) were abnormally enriched in the gut of Pakistani men. Our investigations reveal serious issues with the dietary habits and lifestyle of Pakistani individuals of consuming food enriched in high carbohydrates and fats, overcooked in oil and spices, following a sedentary lifestyle, little or no daily intake of fresh fruits, over-consumption of antibiotics from a very early age, and health and hygiene standards that do not meet international standards. Our sequencing is the first step towards generating a country-wide understanding of the impact of the local diet and lifestyle on Pakistani gut microbiota and can help understand its overall association with health and wellness.
Genetics of essential oil yield and their component traits in vetiver (Chrysopogon zizanioides (L.) Roberty)

The thirteen lines and five testers used for Line × tester analysis in vetiver (Chrysopogon zizanioides (L.) Roberty) to estimate the general and specific combining ability and the other allied genetic parameters with respect to physiological traits, essential oil contents, yield of essential oil and other components. The mean squares of all the eleven traits were significant for variances GCA and SCA stipulating that additive and non-additive genes control these characters. The character root yield/plot (ml), female lines L4 (g.c.a.= 71.585, x/Mean= 553.33), L13 (g.c.a.= 63.918, x/Mean= 383.33), and among testers T3 (g.c.a.= 31.149, x/Mean= 583.33) followed by T1 (g.c.a.= 26.046, x/Mean= 433.33) were the better general combiners; In the essential oil trait the female lines L1 (g.c.a.= 0.240, x/Mean= 0.80) followed by L3 (g.c.a.= 0.143, x/Mean= 0.81), L2 (g.c.a.= 0.111, x/Mean= 0.85), L9 (g.c.a.= 0.203, x/Mean= 0.78) were the better general combiners. For the character the essential oil/plot (g) the female lines L10 (g.c.a.= 1.156, x/Mean= 0.97), L7 (g.c.a.= 0.869, x/Mean= 3.50), L11 (g.c.a. = 0.802, x/Mean=5.00), L9 (g.c.a.= 0.669, x/Mean= 1.67), and L2 (g.c.a. = 0.556, x/Mean=2.57), and among testers T3 (g.c.a.= 0.391, x/Mean= 4.67) and T4 (g.c.a.=0.330, x/Mean=5.67) were the better general combiners. The heritability in the narrow sense was low in all the traits (008-3.796 %) and in most of the traits genetic advance was poor (0.008-2.93) except the two traits i.e. high namely root yield/plot (ml) 180.44 and stomatal conductance (160.99) %. The relative magnitude of SCA variance was higher than GCA for all the traits in the present investigation, depicting the predominance of non-additive gene action for inheritance of these characters. The hybrids L7× T3 followed by L10× T5, L2×T3 and L4×T5 were best for the essential oil yield of better quality and the three hybrids showed high mean performance for the khusimol content (%) namely, L8 × T4 (34.50), L3 × T1 (34.30) and L13 × T4 (34.17) % with high s.c. a. could be exploited for large area cultivation.
SWI/SNF coordinates transcriptional activation through Rpd3-mediated histone hypoacetylation during quiescence entry

Whether or not a cell chooses to divide is a tightly regulated and extremely important decision. Cells from yeast to human are able to reversibly exit the cell cycle in response to environmental changes such as nutritional changes or removal of growth cues to become quiescent. An inappropriate response to environmental cues can result in overproliferation which can lead to cancer, or a failure to proliferate which can result in developmental defects, premature aging and defects in wound healing. While many of the cell signaling pathways involved in regulating cellular quiescence have been identified, how these pathways translate their messages into transcriptional outputs is not well characterized. We previously showed that the histone deacetylase Rpd3 mediates global histone deacetylation and transcription repression upon quiescence entry. How the activation of quiescence-specific genes occurs in the midst of this transcriptionally repressive environment is not well understood. We show that the SWI/SNF chromatin remodeling complex activates quiescence specific genes to promote entry into quiescence. We additionally show that SWI/SNF binding early during quiescence entry is important for facilitating localization of the transcriptional activator Gis1, as well as histone H4 hypoacetylation in coding regions later on. The increase in H4 acetylation that we observe at Snf2-regulated genes upon Snf2 depletion corresponds to a decrease in promoter-bound Rpd3, suggesting that Snf2 remodels chromatin not only to facilitate activator binding, but also the binding of Rpd3. These observations provide mechanistic insight as to how quiescence-specific genes can be activated in the face of global deacetylation and transcription repression.
Depressive disorders in type 2 diabetes – initial reports

Introduction: Diabetes patients experience burdens associated with adherence to treatment, self-control, and taking preventive measures against diabetic complications. These can contribute to the development of depressive disorders. Aim of the study: To assess the occurrence and severity of depressive disorders and factors connected with them among diabetes type 2 patients aged 35-64 years. Material and methods: The research was done with the use of a diagnostic survey method among 70 patients in the Metabolic Disease Department of the University Hospital in Krakow. The Beck Depression Inventory and the authors’ own interview questionnaire were used. Statistical analysis was carried out using Statistica 13.1, and p < 0.05 was the significance level. Results: The average number of points in the Beck Depression Inventory was 12.81 (moderate level of depressive disorders). Greater severity of depressive disorders was present in people who were professionally inactive, who defined their monthly income as insufficient, who felt uncertainty after diabetes diagnosis, whose treatment included both diet and insulin intake, who had problems with foot care, and who did not follow the diabetes treatment principles. The respondents who declared lack of support from their spouses felt the impact of diabetes on their mental well-being and confirmed the need for help in connection with the disease and had increased levels of depressive disorders. Conclusions: Due to the occurrence of depressive symptoms among diabetes patients it is necessary to conduct screening research for depressive disorders. It should be an indispensable element of the therapeutic team’s activities. enable action to be taken in order to prevent their aggravation and provide holistic care to patients. The presented results are fragments of research carried out as a part of statutory project disorders in
Heat killed Dietzia maris reduces lipopolysaccharide-induced inflammatory responses in murine adherent peritoneal cells

Dietzia maris (D. maris) is a gram-positive, aerobic, mycolic acid-containing actinomycete without mycelium. Actinomycetes such as Tsukamurella inchonensis reduce lipopolysaccharideinduced inflammatory responses in activated murine peritoneal macrophages. Here, the effects of D. maris on LPS-induced inflammatory responses were examined in mouse adherent peritoneal cells. D. maris was grown, harvested, and washed. Suspensions were standardized by wet weight, re-suspended in borate-buffered saline, and autoclaved. For in vivo study, each mouse was orally administered by bacterial suspension (5 × 107, 1 × 108 and 2 × 108 CFU/Mouse) consecutively for seven days. Control animals received the same amount of phosphate-buffered saline (PBS). Adherent peritoneal cells were harvested for in vitro experiments. Cells were lavaged and plated in RPMI 1640 medium, stimulated with LPS (100 ng/ml), and incubated for 2 h. Afterward, non-adherent cells were removed followed by adding freshly prepared medium. Supernatants (50 μl) were collected, centrifuged, mixed with Griess reagent, and the absorbance was measured at 560 nm. D . maris inhibited LPS-stimulated nitric oxide (NO) production in murine macrophages at concentrations of 5 × 107, 1 × 108 and 2 × 108 CFU/Mouse. Also, D. maris decreased LPS-induced production of pro-inflammatory cytokines of interleukin (IL)-6 at all doses. By contrast, tumor necrosis factor (TNF)-α was not effected by D. maris treatment of mice. Our results indicate that D. maris is a potent inhibitor of LPS-induced NO production. D. maris may be useful as a novel agent for the chemoprevention of inflammatory disease.
Fundamentals of Acute Relay CSI Severity

A probability density function (pdf) of bivariate exponential-correlated (exp.c.) Rayleigh fading—the simplest under correlated fading—has chronically been employed to model decode-and-forward relay networks under outdated channel state information (CSI) conditions. In addition to CSI outdatedness, CSI imperfection exists, however, their compound co-modelling—defined as acute imperfect CSI-outdated CSI—has not yet been performed in the existing literature. Using a joint pdf of trivariate exp.c. Nakagami- $m$ fading—which is more advanced than the pdf of bivariate exp.c. Rayleigh fading—this article models acute imperfect CSI-outdated CSI, and examines its impact on relay networks. Selection combining (SC) is also employed to improve the practicality of this work. Using a pdf of bivariate exp.c. Nakagami- $m$ fading, conditional pdfs of relay SNRs under acute-CSI severity are derived. Using the newly-derived conditional functions, pdfs of Rayleigh fading for SC deployment under acute imperfect CSI-outdated CSI severity are then obtained. Ergodic channel capacity, diversity gains, average-SNR gains, and outage probability are then computed to (a) obtain insight into the proposed findings, and (b) examine the impact of acute-CSI conditions on network performance. Existing results are employed for clarification purposes, and to show the advantage of the proposed work. Monte Carlo simulation is given, which matches theoretical predictions.
Performance and inheritance of yield and maize streak virus disease resistance in white maize and yellow conversions

In sub Saharan Africa, past effort has registered success in developing high yielding and foliar disease resistant maize (Zea mays L.) varieties, which are deficient in pro-vitamin A. A new initiative is to develop maize varieties, tolerant to foliar diseases and rich in pro-vitamin A carotenoids. To achieve this, yellow conversions of white testers and other elite maize varieties have been developed by the International Center for Maize and Wheat Development (CIMMYT). Unlike the white lines, limited information on agronomic performance and disease resistance is available for yellow maize conversions. This study was conducted to evaluate the performance of white maize and their corresponding yellow maize conversions for yield and tolerance to Maize streak virus (MSV) disease; and determine the inheritance patterns of these traits. Fourty seven three-way hybrids generated in a Line by tester mating design (North Carolina 2), 12 inbred lines (used as male parents), 4 single crosses (used as female parents) and 3 commercials checks were screened for resistance to Maize streak virus (MSV) disease at the National Crop Resources Research Institute (NaCRRI) in Uganda. The same genotypes were evaluated in a 9x5 alpha lattice design in three locations of Uganda (National Crop Resources Research Institute (NACRRI), National Semi Arid Resources Research Institute (NaSARRI) and Bulambuli) for agronomic performance. Results confirmed tolerance to MSV in testers CML202, CML395, CML444, CML445 and CML312-SR (white). Genotypes performed significantly differently for yield, anthesis days, plant height, ear height, husk cover, grain texture, reaction to Gray leaf spot (GLS) (P 0.05) in agronomic performance and tolerance to diseases. General combining ability (GCA) was more important than specific combining ability (SCA) for most traits, except for anthesis days, Turcicum leaf blight (TLB), GLS and yield. GCA effects for yield were not significant in both lines (male parents) and single cross testers (female parents) of white and yellow conversions. However, two unique cases were observed for diseases; yellow conversion of line CML444 significantly combined for susceptibility to TLB; while tester CML312/CML442 combined for resistance to GLS. Additionally, there was low heritably estimates for tolerance to MSV and yield. Generally, there was no significant difference between white and corresponding yellow maize conversion, implying that there is no significant loss in MSV resistance and yield performance while converting white into yellow maize.
Relationships between ecological niche and expected shifts in elevation and latitude due to climate change in South American temperate forest plants

Niche properties, such as breadth and position along environmental gradients, are hypothesized to determine plant responses to climate change. We explored the properties of different plant niches in a biodiversity hotspot, over a wide span of elevational and latitudinal ranges, to assess the relationship between niche characteristics and the modelled distributional shifts due to climate change.
Potential Protective Effect of Vitamin D on Cardiac Extrinsic pathways of apoptosis in Male Rats Fed with high fat diet

Background: Obesity and vitamin D deficiency are increasing in Kingdom of Saudi Arabia (KSA) in last decades. Researchers have shown a relation between both disorders and cardiovascular disease (CVD). The present work aimed to investigate the possible protective effect of vitamin D on cardiac apoptosis in rats fed with a high fat diet. Methods: This study included 30 male wistar rats and was divided in four groups. One group fed standard diet [control (C)], second group fed standard diet with vitamin D, third group fed hypercaloric diets [obese (Ob], and fourth group fed hypercaloric diets with vitamin D, for 22 weeks. The weight and length were measured to assess BMI and repeated every 45 days. Food intake and body weight were monitored. Heart tissues were collected for Quantitative Real-time polymerase chain reaction (qRT-PCR) to detect different genetic markers of apoptosis (FAS, FAS-L). Results: A significant increase in FAS, FAS-L gene expression in rats fed with high fat diet was found. Conclusion: The cardiac Extrinsic pathways of apoptosis were activated in rats fed with high fat diet. It was found that vitamin D protects the heart from the cardiac Independent pathways of apoptosis.
Impact of Complex Permeability Measurements Up to Millimeter-Wave Frequency Range

A highly sensitive microstrip-line-type probe using a flexible substrate was developed to measure thin-film permeability continuously up to the millimeter-wave frequency range (over 30 GHz). The probe enables broad bandwidth and highly sensitive permeability measurements without sample size limitations. The complex permeability of the CoFeB film (45 mm <inline-formula> <tex-math notation="LaTeX">$\times25$ </tex-math></inline-formula> mm and <inline-formula> <tex-math notation="LaTeX">$0.5~\mu \text{m}$ </tex-math></inline-formula> in thickness), CoNbZr film (25 mm <inline-formula> <tex-math notation="LaTeX">$\times25$ </tex-math></inline-formula> mm and 3 nm in thickness), and nickel ferrite film (8 mm <inline-formula> <tex-math notation="LaTeX">$\times5$ </tex-math></inline-formula> mm, and <inline-formula> <tex-math notation="LaTeX">$1.2~\mu \text{m}$ </tex-math></inline-formula> in thickness) were optimized. The measured permeability spectrum and ferromagnetic resonance frequency showed good agreement with the theoretical values based on the Landau–Lifshitz–Gilbert equation and eddy current generation up to 67 GHz.
Anatomically Constrained Deep Learning for Automating Dental CBCT Segmentation and Lesion Detection

Compared with the rapidly growing artificial intelligence (AI) research in other branches of healthcare, the pace of developing AI capacities in dental care is relatively slow. Dental care automation, especially the automated capability for dental cone beam computed tomography (CBCT) segmentation and lesion detection, is highly needed. CBCT is an important imaging modality that is experiencing ever-growing utilization in various dental specialties. However, little research has been done for segmenting different structures, restorative materials, and lesions using deep learning. This is due to multifold challenges such as content-rich oral cavity and significant within-label variation on each CBCT image as well as the inherent difficulty of obtaining many high-quality labeled images for training. On the other hand, oral-anatomical knowledge exists in dentistry, which shall be leveraged and integrated into the deep learning design. In this article, we propose a novel anatomically constrained Dense U-Net for integrating oral-anatomical knowledge with data-driven Dense U-Net. The proposed algorithm is formulated as a regularized or constrained optimization and solved using mean-field variational approximation to achieve computational efficiency. Mathematical encoding for transforming descriptive knowledge into a quantitative form is also proposed. Our experiment demonstrates that the proposed algorithm outperforms the standard Dense U-Net in both lesion detection accuracy and dice coefficient (DICE) indices in multilabel segmentation. Benefited from the integration with anatomical domain knowledge, our algorithm performs well with data from a small number of patients included in the training. Note to Practitioners—This article proposes a novel deep learning algorithm to enable the automated capability for cone beam computed tomography (CBCT) segmentation and lesion detection. Despite the growing adoption of CBCT in various dental specialties, such capability is currently lacking. The proposed work will provide tools to help reduce subjectivity and human errors, as well as streamline and expedite the clinical workflow. This will greatly facilitate dental care automation. Furthermore, due to the capacity of integrating oral-anatomical knowledge into the deep learning design, the proposed algorithm does not require many high-quality labeled images to train. The algorithm can provide good accuracy under limited training samples. This ability is highly desirable for practitioners by saving labor-intensive, costly labeling efforts, and enjoying the benefits provided by AI.
Detection and assembly of novel sequence insertions using Linked-Read technology

Motivation Emerging Linked-Read (aka read-cloud) technologies such as the 10x Genomics Chromium system have great potential for accurate detection and phasing of largescale human genome structural variations (SVs). By leveraging the long-range information encoded in Linked-Read sequencing, computational techniques are able to detect and characterize complex structural variations that are previously undetectable by short-read methods. However, there is no available Linked-Read method for detection and assembly of novel sequence insertions, DNA sequences present in a given sequenced sample but missing in the reference genome, without requiring whole genome de novo assembly. In this paper, we propose a novel integrated alignment-based and local-assembly-based algorithm, Novel-X, that effectively uses the barcode information encoded in Linked-Read sequencing datasets to improve detection of such events without the need of whole genome de novo assembly. We evaluated our method on two haploid human genomes, CHM1 and CHM13, sequenced on the 10x Genomics Chromium system. These genomes have been also characterized with high coverage PacBio long-reads recently. We also tested our method on NA12878, the wellknown HapMap CEPH diploid genome and the child genome in a Yoruba trio (NA19240) which was recently studied on multiple sequencing platforms. Detecting insertion events is very challenging using short reads and the only viable available solution is by long-read sequencing (e.g. PabBio or ONT). Our experiments, however, show that Novel-X finds many insertions that cannot be found by state of the art tools using short-read sequencing data but present in PacBio data. Since Linked-Read sequencing is significantly cheaper than long-read sequencing, our method using Linked-Reads enables routine large-scale screenings of sequenced genomes for novel sequence insertions. Availability Software is freely available at https://github.com/1dayac/novel_insertions Contact imh2003@med.cornell. edu Supplementary information Supplementary data are available at https://github.com/1dayac/novel_insertions_supplementary
CONNECTION g.307 G > A SNP POLYMORPHISM OF THE ALPHA-FUKOZYLTRASFERAZA 1 GENE WITH ECONOMIC-USEFUL TRAITS IN THE LARGE WHITE PIG BREED

Г. С. РУДОМАН, В. М. БАЛАЦЬКИЙ, В. Ю. НОР, В. О. ВОВК Інститут свинарства і агропромислового виробництва НААН (Полтава, Україна) rudoman.halyna@gmail.com Здійснена оцінка поліморфізму g.307 G > A SNP гену FUT1, що асоційований із резистентністю тварин до ентеропатогенних штамів бактерії Escherichia colі та із показниками продуктивності у свиней великої білої породи методом ПЛР-ПДРФ. Встановлені основні генетико-популяційні параметри стада за обраним локусом. Розподіл частот алелів показав домінування алелю G у даній вибірці. За результатом однофакторного дисперсійного аналізу виявлений вплив генотипів гену FUT1 (g.307 G > A SNP) на показники середньодобового приросту (р ≤ 0,001), віку досягнення живої маси 100 кг (р ≤ 0,001), товщини шпику на рівні VI – VII хребців (р ≤ 0,01) та селекційного індексу відгодівельних якостей (р ≤ 0,01). Ключові слова: ген FUT1, свині, велика біла порода, поліморфізм, колібактеріоз, показники продуктивності