Miracle-dz/UniFAR-FTUs huggingface dataset:
Ethical Challenges of Embryo Donation in Embryo Donors and Recipients

Background: Embryo donation, as one of the novel assisted reproductive technologies (ART), has remained a controversial issue. This is due to this methods' need for individuals from outside the family circle. Their presence can cause many ethical issues and complicate the designing and planning of the embryo donation process. The present study was conducted with the aim to assess the ethical challenges of embryo donation from the view point of embryo donors and recipients. Material and Methods: This descriptive, cross-sectional study was conducted on 192 couples (96 embryo donators and 96 embryo recipients) referring to Isfahan Fertility and Infertility Center and Royan Institute, Iran. The subjects were selected through convenience sampling. The data collection tool was the researcher-made Ethical Challenges Questionnaire. Data were analyzed in SPSS software. Results: Embryo donors and recipients expresses the most important ethical challenges of embryo donation in the principle of justice (70.20%) and respect for autonomy (42.57%), respectively. Conclusions: The four ethical principles are important in the view of embryo donors and recipients; however, they highlighted the importance of the principle of respect for autonomy considering the existing barriers in the services of infertility centers. Legislators and relevant authorities must take measures toward the development of guidelines for this treatment method in the framework of ethics principles and incorporate all four principles independently.
LY2405319, an Engineered FGF21 Variant, Improves the Metabolic Status of Diabetic Monkeys

Fibroblast growth factor 21 (FGF21) is a novel metabolic regulator that represents a promising target for the treatment of several metabolic diseases. Administration of recombinant wild type FGF21 to diabetic animals leads to a dramatic improvement in glycaemia and ameliorates other systemic measures of metabolic health. Here we report the pharmacologic outcomes observed in non-human primates upon administration of a recently described FGF21 analogue, LY2405319 (LY). Diabetic rhesus monkeys were treated subcutaneously with LY once daily for a period of seven weeks. The doses of LY used were 3, 9 and 50 mg/kg each delivered in an escalating fashion with washout measurements taken at 2, 4, 6 and 8 weeks following the final LY dose. LY therapy led to a dramatic and rapid lowering of several important metabolic parameters including glucose, body weight, insulin, cholesterol and triglyceride levels at all doses tested. In addition, we observed favorable changes in circulating profiles of adipokines, with increased adiponectin and reduced leptin indicative of direct FGF21 action on adipose tissue. Importantly, and for the first time we show that FGF21 based therapy has metabolic efficacy in an animal with late stage diabetes. While the glycemic efficacy of LY in this animal was partially attenuated its lipid lowering effect was fully preserved suggesting that FGF21 may be a viable treatment option even in patients with advanced disease progression. These findings support continued exploration of the FGF21 pathway for the treatment of metabolic disease.
Hardening by partial dehydration and ABA increase desiccation tolerance in the cyanobacterial lichen Peltigera polydactylon.

BACKGROUND AND AIMS The ability of partial dehydration and abscisic acid pretreatments to increase desiccation tolerance in the cyanobacterial lichen Peltigera polydactylon was tested. * METHODS Net photosynthesis and respiration were measured using infrared gas analysis during a drying and rehydration cycle. At the same time, the efficiency of photosystem two was measured using chlorophyll fluorescence, and the concentrations of chlorophyll a were spectrophotometrically assayed. Heat production was also measured during a shorter drying and rehydration cycle using differential dark microcalorimetry. * KEY RESULTS Pretreating lichens by dehydrating them to a relative water content of approx. 0.65 for 3 d, followed by storing thalli hydrated for 1 d in the light, significantly improved their ability to recover net photosynthesis during rehydration after desiccation for 15 but not 30 d. Abscisic acid pretreatment could substitute for partial dehydration. The improved rates of photosynthesis during the rehydration of pretreated material were not accompanied by preservation of photosystem two activity or chlorophyll a concentrations compared with untreated lichens. Partial dehydration and ABA pretreatments appeared to have little direct effect on the desiccation tolerance of the mycobiont, because the bursts of respiration and heat production that occurred during rehydration were similar in control and pretreated lichens. * CONCLUSIONS Results indicate that the photobiont of P. polydactylon possesses inducible tolerance mechanisms that reduce desiccation-induced damage to carbon fixation, and will therefore improve the supply of carbohydrates to the whole thallus following stress. In this lichen, ABA is involved in signal transduction pathways that increase tolerance of the photobiont.
Correlation of Vitamin D and Body Mass Index with Modic Changes in Patients with Non-Specific Low Back Pain in a Sub-Tropical Asian Population

Study Design Cross-sectional study by non-probability consecutive sampling. Purpose The objective of this study was to assess body mass index (BMI) and investigate vitamin D levels in patients with low back pain (LBP) and study a possible relationship with myopathy-related symptoms and Modic changes. Overview of Literature LBP is a multifactorial problem and the search for its patho-anatomical causes is ongoing. Modic changes seem to be a cause of back pain but the pathological mechanisms underlying this are not completely defined. Hypovitaminosis D and obesity have also been shown to cause chronic musculoskeletal pain. The relationship between vitamin D deficiency and BMI with Modic changes has not been studied in detail. Methods Three hundred and sixteen patients with chronic LBP was selected for the study by non-probability consecutive sampling. The study was conducted over a period of 12 months from January 2014 to December 2014 at St. John's Medical College, Banglore. Questionnaires were provided to the participants and demographic information, symptoms, weight and height were recorded from the study subjects. BMI was calculated. Serum vitamin D level was assessed and Modic changes studied on magnetic resonance imaging. Correlations between vitamin D, BMI and Modic changes were studied using correlation coefficients and odds ratios obtained from logistic regression. Results Two hundred and fifty-six out of 316 patients (80%) had low vitamin D. 83% of patients with BMI>25 kg/m2 had low vitamin D levels as compared to 69% with BMI<25 kg/m2. Statistically significant correlation coefficients were found between vitamin D levels, BMI and Modic changes. Significant association was found between low vitamin D levels and Modic changes (odds ratio 1.75). Conclusions Vitamin D deficiency and obesity have significant relations with LBP. Low vitamin D levels is associated with Modic changes but whether they represent a subgroup of patients whose low backpain is associated with low vitamin D needs to be further evaluated.
The Am-tra2 Gene Is an Essential Regulator of Female Splice Regulation at Two Levels of the Sex Determination Hierarchy of the Honeybee

Heteroallelic and homo- or hemiallelic Complementary sex determiner (Csd) proteins determine sexual fate in the honeybee (Apis mellifera) by controlling the alternative splicing of the downstream gene fem (feminizer). Thus far, we have little understanding of how heteroallelic Csd proteins mediate the splicing of female fem messenger RNAs (mRNAs) or how Fem proteins direct the splicing of honeybee dsx (Am-dsx) pre-mRNAs. Here, we report that Am-tra2, which is an ortholog of Drosophila melanogaster tra2, is an essential component of female splicing of the fem and Am-dsx transcripts in the honeybee. The Am-tra2 transcripts are alternatively (but non-sex-specifically) spliced, and they are translated into six protein isoforms that all share the basic RNA-binding domain/RS (arginine/serine) domain structure. Knockdown studies showed that the Am-tra2 gene is required to splice fem mRNAs into the productive female and nonproductive male forms. We suggest that the Am-Tra2 proteins are essential regulators of fem pre-mRNA splicing that, together with heteroallelic Csd proteins and/or Fem proteins, implement the female pathway. In males, the Am-Tra2 proteins may enhance the switch of fem transcripts into the nonproductive male form when heteroallelic Csd proteins are absent. This dual function of Am-Tra2 proteins possibly enhances and stabilizes the binary decision process of male/female splicing. Our knockdown studies also imply that the Am-Tra2 protein is an essential regulator for Am-dsx female splice regulation, suggesting an ancestral role in holometabolous insects. We also provide evidence that the Am-tra2 gene has an essential function in honeybee embryogenesis that is unrelated to sex determination.
Telomere Erosion in Memory T Cells Induced by Telomerase Inhibition at the Site of Antigenic Challenge In Vivo

The extent of human memory T cell proliferation, differentiation, and telomere erosion that occurs after a single episode of immune challenge in vivo is unclear. To investigate this, we injected tuberculin purified protein derivative (PPD) into the skin of immune individuals and isolated responsive T cells from the site of antigenic challenge at different times. PPD-specific CD4+ T cells proliferated and differentiated extensively in the skin during this secondary response. Furthermore, significant telomere erosion occurred in specific T cells that respond in the skin, but not in those that are found in the blood from the same individuals. Tissue fluid obtained from the site of PPD challenge in the skin inhibited the induction of the enzyme telomerase in T cells in vitro. Antibody inhibition studies indicated that type I interferon (IFN), which was identified at high levels in the tissue fluid and by immunohistology, was responsible in part for the telomerase inhibition. Furthermore, the addition of IFN-α to PPD-stimulated CD4+ T cells directly inhibited telomerase activity in vitro. Therefore, these results suggest that the rate of telomere erosion in proliferating, antigen-specific CD4+ T cells may be accelerated by type I IFN during a secondary response in vivo.
Sex hormone regulation of systemic endothelial and renal microvascular reactivity in type‐2 diabetes: studies in gonadectomized and sham‐operated Zucker diabetic rats

Background Male Zucker diabetic rats exhibit a more severe endotheliopathy in comparison with their female diabetic litter mates. The plasma concentrations of both thromboxanes and endothelins are elevated in diabetes, and the receptor cross‐talk between TXA2 and ET‐1 receptors may be enhanced in type‐2 diabetic Zucker rats.
Strain Effects by Surface Oxidation of Cu3N Thin Films Deposited by DC Magnetron Sputtering

We report the self-buckling (or peeling off) of cubic Cu3N films deposited by DC magnetron sputtering of a Cu target in a nitrogen environment at a gas pressure of 1 Pa. The deposited layer partially peels off as it is exposed to ambient air at atmospheric pressure, but still adheres to the substrate. The chemical composition of the thin film as investigated by means of X-ray photoelectron spectroscopy (XPS) shows a considerable surface oxidation after exposure to ambient air. Grazing incidence X-ray diffraction (GIXRD) confirms the formation of a crystalline Cu3N phase of the quenched film. Notable are the peak shifts in the deposited film to smaller angles in comparison to stress-free reference material. The X-ray pattern of Cu3N exhibits clear differences in the integral width of the line profiles. Changes in the film microstructure are revealed by X-ray diffraction, making use of X-ray line broadening (Williamson–Hall and Stokes–Fourier/Warren–Averbach method); it indicates that the crystallites are anisotropic in shape and show remarkable stress and micro-strain.
A High Recall Error Identification Tool for Hindi Treebank Validation

This paper describes the development of a hybrid tool for a semi-automated process for validation of treebank annotation at various levels. The tool is developed for error detection at the part-of-speech, chunk and dependency levels of a Hindi treebank, currently under development. The tool aims to identify as many errors as possible at these levels to achieve consistency in the task of annotation. Consistency in treebank annotation is a must for making data as error-free as possible and for providing quality assurance. The tool is aimed at ensuring consistency and to make manual validation cost effective. We discuss a rule based and a hybrid approach (statistical methods combined with rule-based methods) by which a high-recall system can be developed and used to identify errors in the treebank. We report some results of using the tool on a sample of data extracted from the Hindi treebank. We also argue how the tool can prove useful in improving the annotation guidelines which would in turn, better the quality of annotation in subsequent iterations.
Ischemia Enhances Activation by Ca2+ and Redox Modification of Ryanodine Receptor Channels from Rat Brain Cortex

Cerebral ischemia stimulates Ca2+ influx and thus increases neuronal intracellular free [Ca2+]. Using a rat model of cerebral ischemia without recirculation, we tested whether ischemia enhances the activation by Ca2+ of ryanodine receptor (RyR) channels, a requisite feature of RyR-mediated Ca2+-induced Ca2+ release (CICR). To this aim, we evaluated how single RyR channels from endoplasmic reticulum vesicles, fused into planar lipid bilayers, responded to cytoplasmic [Ca2+] changes. Endoplasmic reticulum vesicles were isolated from the cortex of rat brains incubated without blood flow for 5 min at 37°C (ischemic) or at 4°C (control). Ischemic brains displayed increased oxidative intracellular conditions, as evidenced by a lower ratio (∼130:1) of reduced/oxidized glutathione than controls (∼200:1). Single RyR channels from ischemic or control brains displayed the same three responses to Ca2+ reported previously, characterized by low, moderate, or high maximal activity. Relative to controls, RyR channels from ischemic brains displayed with increased frequency the high activity response and with lower frequency the low activity response. Both control and ischemic cortical vesicles contained the RyR2 and RyR3 isoforms in a 3:1 proportion, with undetectable amounts of RyR1. Ischemia reduced [3H]ryanodine binding and total RyR protein content by 35%, and increased at least twofold endogenous RyR2 S-nitrosylation and S-glutathionylation without affecting the corresponding RyR3 endogenous levels. In vitro RyR S-glutathionylation but not S-nitrosylation favored the emergence of high activity channels. We propose that ischemia, by enhancing RyR2 S-glutathionylation, allows RyR2 to sustain CICR; the resulting amplification of Ca2+ entry signals may contribute to cortical neuronal death.
Model explaining the relation between distal nephron Li+ reabsorption and urinary Na+ excretion in rats.

Li+ may be reabsorbed via an amiloride-sensitive mechanism in the collecting ducts of rats administered a low-Na+ diet. This was investigated by measuring the increase in fractional urinary excretion of Li+(FELi) in response to amiloride in conscious rats at two different levels of plasma Li+ concentration and after administration of bendroflumethiazide (BFTZ), angiotensin III (ANG III), and aldosterone (Aldo). The results confirmed that amiloride increased (FELi) in rats on a low-Na+ diet (20 ± 1 to 35 ± 1%, means ± SE), whereas no increase was observed in rats on a normal Na+ diet (37 ± 1 to 38 ± 1%). The lithiuretic effect of amiloride was 1) abolished by preadministration of BFTZ (32 ± 1 to 33 ± 2%) to Na+-deprived rats and 2) increased by ANG III (27 ± 3 to 33 ± 2%) and Aldo (25 ± 2 to 37 ± 2%) in Na+-replete rats. Amiloride-induced changes in FELiwere independent of plasma Li+concentration but inversely related to the fractional excretion of Na+ and the amiloride-sensitive excretion of K+. These results are compatible with the hypothesis that a low tubular Na+ concentration reduces end-tubular Na+ reabsorption and results in hyperpolarization of the apical membrane, thus favoring Li+ uptake into the cells.
Biosynthetic Pathway of Pseudomonas aeruginosa 4-Hydroxy-2-Alkylquinolines

ABSTRACT The role of intercellular communication in the regulation of bacterial multicellular behavior has received widespread attention, and a variety of signal molecules involved in bacterial communication have been discovered. In addition to the N-acyl-homoserine lactones, 4-hydroxy-2-alkylquinolines (HAQs), including the Pseudomonas quinolone signal, have been shown to function as signal molecules in Pseudomonas aeruginosa. In this study we unraveled the biosynthetic pathway of HAQs using feeding experiments with isotope-labeled precursors and analysis of extracted HAQs by gas chromatography-mass spectrometry and nuclear magnetic resonance spectroscopy. Our results show that the biosynthesis of various HAQ metabolites is directed via a common metabolic pathway involving a “head-to-head” condensation of anthranilic acid and β-keto fatty acids. Moreover, we provide evidence that the β-keto-(do)decanoic acids, crucial for the biosynthesis of the heptyl and nonyl derivatives of the 4-hydroxyquinolines in P. aeruginosa, are at least in part derived from a common pool of β-hydroxy(do)decanoic acids involved in rhamnolipid biosynthesis.
Causes of severe visual impairment and blindness in children in schools for the blind in Ethiopia

Aims: To determine the causes of severe visual impairment and blindness in children in schools for the blind in Ethiopia, to aid in planning for the prevention and management of avoidable causes. Methods: Children attending three schools for the blind in Ethiopia were examined during April and May 2001 using the standard WHO/PBL eye examination record for children with blindness and low vision protocol. Data were analysed for those children aged less than 16 years using the epi-info-6 programme. Results: Among 360 pupils examined, 312 (96.7%) were aged <16 years. Of these children, 295 (94.5%) were blind or severely visually impaired. The major anatomical site of visual loss was cornea/phthisis (62.4%), followed by optic nerve lesions (9.8%), cataract/aphakia (9.2%), and lesions of the uvea (8.8%). The major aetiology was childhood factors (49.8%). The aetiology was unknown in 45.1% of cases. 68% of cases were considered to be potentially avoidable. Conclusions: Vitamin A deficiency and measles were the major causes of severe visual impairment/blindness in children in schools for the blind in Ethiopia. The majority of causes acquired during childhood could be avoided through provision of basic primary healthcare services.
Constructing Subtle Faults Using Higher Order Mutation Testing

Traditional mutation testing considers only first order mutants, created by the injection of a single fault. Often these first order mutants denote trivial faults that are easily killed. This paper investigates higher order mutants (HOMs). It introduces the concept of a subsuming HOM; one that is harder to kill than the first order mutants from which it is constructed. By definition, subsuming HOMs denote subtle fault combinations. The paper reports the results of an empirical study into subsuming HOMs, using six benchmark programs. This is the largest study of mutation testing to date. To overcome the exponential explosion in the number of mutants considered, the paper introduces a search based approach to the identification of subsuming HOMs. Results are presented for a greedy algorithm, a genetic algorithm and a hill climbing algorithm.
Sequence Comparison Alignment-Free Approach Based on Suffix Tree and L-Words Frequency

The vast majority of methods available for sequence comparison rely on a first sequence alignment step, which requires a number of assumptions on evolutionary history and is sometimes very difficult or impossible to perform due to the abundance of gaps (insertions/deletions). In such cases, an alternative alignment-free method would prove valuable. Our method starts by a computation of a generalized suffix tree of all sequences, which is completed in linear time. Using this tree, the frequency of all possible words with a preset length L—L-words—in each sequence is rapidly calculated. Based on the L-words frequency profile of each sequence, a pairwise standard Euclidean distance is then computed producing a symmetric genetic distance matrix, which can be used to generate a neighbor joining dendrogram or a multidimensional scaling graph. We present an improvement to word counting alignment-free approaches for sequence comparison, by determining a single optimal word length and combining suffix tree structures to the word counting tasks. Our approach is, thus, a fast and simple application that proved to be efficient and powerful when applied to mitochondrial genomes. The algorithm was implemented in Python language and is freely available on the web.
Is human T-cell lymphotropic virus type I more clever than human immunodeficiency virus type 1?

SIR—Casseb [1] hypothesizes that human T-cell lymphotropic virus type I (HTLV-I) is “more clever” than human immunodeficiency virus type 1 (HIV-1). One of his reasons is that HTLV-I, unlike HIV-1, has “an exceptionally low capability for causing death in the host. ” “Cleverness” is not a biological concept but rather an anthropomorphism. Casseb probably is referring to the biological success of a virus. The only measure of the success of an organism is Darwinian—that is, successful viruses transmit more copies of their genes to new hosts, and unsuccessful ones transmit fewer (or none, thus dying out completely). As has been pointed out, it is not necessarily in the evolutionary interest of a virus to have low pathogenicity [2]. For example, some arthropod-borne viruses are transmitted more efficiently when their host is debilitated and unable to fend off insect vectors. HIV-1 seems to be particularly successful in transmitting itself to new hosts, although most transmissions probably take place when the host is feeling well. It is probable that host death caused by HIV-1 is merely an unfortunate (from the host’s point of view) epiphenomenon, although in fact we do not know if this is the case. HTLV-I may seem “clever” because it does not cause host mortality, but we cannot say that HIV-1 is less “clever” because it often kills its host. HIV-1, however deadly, seems to be remarkably evolutionarily successful at this point in time, and there seems to be no shortage of hosts for the virus to infect in the future.
On imperfect CSI for the downlink of a two-tier network

In this paper, we consider a hierarchical two-tier cellular network where a macrocell is overlaid with a tier of randomly distributed femtocells. We evaluate the combined effect of uncoordinated cross-tier interference, feedback delay, and quantization errors on the achievable rate of transmit beamforming with imperfect channel state information (CSI). We model the femtocell spatial distribution as a Poisson point process (PPP) and the temporal correlation of the channel according to a Gauss-Markov model. Using stochastic geometry tools, we derive the probability of outage at the macrocell users as a function of the temporal correlation, the femtocell density, and the feedback rate. We compute the maximum average achievable rate on the downlink of the macrocell network using a properly designed rate backoff scheme. We show that transmit beamforming with imperfect CSI is a viable option for the downlink of a two-tier cellular network, and that rate backoff recovers the loss in rate due to packet outage.