Miracle-dz/UniFAR-FTUs huggingface dataset:
The Use of Teat-End Hyperkeratosis to Predict Somatic Cell Count and Milk Quality of Holstein Cows Raised in Egypt

The study aimed to investigate the association between teat-end hyperkeratosis (THK) and somatic cell count (SCC) and to assess the effect of SCC on milk yield, fat, and protein percentages of Holstein cows. A total of 740 udder quarters of 185 Holstein cows kept in three commercial herds in Egypt were enrolled in the study from May to September 2019. Foremilk samples were collected from udder quarters for assessing milk SCC, fat, and protein percentages. On the same cows, a digital picture of each teat end orifice was taken with a digital camera. Cows’ teats were assessed for THK and classified into two different groups of hyperkeratosis; mild and severe THK. SCC was converted to five classes of somatic cell score (SCS). Simple linear regression was performed to determine the loss of milk yield, fat, and protein percentages. SCC was significantly affected by THK (p<0.0001). About 57% of teats were classified as mild THK and 43% as severe THK. The teats with severe THK recorded higher SCC in milk. It was observed that SCS had a significant effect on fat and protein percentages (p<0.0001). A similar trend was shown for the effect of SCS on milk yield (p<0.05), where the highest values of milk traits were obtained for the lowest SCS. The loss of milk was 220 g/day. Also, fat and protein percentages decreased by 0.11% and 0.08%, respectively, for each unit increase in SCS, from zero to four. In conclusion, severe THK can lead to high SCC, which negatively affects milk traits.
Hospital competition and quality for non‐emergency patients in the English NHS

We investigate the effect on the quality of three high-volume non-emergency treatments of a reform that relaxed restrictions on patient choice of hospital. We employ a quasi difference-in-difference strategy and use control functions allowing for patient selection into providers correlated with unobserved morbidity. Public hospitals facing more rivals reduced quality, increased waiting times, and reduced length of stay for hip and knee replacements. This is likely due to regulated prices implying larger losses on these treatments compared to coronary artery bypass grafts, where no effects were found. Our ﬁndings are robust to estimation methods and competition measures, allowing for private providers’ entry.
A method for mapping morphological convergence on three‐dimensional digital models: the case of the mammalian sabre‐tooth

Morphological convergence can be assessed using a variety of statistical methods. None of the methods proposed to date enable the visualization of convergence. All are based on the assumption that the phenotypes either converge, or do not. However, between species, morphologically similar regions of a larger structure may behave differently. Previous approaches do not identify these regions within the larger structures or quantify the degree to which they may contribute to overall convergence. Here, we introduce a new method to chart patterns of convergence on three‐dimensional models using the R function conv.map. The convergence between pairs of models is mapped onto them to visualize and quantify the morphological convergence. We applied conv.map to a well‐known case study, the sabre‐tooth morphotype, which has evolved independently among distinct mammalian clades from placentals to metatherians. Although previous authors have concluded that sabre‐tooths kill using a stabbing ‘bite’ to the neck, others have presented different interpretations for specific taxa, including the iconic Smilodon and Thylacosmilus. Our objective was to identify any shared morphological features among the sabre‐tooths that may underpin similar killing behaviours. From a sample of 49 placental and metatherian carnivores, we found stronger convergence among sabre‐tooths than for any other taxa. The morphological convergence is most apparent in the rostral and posterior parts of the cranium. The extent of this convergence suggests similarity in function among these phylogenetically distant species. In our view, this function is most likely to be the killing of relatively large prey using a stabbing bite.
Association of the presence of estrogen and progesterone receptors in uterine carcinosarcoma with improved survival and increased immunogenicity.

5588 Background: Recent data has shed light on molecular profiles of uterine carcinosarcoma (UCS), but few have correlated molecular profiles with prognosis. In a preliminary data analysis, we found that hormone receptors (HR)—estrogen receptor (ER) and progesterone receptor (PR)—expression was associated with improved OS. Here, we investigate the molecular profile differences between ER+/- and PR +/- tumors. Methods: Tumor samples were analyzed using Next-Generation sequencing of DNA (NextSeq, 592 genes or NovaSeq, whole exome sequencing) and RNA (NovaSeq, whole transcriptome sequencing) and immunohistochemistry (IHC) at the Caris Life Sciences Laboratory (Phoenix, AZ). ER and PR tested by IHC on whole tumor (cut-off: +1, 10%). PD-L1 IHC used SP-142 (cut-off >1%). MSI was tested by FA, IHC an NGS. TMB was measured by totaling somatic mutations per tumor (high > 10 mutations per MB). Immune cell fraction was calculated by QuantiSeq. Overall survival (OS) information was obtained from insurance claims data and Kaplan-Meier estimates were calculated for molecularly defined cohorts. Statistical significance was determined by chi-square and Wilcoxon rank sum test and p-values adjusted for multiple comparisons (q) to be <0.05. Results: 1,144 UCS tumors were included. (ER+, n=261; PR+, n=197; HR+ (ER+ and PR+), n=168). Median OS for patients with hormone receptor (HR)+ tumors was significantly longer than for patients with HR- tumors (months: 34.8 vs 17.4; HR(95% CI): 0.67 (0.53-0.84), p<0.01). This remained significant for ER (29.4 vs 17.3) and PR (25.3 vs 18.7) individually. ER+ tumors had fewer alterations in the TP53 pathway (71.4% vs 82.1%) in the WNT (19.5% vs 5.8%) pathway than ER- tumors (q<0.05). PR+ tumors had similar findings in the TP53 and WNT pathways, and also more alterations in the DNA damage sensor pathway. Both ER+ and PR+ UCS tumors had significantly increased MSI-H (ER: 10.9% vs 5.5%, PR: 12.9% vs 5.5%) and TMB-H (ER: 16.8% vs 6.0%; PR: 19.5% vs 6.1%) (all q<0.05) compared to ER- and PR- tumors. They also had increased T-reg cells in their immune micro-environment and increased expression of the immune checkpoint gene IDO1 (q<0.05; Table). Conclusions: HR+ tumors have distinct molecular profiles from HR- tumors. ER+ and PR+ UCS tumors appear more immunogenic with more frequent MSI-H status, TMB-H, increased infiltrating regulatory T-cells and IDO1 expression, suggesting possible benefit with immune-oncology (IO) therapy. This may contribute to the observed improved OS, but more data are needed to determine if HR status is a marker of response to IO therapy. [Table: see text]
Prolyl 4-hydroxylase : genomic cloning of the human and mouse α(II) subunit, tissue distribution of type I and II isoenzymes, and cloning and characterization of a novel prolyl 4-hydroxylase from Caenorhabditis elegans

The collagens are a family of extracellular matrix proteins with a widespread tissue distribution. Collagen biosynthesis requires the hydroxylation of a number of proline residues by prolyl 4hydroxylase. This posttranslational modification is essential for the synthesis of all collagens, as 4hydroxyproline deficient collagens cannot form stable triple helices at body temperature. The genes for the human and mouse prolyl 4-hydroxylase α(II) subunits were cloned and characterized in this study. The human and mouse genes are 34.6 and 30.3 kb in size, respectively, consisting of 16 exons and 15 introns. The intron sizes vary from 48-49 bp to over 8 kb in both genes. The 5' flanking regions contain no TATA box, but there are several motifs that may act as transcription factor binding sites. A novel mutually exclusively spliced exon 12a was identified in both genes. Both variants of the α(II) subunit were found to be expressed in a variety of tissues and both formed a fully active recombinant tetramer with the β subunit when expressed in insect cells. Tissue distribution of the type I and type II prolyl 4-hydroxylase isoenzymes was studied in developing, mature, and malignant cells and tissues by immunofluorescence and Western blotting. The results indicate that the type I isoenzyme is the main form in many cell types. Skeletal myocytes and smooth muscle cells appeared to have the type I isoenzyme as their only prolyl 4-hydroxylase form, whereas the type II isoenzyme was clearly the main form in chondrocytes. A strong signal for the type II enzyme was detected in cultured umbilical and capillary endothelial cells, whereas the type I isoenzyme could not be detected in these cells by immunostaining or Western blotting. Similar studies on primary chondroand osteosarcomas and benign bone tumours indicated that the type I isoenzyme is the predominant form in both types of bone sarcoma, whereas the type II isoenzyme was more abundantly expressed in benign tumours. In chondrosarcomas, the type II isoenzyme was expressed in the nonmalignant chondrocytes, whereas their malignant counterparts switched their expression pattern to that of the type I isoenzyme. Two isoforms of the catalytic prolyl 4-hydroxylase α subunit, PHY-1 and PHY-2, have previously been characterized from Caenorhabditis elegans. This study reports the cloning and characterization of a third C. elegans α subunit isoform, PHY-3, which is much shorter than the previously characterized vertebrate and C. elegans α subunits. Nematodes homozygous for a phy-3 deletion were phenotypically wild type and fertile, but the 4-hydroxyproline content of their early embryos was reduced by about 90%. The expression of PHY-3 was found to be restricted to spermatheca of late larvae and adult nematode, indicating that PHY-3 is likely to be involved in the synthesis of collagens of the early embryo egg shells.
Demographic stability of the Australian temperate exoneurine bees (Hymenoptera: Apidae) through the Last Glacial Maximum

The period of the Last Glacial Maximum (LGM) is characterised by severe cooling and extreme aridity in Australia. Australian temperate‐adapted bees experienced entirely new conditions over the LGM; however, few studies focused on the response of these key pollinators and their dependent plants to the LGM in Australia. In this study, we investigated the impact of the LGM climatic conditions on the population histories of the Australian temperate exoneurine bees regarded as critical native pollinators in the continent. To address this issue, we first identified the bee species using a combination of morphological and molecular approaches including phylogenetic and species delimitation methods. The analyses revealed three exoneurine genera, including Brevineura, Exoneura and Inquilina. Our estimated divergence time between Exoneura and Inquilina was close to that of previous phylogenetic studies of the exoneurine bees, which used different dating methods. The haplotype network analyses indicated the geographical structuring of the haplotypes within Exonuera and Inquilina species. We then utilised Bayesian skyline analyses to reconstruct demographic histories of the genus Exoneura for which sufficient haplotype diversity was found. The results showed that the population size of Exoneura species remained unchanged over the LGM or even increased shortly before it. The wide geographical distribution of the exoneurine species in Australia and earlier development of genetic and physiological adaptations are discussed as possibilities that enabled the species to maintain their population sizes over the LGM.
COVID-19 Pandemic and Higher Education: Leveraging on Digital Technologies and Mobile Applications for Online Learning in Ghana

Since mid-March 2020, educational systems worldwide and particularly Ghana were under increasing pressure to use the new Digital Technologies (DTs) and mobile applications (apps) to assist teachers in guiding students to continue with online learning activities due to the COVID-19 pandemic. The study is aimed at assessing the utilization of DTs and apps tools by students during the COVID-19 pandemic and how those technologies have affected online learning in institutions of higher education in Ghana. The researcher adopted an online survey and exploratory-based design that utilized quantitative and qualitative approaches to purposively collect data from N=784 students from three major public universities in Ghana. Also, the study applied Uses and Gratification as the theoretical basis in understanding the utilization of DTs and their possible limitations for remote learning during the peak of COVID-19 in Ghana. This study reported that the specific DMTs and mobile apps used by students in higher education for online learning are smarts phones and apps such as Class In, Zoom, Skype, and Instagram live stream. This study also revealed that Personal Learning Network (PLN) such as WhatsApp, Facebook, Twitter were also actively used by students for remote online learning. Again, the study shows that 77.1% of students in the sampled three universities were fully aware of the DTs and apps utilized for online learning during COVID-19. Also, the findings from this study report that students in higher institutions identified unstable electricity for continuous online learning, especially for those students in rural areas, unreliable internet service, poor WiFi connections, expensive smartphones /laptops, and high cost of inter bundle as key challenges of using DMTs and mobile apps for online learning during the COVID-19 pandemic. Finally, on the perceived usefulness of DTs and mobile apps among students for online learning in higher educational institutions, the findings from this study suggest that DMT's and apps were of great benefit to students for remote online learning.
Correlation between Urinary Bisphenol A, Serum 25 OH Vitamin D Levels and Preterm Birth in Egyptian Pregnant Women

Introduction: Preterm birth (PTB) is a worldwide cause of infant mortality and morbidity. Prenatal exposure to endocrine disrupting chemicals (EDCs) especially bisphenol A (BPA) is questioned as a potential risk factor for PTB. Lower gestational vitamin D levels are associated with various maternal and fetal complications. Aim of the Work: This study aimed to evaluate the gestational exposure to BPA and the potential association between urinary BPA and serum vitamin D levels in a sample of Egyptian women having spontaneous PTB. Subjects and Methods: This study was conducted on 106 reproductive aged females divided into Group I with full term delivery (37-42 weeks gestational age) as “control group” and Group II with spontaneous preterm contractions (24 - ˂37 weeks gestational age) that ended with preterm delivery as “PTB group”. Results: The median level of urinary uncorrected and specific gravity (SG)-corrected BPA was found to be higher in PTB group with high statistically significant difference between both studied groups (P<0.001). Vitamin D deficiency (≤ 20 ng/ml) was detected in 35.8% of PTB cases with a statistically significant difference (P=0.001) among the studied groups. There was statistically significant strong negative correlation (P<0.001) between serum vitamin D and both urinary uncorrected and SG-corrected BPA among the PTB group. Conclusions: high Urinary BPA and low vitamin D levels represent possible predictive environmental risk factors for PTB.
Do Teachers’ Qualifications and Experience Influence Academic Performance of Students in Basic Science in Junior Secondary Schools in Nigeria?

This study investigated the influence of teachers’ qualification and experience on students’ academic performance in basic science in junior secondary schools in Nigeria. The study was a descriptive survey type of research. Simple random sampling was used to select eight Junior Secondary Schools (J.S.S.) in Ogun East senatorial district of Ogun State. It included 18basic science teachers and 540 junior secondary school students. The data were collected using a questionnaire and basic science achievement test. The data collected were analysed using descriptive statistics, one-way analysis of variance and Pearson Product-Moment Correlation. The findings of this study revealed that most of the basic science teachers at the J.S. S. level were not trained as basic science teachers; science teachers’ qualifications influenced students’ academic performance in basic science; basic science teachers’ years of teaching experience did not have a positive correlation with students’ academic performance in basic science.
Association between antibiotic exposure and survival in patients with hepatocellular carcinoma treated with nivolumab.

e16186 Background: Nivolumab, an immune checkpoint inhibitor, has improved the outcomes of patients with hepatocellular carcinoma (HCC). It is approved for HCC patients previously treated with sorafenib. Outcomes have been reported in previous studies, in malignancies other than HCC, to be worse when patients have been exposed to antibiotics while receiving immune checkpoint inhibitors. We aimed to evaluate the effects of antibiotics on survival in HCC patients treated with nivolumab. Methods: We performed a retrospective review of 59 patients with advanced HCC that have been treated with nivolumab in two academic centers in Saudi Arabia. Patient characteristics, tumor data, antibiotic use (2 weeks prior, during, and 4 weeks after nivolumab therapy), survival data, and other factors were collected. Log-rank test analysis was performed to test the difference in overall survival (OS) time with and without antibiotics use. Results: The majority of patients were males (n=51, 85%), and 38 were Child-Pugh A (64%). A large number of patients had Barcelona Clinic Liver Cancer (BCLC) stage C tumors (n=42, 71%), and 20 patients (34%) used antibiotics. Most patients received nivolumab as second-line therapy after exposure to sorafenib (n=49, 83%). In patients who received nivolumab as first- or second-line therapy (n=57) and did not receive antibiotics, the median OS was double that of patients who received antibiotics (10 vs. 4.5 months, P=0.04). In child A patients who received nivolumab as second-line therapy (n=32), those who were exposed to antibiotics had a statistically significant shorter median OS compared to those who did not (5.5 vs. 20 months, P=0.04). More patients achieved partial response, or complete response (as per modified RECIST criteria) in the cohort that did not receive antibiotics compared to patients who received antibiotics (21% vs. 15%) but that was not statistically significant (P=0.6). Conclusions: This study shows that HCC patients receiving nivolumab have worse survival if they received antibiotics. Antibiotic mediated alteration of the gut microbiome may impact nivolumab response and shorten patient survival. Although this finding may warrant a prospective larger study but it is consistent with other previous studies. Antibiotics should be used very cautiously when treatment with checkpoint inhibitors is considered.
Optimising Sentinel-2 MSI spatial resolution for estimating foliar nitrogen concentration in miombo woodlands

ABSTRACT The landscape-level estimation of nitrogen will constitute a significant input in global change models. High resolution broadband satellite technology is a promising solution to the limitation of spatial coverage. This study sought to identify an optimal spatial resolution for estimating foliar nitrogen in dry miombo woodlands. The contrast texture measure, calculated at increasing window size on Sentinel-2 imagery, was related to field measured nitrogen via random forest regression models. Our results show that the optimum size for estimating nitrogen is 50m. This result is significant in understanding the scale at which dynamics in foliar nitrogen concentration can be remotely measured.
Urban green space soundscapes and their perceived restorativeness

1. The positive influence of urban green spaces on human health and well- being is well known while the pathways are little understood. Past research has largely focused on visual stimuli, yet the auditory pathway is also an important means for contact with nature. 2. The sonic environments of urban green spaces, however, are rarely entirely natural and many differ in their composition of natural sounds and anthropogenic noise. Few studies have investigated how these differences may impact the restorative potential of these soundscapes and, following questions: (a) Do perceived restorativeness and perceived restorative outcomes vary in park soundscapes differing in perceived bird and traffic sounds? (b) How do perceived restorativeness and perceived restorative outcomes vary with perceived awareness, volume and pleasantness of bird calls and traffic sounds? (c) Do perceived traffic sounds constrain restoration by moderating the effect of perceived bird pleasantness on perceived restorativeness and perceived restorative outcomes? (d) How do perceptions of environmental characteristics of the soundscapes influence perceived restorativeness and perceived restorative outcomes? (e) Do noise sensitivity, environmental knowledge and the amount of time lived in the city moderate the effect of bird calls on perceived restorativeness and perceived restorative outcomes?
Slab Transport of Fluids to Deep Focus Earthquake Depths—Thermal Modeling Constraints and Evidence From Diamonds

The nature and cause of deep earthquakes remain enduring unknowns in the field of seismology. We present new models of thermal structures of subducted slabs traced to mantle transition zone depths that permit a detailed comparison between slab pressure/temperature (P/T) paths and hydrated/carbonated mineral phase relations. We find a remarkable correlation between slabs capable of transporting water to transition zone depths in dense hydrous magnesium silicates with slabs that produce seismicity below ∼300‐km depth, primarily between 500 and 700 km. This depth range also coincides with the P/T conditions at which oceanic crustal lithologies in cold slabs are predicted to intersect the carbonate‐bearing basalt solidus to produce carbonatitic melts. Both forms of fluid evolution are well represented by sublithospheric diamonds whose inclusions record the existence of melts, fluids, or supercritical liquids derived from hydrated or carbonate‐bearing slabs at depths (∼300–700 km) generally coincident with deep‐focus earthquakes. We propose that the hydrous and carbonated fluids released from subducted slabs at these depths lead to fluid‐triggered seismicity, fluid migration, diamond precipitation, and inclusion crystallization. Deep focus earthquake hypocenters could track the general region of deep fluid release, migration, and diamond formation in the mantle. The thermal modeling of slabs in the mantle and the correlation between sublithospheric diamonds, deep focus earthquakes, and slabs at depth demonstrate a deep subduction pathway to the mantle transition zone for carbon and volatiles that bypasses shallower decarbonation and dehydration processes.