Miracle-dz/UniFAR-FTUs huggingface dataset:
HIV‐1 transmitted drug resistance surveillance: shifting trends in study design and prevalence estimates

HIV‐1 transmitted drug resistance (TDR) prevalence increased during the initial years of the antiretroviral therapy (ART) global scale‐up. Few studies have examined recent trends in TDR prevalence using published genetic sequences and described the characteristics of ART‐naïve persons from whom these published sequences have been obtained.
Relationship between environmental conditions and nocturnal activity of the terrestrial frog, Leiopelma archeyi

The number of frogs emerging at night in a field population of the terrestrial frog Leiopelma archeyi was examined in relation to environmental conditions. Frogs emerge at or about dusk from retreat sites on the forest floor, climbing up to 2 m high in the vegetation before returning to their retreats at dawn. Emergence is strongly and positively correlated (P 0.1). Frogs which emerged on nights when the vegetation was dry probably suffered little water loss by evaporation, because of the high humidities and cool temperatures which prevailed in the forest habitat. Experimentally dehydrated L. archeyi rehydrated rapidly from wet foliage, increasing from 92 to 99% of original body weight over 4 hr. Although emergence of most L. archeyi was limited to times of high moisture availability, rapid water uptake through ventral skin allowed this species to utilize sources of water which were only present ephemerally. The availability of moisture is widely assumed to limit the temporal and spatial activity of permeable-skinned amphibians in natural habitats, and thus their ability to carry out important ecological activities such as feeding and reproduction (Keen, 1984). When confronted with a water shortage, many amphibians remain in or rapidly seek moist microenvironments (e.g., Heatwole, 1962; Jaeger, 1971; Degani and Warburg, 1978). However, the Puerto Rican frog, Eleutherodactylus coqui, is considered an exception (Pough et al., 1983). Eleutherodactylus coqui inhabits subtropical rainforests and emerges by night to engage in foraging, territorial defence, and reproductive activity. Despite losing water by evaporation, individuals continue to emerge on dry nights for at least the first 7 days without rain, occupying the same arboreal perches as they do on wet nights. Behavioral adjustments are made on dry nights to minimize evaporative water loss (EWL). By day, coquis return to their retreat sites and make up for water lost overnight by absorbing moisture from their retreat site substrates (van Berkum et al., 1982; Pough et al., 1983). Leiopelma archeyi Turbott is a member of the anatomically primitive family Leiopelmatidae and is restricted to mountain ranges on or in the vicinity of the Coromandel Peninsula, New Zealand (Bell et al., 1985). Like E. coqui, L. archeyi is terrestrial, inhabiting high rainfall forest and Present Address: Department of Zoology, Victoria University of Wellington, Private Bag, Wellington, New Zealand. usually remaining in cool, humid retreat sites by day (Cree, 1986). However, apart from reports that L. archeyi (Turbott, 1942) or leiopelmatid frogs in general (Bell et al., 1985) climb trees and vegetation on wet nights, little is known about factors affecting emergence of this species. My study examines the relationship between environmental conditions and nocturnal activity of L. archeyi in a field population, and demonstrates the ability of experimentally dehydrated L. archeyi to make use of a natural moisture source (wet vegetation) for rehydration.
Spatial–Spectral Feature Refinement for Hyperspectral Image Classification Based on Attention-Dense 3D-2D-CNN

Convolutional neural networks provide an ideal solution for hyperspectral image (HSI) classification. However, the classification effect is not satisfactory when limited training samples are available. Focused on “small sample” hyperspectral classification, we proposed a novel 3D-2D-convolutional neural network (CNN) model named AD-HybridSN (Attention-Dense-HybridSN). In our proposed model, a dense block was used to reuse shallow features and aimed at better exploiting hierarchical spatial–spectral features. Subsequent depth separable convolutional layers were used to discriminate the spatial information. Further refinement of spatial–spectral features was realized by the channel attention method and spatial attention method, which were performed behind every 3D convolutional layer and every 2D convolutional layer, respectively. Experiment results indicate that our proposed model can learn more discriminative spatial–spectral features using very few training data. In Indian Pines, Salinas and the University of Pavia, AD-HybridSN obtain 97.02%, 99.59% and 98.32% overall accuracy using only 5%, 1% and 1% labeled data for training, respectively, which are far better than all the contrast models.
APC/CCdh1 is required for the termination of chromosomal passenger complex activity upon mitotic exit

ABSTRACT During mitosis, the chromosomal passenger complex (CPC) ensures the faithful transmission of the genome. The CPC is composed of the enzymatic component Aurora B (AURKB) and the three regulatory and targeting components borealin, INCENP, and survivin (also known as BIRC5). Although the CPC is known to be involved in diverse mitotic events, it is still unclear how CPC function terminates after mitosis. Here we show that borealin is ubiquitylated by the anaphase promoting complex/cyclosome (APC/C) and its cofactor Cdh1 (also known as FZR1) and is subsequently degraded in G1 phase. Cdh1 binds to regions within the N terminus of borealin that act as a non-canonical degron. Aurora B has also been shown previously to be degraded by the APC/CCdh1 from late mitosis to G1. Indeed, Cdh1 depletion sustains an Aurora B activity with stable levels of borealin and Aurora B throughout the cell cycle, and causes reduced efficiency of DNA replication after release from serum starvation. Notably, inhibition of Aurora B kinase activity improves the efficiency of DNA replication in Cdh1-depleted cells. We thus propose that APC/CCdh1 terminates CPC activity upon mitotic exit and thereby contributes to proper control of DNA replication. Summary: APC/CCdh1 ubiquitylates both borealin, via a non-canonical degron motif, and Aurora B to terminate activity of the CPC in G1 phase. Disruption of this ubiquitylation reduces the efficiency of DNA replication.
Clinical evaluation of a new monofocal intraocular lens with enhanced intermediate function in cataract patients.

PURPOSE To evaluate the effectiveness and safety of 2 enhanced monofocal intraocular lenses (IOLs). The TECNIS Eyhance IOL(Model ICB00) was compared with a standard monofocal IOL (TECNIS monofocal, Model ZCB00). SETTING European multicenter study. DESIGN Prospective, bilateral, randomized, comparative/evaluator-masked, controlled study. METHODS Adult subjects scheduled to undergo bilateral, primary phacoemulsification cataract extraction and posterior IOL implantation were randomized to receive the enhanced monofocal ICB00 IOL or the ZCB00 monofocal IOL in both eyes. Monocular endpoints at 6 months included distance corrected intermediate visual acuity (DCIVA), photopic corrected distance visual acuity (CDVA), and uncorrected intermediate visual acuity (UCIVA). Binocular visual acuities, monocular corrected distance contrast sensitivity (first eyes), patient-reported outcomes, and safety were assessed at 6 months. RESULTS Overall, 139 patients were bilaterally implanted with the enhanced monofocal IOL (n = 67) or standard monofocal IOL (n = 72) and available for the 6-month visit. The enhanced monofocal IOL significantly improved mean monocular and binocular DCIVA and UCIVA by at least 1-line logMAR vs the standard monofocal IOL (all P ≤ .0001). Distance vision for the enhanced monofocal IOL was 20/20 or better and comparable to that of the standard monofocal lens at 6 months. Contrast sensitivity, photic phenomena outcomes, and rates of adverse events were similar between the 2 groups. CONCLUSIONS In patients undergoing cataract surgery, TECNIS Eyhance IOL Model ICB00 provided enhanced intermediate vision and similar distance performance and photic phenomena compared with a standard monofocal IOL, along with improved functional performance in daily life.
An Evolutionary Cancer Epigenetic Approach Revealed DNA Hypermethylation of Ultra-Conserved Non-Coding Elements in Squamous Cell Carcinoma of Different Mammalian Species

Background: Ultra-conserved non-coding elements (UCNEs) are genomic sequences that exhibit > 95% sequence identity between humans, mammals, birds, reptiles, and fish. Recent findings reported their functional role in cancer. The aim of this study was to evaluate the DNA methylation modifications of UNCEs in squamous cell carcinoma (SCC) from different mammal species. Methods: Fifty SCCs from 26 humans, 17 cats, 3 dogs, 1 horse, 1 bovine, 1 badger, and 1 porcupine were investigated. Fourteen feline stomatitis and normal samples from 36 healthy human donors, 7 cats, 5 dogs, 5 horses, 2 bovines and 1 badger were collected as normal controls. Bisulfite next generation sequencing evaluated the DNA methylation level from seven UCNEs (uc.160, uc.283, uc.416, uc.339, uc.270, uc.299, and uc.328). Results: 57/59 CpGs were significantly different according to the Kruskal–Wallis test (p < 0.05) comparing normal samples with SCC. A common DNA hypermethylation pattern was observed in SCCs from all the species evaluated in this study, with an increasing trend of hypermethylation starting from normal mucosa, through stomatitis to SCC. Conclusions: Our findings indicate that UCNEs are hypermethylated in human SCC, and this behavior is also conserved among different species of mammals.
Impact d’une infection intra-mammaire causée par Staphylococcus aureus ou un staphylocoque coagulase-négative présente en début de lactation chez les taures laitières

The objective of this study was to determine the effect of a subclinical intramammary infection (IMI) caused by coagulase-negative staphylococci (CNS) or Staphylococcus aureus diagnosed during the first month of lactation in heifers on somatic cell count (SCC), milk production and culling risk during the entire first lactation. Bacteriological analysis data of composite milk samples taken from 2,273 Hostein heifers among 50 dairy herds were interpreted according to the National Mastitis Council guidelines. Among the 1,691 heifers meeting the selection criteria, 90 (5%) were diagnosed with S. aureus, 168 (10%) with CNS, and 153 (9%) were negative (no pathogen isolated). Test-day SCC transformed in natural logarithm (lnCCS) was fit in a linear regression model with herd as random effect. The lnSCC in S. aureus and CNS groups were significantly higher than in negative group from 40 to 300 days in milk (DIM) (P < 0.0001 for all contrasts). At test-day level, lnSCC in S. aureus and CNS groups was on average 1.2 and 0.6 higher than the negative group respectively. A similar model was used for milk yield with age at calving, parent average genetic value for milk yield and natural logarithm of tested DIM included. Milk yield was not statistically different between culture groups from 40 to 300 DIM (P ≥ 0.12). Compared with negative heifers, the culling hazard ratio estimated using Cox survival analysis in S. aureus and CNS infected heifers was not significant (P ≥ 0.16). Prevention of CNS or S. aureus IMI in early lactation remains important for its association with SCC during the ensuing lactation.
Incubation rhythms of ring-necked ducks

Incubation behavior of Ring-necked Ducks (Aythya collaris) was studied in northwestern Minnesota from 1978 to 1980. Incubation constancy was similar for all birds (85%), but recess duration and frequency differed for females nesting along cattail/open water edges (X = 47 min, 5.1 recesses/day) and in flooded sedge meadow (x = 73 min, 2.7 recesses/day) away from open-water feeding areas. Timing of recesses also was influenced by nest site location. Nest attentiveness of Ring-necked Ducks apparently is influenced by nutrient reserve levels in females at the onset of incubation and food availability in wetlands used by breeding birds. My findings are consistent with Afton's (1979, 1980) prediction that in smaller species, environmental factors increasingly affect anatid incubation rhythms, and they generally support his conclusion that the relationship of fasting endurance to body size has been very important in the evolution of avian incubation behavior.
Evaluating the Impact of Telehealth-Based, Diabetes Medication Training for Community Health Workers on Glycemic Control

Background: Diabetes is a major contributor to morbidity and mortality. Community Health Workers (CHWs) have been instrumental in improving patient outcomes. However, CHW training largely focuses on general diabetes concepts rather than medications. Providing accessible, diabetes medication training for CHWs has the potential to increase patient understanding, personalized care, and adherence, thereby improving outcomes. Objective: To evaluate the impact of a telehealth-based diabetes medication training for CHWs on patient outcomes as measured by HbA1c changes. Methods: We provided a 12-month weekly, telehealth (videoconference) medication training for CHWs who led 6-month diabetes programs for low-income Latino(a)s in community clinics. We measured participant HbA1c (primary outcome), blood pressure, and body mass index (BMI) changes. We evaluated CHW knowledge via two pre/post-tests: medication adverse events/side effects (TEST-1, months 1–6) and dosing, titration, and emergencies (TEST-2, months 7–12). We assessed CHW training application by their ability to identify patient, provider, and healthcare system medication barriers. Results: Participants’ (n = 55) HbA1c improved (9.0% (75 mmol/mol) to 7.8% (62 mmol/mol) (p = 0.001)). Blood pressure and BMI changes were not significant. CHWs improved their knowledge: TEST-1: 10.5-18.2/20.0 (p = 0.002), TEST-2: 10.3–17.3/19.0 (p = 0.0019). CHWs identified 984 patients (n = 610), providers (n = 151), and healthcare systems (n = 223) medication barriers during the 12-month training. Conclusions: Providing a telehealth-based, diabetes medication training program for CHWs allowed a personalized approach to identify barriers to care at several levels, which was associated with significant participant HbA1c reductions and improved CHW knowledge. This is a promising cost-effective, culturally sensitive strategy to improve diabetes care. Larger longitudinal evaluations are needed to fully understand the impact of CHW medication training.
Aryl Hydrocarbon Receptor (AHR) Ligands as Selective AHR Modulators (SAhRMs)

The aryl hydrocarbon receptor (AhR) was first identified as the intracellular protein that bound and mediated the toxic effects of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD, dioxin) and dioxin-like compounds (DLCs). Subsequent studies show that the AhR plays an important role in maintaining cellular homeostasis and in pathophysiology, and there is increasing evidence that the AhR is an important drug target. The AhR binds structurally diverse compounds, including pharmaceuticals, phytochemicals and endogenous biochemicals, some of which may serve as endogenous ligands. Classification of DLCs and non-DLCs based on their persistence (metabolism), toxicities, binding to wild-type/mutant AhR and structural similarities have been reported. This review provides data suggesting that ligands for the AhR are selective AhR modulators (SAhRMs) that exhibit tissue/cell-specific AhR agonist and antagonist activities, and that their functional diversity is similar to selective receptor modulators that target steroid hormone and other nuclear receptors.
Ultrasonographic Diagnosis of Intussusception in Children

Ultrasonography offers a unique advantage in the clinical diagnosis of intussusception. We aimed to evaluate the diagnostic accuracy of ultrasonography in pediatric intussusception. The PubMed, Embase, Web of Science, Cochrane Library databases, and African Journals Online database were searched for studies pertaining to ultrasonographic diagnosis of intussusception in children. Finally, 14 studies (combined n = 2367) were found eligible for inclusion. Pooled sensitivity and specificity were 0.94 (95% confidence interval: 0.91–0.96) and 0.96 (95% confidence interval: 0.93–0.98), respectively. In conclusion, ultrasonography has high sensitivity and specificity in the diagnosis of intussusception.
Genomic and chemical evidence for local adaptation in resistance to different herbivores in Datura stramonium

Because most species are collections of genetically variable populations distributed to habitats differing in their abiotic/biotic environmental factors and community composition, the pattern and strength of natural selection imposed by species on each other's traits are also expected to be highly spatially variable. Here, we used genomic and quantitative genetic approaches to understand how spatially variable selection operates on the genetic basis of plant defenses to herbivores. To this end, an F2 progeny was generated by crossing Datura stramonium (Solanaceae) parents from two populations differing in their level of chemical defense. This F2 progeny was reciprocally transplanted into the parental plants’ habitats and by measuring the identity by descent (IBD) relationship of each F2 plant to each parent, we were able to elucidate how spatially variable selection imposed by herbivores operated on the genetic background (IBD) of resistance to herbivory, promoting local adaptation. The results highlight that plants possessing the highest total alkaloid concentrations (sum of all alkaloid classes) were not the most well‐defended or fit. Instead, specific alkaloids and their linked loci/alleles were favored by selection imposed by different herbivores. This has led to population differentiation in plant defenses and thus, to local adaptation driven by plant‐herbivore interactions.
Occupation-based group programs in the inpatient hospital rehabilitation setting: a scoping review

Abstract Purpose Occupation-based practice involves the inclusion of meaningful occupations in the therapeutic process and is promoted within hospital-based general rehabilitation contexts for individual clients or within a group setting. The purpose of this paper is to summarise the current literature regarding the types of occupation-based group programs used within general inpatient rehabilitation and the reported outcomes. Methods A scoping review was conducted and included papers if they described an occupation-based intervention, delivered in a group setting, conducted in an inpatient rehabilitation hospital context, with an adult population. Studies were collated, summarized and key findings are presented. Results Ten articles met inclusion criteria. The results indicate that occupation-based groups are used in inpatient rehabilitation across a variety of settings, the approach is valued by the occupational therapy profession and it appears to have an influence on patient satisfaction and experience. However, the impact on a patient’s confidence and occupational performance outcomes post-inpatient rehabilitation remains unclear. Conclusions There is a dearth of evidence on the impact of occupation-based group service focus in the inpatient rehabilitation setting. Considering the importance of occupation to the profession, further investigation into the use of this approach in a group setting is required. Implications for rehabilitation Occupation-based groups are used in inpatient rehabilitation to achieve more therapy time but there is variability in group processes and outcomes measured. Patient centred occupation-based groups appear to have an influence on patient satisfaction and experience. For the occupation-based groups reviewed, providing explicit links between patient goals, therapeutic activity and real life was important for improving outcomes. There is a growing focus for the use of occupation-based groups in occupational therapy and more research is needed to establish effectiveness.
Pregnancy Losses in Livestock: An Overview of the Physiology and Endocrinology Symposium for the 2020 ASAS-CSAS-WSASAS Virtual Meeting.

This year’s Physiology & Endocrinology Program Committee selected a symposium focusing on Pregnancy Losses in Livestock for the 2020 ASAS-CSAS-WSASAS Virtual Annual Meeting. The symposium was developed to highlight the challenges faced with maintaining pregnancies in cattle and pigs. Methods are available to maximize fertilization success in livestock, but little information exists detailing ways to minimize embryonic and early fetal losses. The magnitude of pregnancy losses during the initial periods of embryo development is extensive in beef cattle and pigs, and the symposia speakers discussed the etiology of these losses, provided insights into the economic consequences of pregnancy losses, proposed developmental mechanisms that may cause these pregnancy losses, and explored how environmental stressors influence pregnancy status.
Lentiviral Vector Pseudotypes: Precious Tools to Improve Gene Modification of Hematopoietic Cells for Research and Gene Therapy

Viruses have been repurposed into tools for gene delivery by transforming them into viral vectors. The most frequently used vectors are lentiviral vectors (LVs), derived from the human immune deficiency virus allowing efficient gene transfer in mammalian cells. They represent one of the safest and most efficient treatments for monogenic diseases affecting the hematopoietic system. LVs are modified with different viral envelopes (pseudotyping) to alter and improve their tropism for different primary cell types. The vesicular stomatitis virus glycoprotein (VSV-G) is commonly used for pseudotyping as it enhances gene transfer into multiple hematopoietic cell types. However, VSV-G pseudotyped LVs are not able to confer efficient transduction in quiescent blood cells, such as hematopoietic stem cells (HSC), B and T cells. To solve this problem, VSV-G can be exchanged for other heterologous viral envelopes glycoproteins, such as those from the Measles virus, Baboon endogenous retrovirus, Cocal virus, Nipah virus or Sendai virus. Here, we provide an overview of how these LV pseudotypes improved transduction efficiency of HSC, B, T and natural killer (NK) cells, underlined by multiple in vitro and in vivo studies demonstrating how pseudotyped LVs deliver therapeutic genes or gene editing tools to treat different genetic diseases and efficiently generate CAR T cells for cancer treatment.