Miracle-dz/UniFAR-FTUs huggingface dataset:
High Prevalence of Multidrug-Resistant Klebsiella pneumoniae in a Tertiary Care Hospital in Ethiopia

Klebsiella pneumoniae poses an urgent public health threat, causing nosocomial outbreaks in different continents. It has been observed to develop resistance to antimicrobials more easily than most bacteria. These days, multidrug-resistant strains are being increasingly reported from different countries. However, studies on the surveillance of multidrug-resistant Klebsiella pneumoniae are very rare in Ethiopia. This study aimed to determine the antimicrobial resistance patterns and magnitude of MDR K. pneumoniae isolates from patients attending or admitted to Tikur Anbessa Specialized Hospital (TASH). A cross-sectional study was conducted from September 2018 to February 2019 at TASH, Addis Ababa, Ethiopia. Identification of K. pneumoniae was done by examining the Gram stain, colony characteristics on MacConkey agar and 5% sheep blood agar, as well as using a series of biochemical tests. Antimicrobial susceptibility testing of the isolates for 21 antimicrobials was done by the Kirby–Bauer disc diffusion technique. Data were double entered using Epidata 3.1 and exported to SPSS version 25 software for analysis. Among the total K. pneumoniae isolates (n = 132), almost all 130 (98.5%) were MDR. Two (1.5%) isolates showed complete non-susceptibility to all antimicrobial agents tested. Moreover, a high rate of resistance was observed to cefotaxime and ceftriaxone 128 (97%), trimethoprim-sulfamethoxazole 124 (93.9%), and cefepime 111 (84.1%). High susceptibility was recorded to amikacin 123 (93.2%), imipenem 107 (81.1%), meropenem 96 (72.7%), and ertapenem 93 (70.5%). K. pneumoniae isolates showed a high rate of resistance to most of the tested antimicrobials. The magnitude of MDR K. pneumoniae was very alarming. Therefore, strengthening antimicrobial stewardship programs and antimicrobial surveillance practices is strongly recommended in TASH.
A Time-Saving Strategy to Generate Double Maternal Mutants by an Oocyte-Specific Conditional Knockout System in Zebrafish

Simple Summary Maternally supplied mRNAs and proteins, termed maternal factors, are produced by over 14,000 coding genes in zebrafish. They play exclusive roles in controlling the formation of oocytes and the development of early embryos. These maternal factors can also compensate for the loss of function of its corresponding zygotic gene products. Thus, eliminating both maternal and zygotic gene products is essential to elucidate the functions of more than half of zebrafish genes. However, it is always challenging to inactivate maternal factors, because traditional genetic methods are either technically demanding or time-consuming. Our recent work established a rapid conditional knockout method to generate maternal or maternal and zygotic mutants in one fish generation. Here, we further test the feasibility of this approach to knock out two maternal genes with functional redundancy simultaneously. As a proof of principle, we successfully generated double maternal mutant embryos for dvl2 and dvl3a genes in three months for the first time. The cell movement defects in mutant embryos obtained by this approach mimic the genuine mutant embryos generated after fifteen months of time-consuming screening following the previously reported mosaic strategy. Therefore, this method has the potential to speed up the functional study of paralogous maternal genes. Abstract Maternal products are those mRNAs and proteins deposited during oogenesis, which play critical roles in controlling oocyte formation, fertilization, and early embryonic development. However, loss-of-function studies for these maternal factors are still lacking, mainly because of the prolonged period of transgenerational screening and technical barriers that prevent the generation of maternal (M) and maternal and zygotic (MZ) mutant embryos. By the transgenic expression of multiple sgRNAs targeting a single gene of interest in the background of a transgenic line Tg(zpc:zcas9) with oocyte-specific cas9 expression, we have successfully obtained maternal or maternal–zygotic mutant for single genes in F1 embryos. In this work, we tandemly connected a maternal GFP marker and eight sgRNA expression units to target dvl2 and dvl3a simultaneously and introduced this construct to the genome of Tg(zpc:zcas9) by meganuclease I-Sce I. As expected, we confirmed the existence of Mdvl2;Mdvl3a embryos with strong defective convergence and extension movement during gastrulation among outcrossed GFP positive F1 offspring. The MZdvl2;MZdvl3a embryos were also obtained by crossing the mutant carrying mosaic F0 female with dvl2+/−;dvl3a−/− male fish. This proof-of-principle thus highlights the potential of this conditional knockout strategy to circumvent the current difficulty in the study of genes with multiple functionally redundant paralogs.
Clinical Applications and Factors Involved in Validating Thermal Windows Used in Infrared Thermography in Cattle and River Buffalo to Assess Health and Productivity

Simple Summary Infrared thermography is a clinically useful method for detecting physiopathological alterations in animals through microvascular changes. It has been adapted for applications with large species, as a support tool in evaluating animal welfare, and can also contribute to productive and reproductive evaluations. This review discusses the thermal windows currently in use and characterizes their differences and limitations as resources for early detection and diagnosis in cattle and river buffaloes. Abstract Infrared thermography (IRT) is a non-ionizing, non-invasive technique that permits evaluating the comfort levels of animals, a topic of concern due to the growing interest in determining the state of health and welfare of production animals. The operating principle of IRT is detecting the heat irradiated in anatomical regions characterized by a high density of near-surface blood vessels that can regulate temperature gain or loss from/to the environment by modifying blood flow. This is essential for understanding the various vascular thermoregulation mechanisms of different species, such as rodents and ruminants’ tails. The usefulness of ocular, nasal, and vulvar thermal windows in the orbital (regio orbitalis), nasal (regio nasalis), and urogenital (regio urogenitalis) regions, respectively, has been demonstrated in cattle. However, recent evidence for the river buffalo has detected discrepancies in the data gathered from distinct thermal regions in these large ruminants, suggesting a limited sensitivity and specificity when used with this species due to various factors: the presence of hair, ambient temperature, and anatomical features, such as skin thickness and variations in blood supplies to different regions. In this review, a literature search was conducted in Scopus, Web of Science, ScienceDirect, and PubMed, using keyword combinations that included “infrared thermography”, “water buffalo”, “river buffalo” “thermoregulation”, “microvascular changes”, “lacrimal caruncle”, “udder”, “mastitis”, and “nostril”. We discuss recent findings on four thermal windows—the orbital and nasal regions, mammary gland in the udder region (regio uberis), and vulvar in the urogenital region (regio urogenitalis)—to elucidate the factors that modulate and intervene in validating thermal windows and interpreting the information they provide, as it relates to the clinical usefulness of IRT for cattle (Bos) and the river buffalo (Bubalus bubalis).
Effects of Different Housing Systems during Suckling and Rearing Period on Skin and Tail Lesions, Tail Losses and Performance of Growing and Finishing Pigs

Simple Summary Weaning involves multiple stressors and is one of the most critical periods for piglets. It is known that pigs try to compensate stressful events by different coping strategies that might culminate in the biting of other pigs. The reduction in the number of stressors by optimizing housing conditions might be a way to reduce tail biting, one huge challenge in modern pig production. Since tail docking as a measure to avoid injuries is banned by EU regulations, this study aims to present alternatives to combat tail biting. The present work shows that the group housing of lactating sows and their litters improves pig welfare after regrouping events in terms of skin lesions. Rearing in the farrowing pen with reduced regrouping positively affected the incidence of tail lesions and losses of undocked pigs. Against expectations, free farrowing and group housing systems had no negative impact on later performance during rearing or fattening. Abstract Feasible alternatives to stressful weaning and tail-docking are needed to inhibit tail biting. Therefore, we investigated the effects of housing systems for 1106 pigs that were weaned from: (1) conventional farrowing crates (FC), (2) free-farrowing pens (FF), or (3) group housing of lactating sows (GH) into (1) conventional rearing pens (Conv) or (2) piglets remained in their farrowing pens for rearing (Reaf). Tails were docked or left undocked batchwise. All pigs were regrouped for the fattening period. Pigs were scored for skin lesions, tail lesions and losses. After weaning, Conv-GH pigs had significantly less skin lesions than Conv-FC and Conv-FF pigs. After regrouping for fattening, Reaf-GH pigs had significantly less skin lesions than Conv pigs, Reaf-FC and Reaf-FF. The frequency of tail lesions of undocked Conv pigs peaked in week 4 (66.8%). Two weeks later, Reaf undocked pigs reached their maximum (36.2%). At the end of fattening, 99.3% of undocked Conv pigs and 43.1% of undocked Reaf pigs lost parts of their tail. In conclusion, the co-mingling of piglets during suckling reduced the incidence of skin lesions. Rearing in the farrowing pen significantly reduced the incidence of tail lesions and losses for undocked pigs. No housing system negatively affected the performance.
Associations between relative grip strength and type 2 diabetes mellitus: The Yangpyeong cohort of the Korean genome and epidemiology study

Objective To investigate the association between relative grip strength and the prevalence of type 2 diabetes mellitus (T2DM) independently and in combination with body mass index (BMI) in Korean adults. Methods The cross-sectional study includes 2,811 men and women (age 40 to 92 years old) with no history of heart disease, stroke, or cancer. Relative grip strength was measured by a handheld dynamometer and calculated by dividing absolute grip strength by body weight. Logistic regression analysis was used to calculate the odds ratios (ORs) and 95% confidence intervals (CIs) of T2DM by sex-specific quintiles of relative grip strength. In a joint analysis, participants were classified into 4 groups: “weak (lowest 20% quintile one) and normal weight (BMI <25.0 kg/m2)”, “weak and overweight/obese (BMI ≥25.0 kg/m2)”, “strong (upper 80% four quintiles) and normal weight” or “strong and overweight/obese”. Results Among the 2,811 participants, 371 were identified as having T2DM. Compared with the lowest quintile of relative grip strength (weakest), the ORs (95% CIs) of T2DM were 0.73 (0.53–1.02), 0.68 (0.48–0.97), 0.72 (0.50–1.03), and 0.48 (0.32–0.74) in upper quintiles two, three, four, and five, respectively, after adjusting for BMI and other potential confounders. In the joint analysis, compared with the “weak and overweight/obese” reference group, the odds of T2DM [ORs (95% CIs)] was lower in the “strong and overweight/obese” group [0.65 (0.46–0.92)] and the “strong and normal weight” group [0.49 (0.35–0.67)], after adjusting for potential confounders. Conclusion In this cross-sectional study, greater relative grip strength was associated with a lower prevalence of T2DM independent of BMI in Korean adults. Additional prospective studies are needed to determine whether a causal association exists between relative grip strength and T2DM prevalence considering BMI.
Acute Lung Injury Biomarkers in the Prediction of COVID-19 Severity: Total Thiol, Ferritin and Lactate Dehydrogenase

SARS-CoV-2 (COVID-19) patients who develop acute respiratory distress syndrome (ARDS) can suffer acute lung injury, or even death. Early identification of severe disease is essential in order to control COVID-19 and improve prognosis. Oxidative stress (OS) appears to play an important role in COVID-19 pathogenesis; we therefore conceived a study of the potential discriminative ability of serum biomarkers in patients with ARDS and those with mild to moderate disease (non-ARDS). 60 subjects were enrolled in a single-centre, prospective cohort study of consecutively admitted patients: 29 ARDS/31 non-ARDS. Blood samples were drawn and marker levels analysed by spectrophotometry and immunoassay techniques. C-reactive protein (CRP), lactate dehydrogenase (LDH), and ferritin were significantly higher in ARDS versus non-ARDS cases at hospital admission. Leukocytes, LDH, ferritin, interleukin 6 (IL-6) and tumour necrosis factor alpha (TNF-α) were also significantly elevated in ARDS compared to non-ARDS patients during the hospital stay. Total thiol (TT) was found to be significantly lower in ARDS. Conversely, D-dimer, matrix metalloproteinase-9 (MMP-9) and advanced glycosylated end products (AGE) were elevated. Leukocytes, LDH, CRP, ferritin and IL-6 were found to be significantly higher in non-survivors. However, lymphocyte, tumour necrosis factor beta (TGF-β), and TT were lower. In summary, our results support the potential value of TT, ferritin and LDH as prognostic biomarkers for ARDS development in COVID-19 patients, distinguishing non-ARDS from ARDS (AUCs = 0.92; 0.91; 0.89) in a fast and cost-effective manner. These oxidative/inflammatory parameters appear to play an important role in COVID-19 monitoring and can be used in the clinical management of patients.
Incidence, Etiology, and Risk Factors of Clinical Mastitis in Dairy Cows under Semi-Tropical Circumstances in Chattogram, Bangladesh

Simple Summary Bovine clinical mastitis is an inflammatory disease of the mammary gland associated with visual changes in the milk and/or the udder. We show that the incidence of clinical mastitis in commercial dairy farms in Bangladesh is high but with large variation between farms. Streptococci and non-aureus Staphylococci were the most frequently isolated bacteria from quarter milk samples. Staphylococcus aureus and non-aureus Staphylococci were often resistant against penicillin and oxacillin. This work suggests an urgent need for improved udder health management and specifically a more prudent use of antimicrobial agents following a treatment protocol. Abstract Clinical mastitis (CM) is an important production disease in dairy cows, but much of the knowledge required to effectively control CM is lacking, specifically in low-income countries where most farms are small and have specific dairy management, such as regular udder cleaning and practicing hand milking. Therefore, we conducted a 6-month-long cohort study to (a) estimate the incidence rate of clinical mastitis (IRCM) at the cow and quarter level, (b) identify risk factors for the occurrence of CM, (c) describe the etiology of CM, and (d) quantify antimicrobial susceptibility (AMS) against commonly used antimicrobial agents in S. aureus and non-aureus Staphylococcus spp. (NAS) in dairy farms in the Chattogram region of Bangladesh. On 24 farms, all cows were monitored for CM during a 6-month period. Cases of CM were identified by trained farmers and milk samples were collected aseptically before administering any antimicrobial therapy. In total, 1383 lactating cows were enrolled, which totaled 446 cow-years at risk. During the study period, 196 new cases of CM occurred, resulting in an estimated crude IRCM of 43.9 cases per 100 cow-years, though this varied substantially between farms. Among the tested CM quarter samples, Streptococci (22.9%) followed by non-aureus staphylococci (20.3%) were the most frequently isolated pathogens and resistance of S. aureus and NAS against penicillin (2 out of 3 and 27 out of 39 isolates, respectively) and oxacillin (2 out of 3 and 38 out of 39 isolates, respectively) was common. The IRCM was associated with a high milk yield, 28 to 90 days in milk, and a higher body condition score. Our results show that there is substantial room for udder health improvement on most farms.
Combined Medical and Minimally Invasive Robotic Surgical Approach to the Treatment and Repair of Cesarean Scar Pregnancies

Background and Objectives: The rise in cesarean deliveries, has led to increase in maternal complications in subsequent pregnancies such as abnormal placental implantation, uterine rupture, hemorrhage and, less commonly, cesarean scar pregnancies (CSP). Our objective was to describe patient characteristics following a combined medical and surgical treatment approach to first trimester cesarean scar pregnancies. Methods: This was a case series approved by the Institutional Review Board of cesarean scar pregnancies over a two-year period at a single academic institution. The study included five patients with diagnosed cesarean scar pregnancies opting for pregnancy termination with the desire for fertility preservation. Medical treatment involved intra-gestational sac injection of lidocaine followed by systemic injection of methotrexate. At a minimum of two months later, surgical resection of cesarean scar pregnancy and repair of the uterus was performed. Results: Median patient age was 36 (range 34 – 42) years, with 4 (3 – 10) prior pregnancies and 2 (1 – 3) prior cesarean deliveries. 40% (2/5) were Hispanic, 20% (1/5) Caucasian, 20% (1/5) African-American, and 20% (1/5) South Asian. After medical intervention, patients waited on average 4.6 ± 2.3 months before surgery. No post-intervention complications or recurrences occurred. Two patients had a subsequent pregnancy. Conclusion: This case series demonstrates an ideal management of cesarean scar pregnancy using combined medical and surgical approach in treating current ectopic pregnancy and repairing the uterine defect successfully without recurrence.
Unraveling the Genetic Diversity and Population Structure of Bangladeshi Indigenous Cattle Populations Using 50K SNP Markers

Simple Summary Indigenous cattle have extraordinary adaptation capability to diverse environments under low input production system. However, the population size is declining rapidly in Bangladesh due to massive imports of high yielding dairy breeds. The genetic diversity measures are important for assessing population architecture as well as for development of conservation strategies. The aim of this study was to investigate genetic variability and population structure of indigenous cattle genetic resources of Bangladesh using Illumina Bovine SNP50K BeadChip genotyped data. Similar to other zebu populations, low genetic diversity measures were found in Bangladeshi cattle populations. Our findings revealed their distinct genetic structure but showed low levels of genetic differentiation among the six indigenous cattle populations. Moreover, admixture and phylogenetic analysis highlighted historical gene flow among the studied populations. Altogether, our findings provide a comprehensive genomic information on indigenous cattle populations of Bangladesh that could be utilized in their future conservation and breeding research. Abstract Understanding the genetic basis of locally adapted indigenous cattle populations is essential to design appropriate strategies and programs for their genetic improvement and conservation. Here, we report genetic diversity measures, population differentiation, and structure of 218 animals sampled from six indicine cattle populations of Bangladesh. Animals were genotyped with Illumina Bovine SNP50K BeadChip along with genotyped data of 505 individuals included from 19 zebu and taurine breeds worldwide. The principal component analysis (PCA) showed clear geographic separation between taurine and indicine lineages where Bangladeshi indigenous cattle clustered with South Asian zebu populations. However, overlapped clusters in PCA, heterozygosity estimates, and Neighbor-Joining phylogenetic tree analysis revealed weak genetic differentiation among the indigenous cattle populations of Bangladesh. The admixture analysis at K = 5 and 9 suggests distinct genetic structure of the studied populations along with 1 to 4% of taurine ancestry. The effective population size suggested a limited pool of ancestors particularly for Sahiwal and North Bengal Grey cattle. In conclusion, these findings shed insights into the genetic architecture of six indigenous cattle populations of Bangladesh for the first time and suggested as distinct gene pools without potential admixture with zebu or taurine populations.
MiRNA-34c Regulates Bovine Sertoli Cell Proliferation, Gene Expression, and Apoptosis by Targeting the AXL Gene

Simple Summary Fertility is one of the essential reproduction traits of bulls, and accurate prediction of fertility potential using a semen sample from a donor bull for artificial insemination is crucial to achieve consistently high reproductive efficiency. Somatic cells, such as Sertoli cells and Leydig cells, are important in testis formation and provide a nurturing and regulatory environment for spermatogenesis. Furthermore, it was suggested that non-coding RNAs, such as microRNAs, long non-coding RNAs, circular RNAs, and Piwi-interacting RNA, function as important regulators of gene expression at post-transcriptional level in spermatogenesis. In this study, microRNA-34c was verified to specifically regulate the AXL gene by targeting a sequence in the 3’ UTR; miRNA-34c can also influence the proliferation, apoptosis, and relative abundance of the transcript of male-reproduction-related genes. Therefore, microRNA-34c can be considered an essential regulator in the process of bull spermatogenesis. These results identify a key microRNA and functional genes in the process of cattle male reproduction, providing useful information for future marker-assisted selection of bulls with excellent sperm quality. Abstract MicroRNAs (miRNAs) play significant roles in mammalian spermatogenesis. Sertoli cells can provide a stable microenvironment and nutritional factors for germ cells, thus playing a vital role in spermatogenesis. However, few studies elucidate the regulation of bovine testicular Sertoli cells by miRNAs. Here, we have reported that miRNA-34c (miR-34c) regulates proliferation, apoptosis, and relative transcripts abundance gene in bovine Sertoli cells. In bovine Sertoli cells, overexpression of miR-34c inhibited proliferation and relative abundance of gene transcripts while promoting apoptosis of Sertoli cells, and the effects were the opposite when miR-34c was knocked down. Receptor tyrosine kinase (AXL) was identified as a direct target gene of miR-34c in Sertoli cells, validated by analysis of the relative abundance of AXL transcript and dual-luciferase reporter assay. The relative abundance of the transcript of genes related to male reproduction in Sertoli cells was changed after the AXL gene was overexpressed, as demonstrated by the RT2 Profiler PCR Array results. In summary, miR-34c specifically regulated the AXL gene by targeting a sequence in the 3′-UTR, which could influence proliferation, apoptosis, and relative abundance of the transcript of male reproduction-related genes. Therefore, miR-34c could be considered an essential regulator in the process of bull spermatogenesis.