Miracle-dz/UniFAR-FTUs huggingface dataset:
Sperm RNA elements as markers of health

ABSTRACT Idiopathic infertility, an etiology not identified as part of standard clinical assessment, represents approximately 20% of all infertility cases. Current male infertility diagnosis focuses on the concentration, motility, and morphology of spermatozoa. This is of limited value when predicting birth success and of limited utility when selecting the optimum treatment. At fertilization, spermatozoa provide their genomic contribution, as well as a set of RNAs and proteins that have distinct roles in development. The potential of spermatozoal RNAs to be used as a prognostic of live birth has been shown [Jodar et al. (2015) Science Translational Medicine 7(295):295re6]. This relied on a set of 648 sperm RNA elements derived from 285 genes that are perhaps indicative of future health status. To address this tenet, the present study correlated the levels of each transcript among all samples to assess linkage between transcript absence, birth success, and possible disease association. Correlations between transcript levels of the 285 genes were analyzed amongst themselves, and within the context of the entire transcript population for these samples. The transcripts ACE, GIGYF2, and ODF2 had many negative correlations and form the majority of correlations, suggesting an important function for these transcripts. Eleven of the 285 queried genes had disease-associated variants within a sperm RNA element. Three genes, GPX4, NDRG1, and RPS24 had SREs were absent in at least one individual from the test cohort. GPX4 and RPS24 are associated with developmental defects and/or neonatal lethality. This leaves the intriguing possibility that, while sperm RNAs delivered to the oocyte inform the success of live birth, they may also be predictors of human health. Abbreviations: GO: Gene Ontology; ART: assisted reproductive technology; IVF: in vitro fertilization; ICSI: intra-cytoplasmic sperm injection; RNA-seq: RNA-sequencing; TIC: timed intercourse; IUI: intrauterine insemination; SRE: sperm RNA elements; HPA: Human Protein Atlas; SMDS: sedaghatian-type spondylometaphyseal dysplasia; DBA: Diamond-Blackfan anemia; RPKM: reads per kilobase per million; TPM: transcripts per million; IPA: Ingenuity Pathway Analysis; OMIM: Online Mendelian Inheritance in Man
Exploring regional economic convergence in Romania. A spatial modeling approach

This paper explores spatial economic convergence in Romania, from the perspective of real GDP/capita, and examines how the shock of the recent economic crisis has affected the convergence process. Given the presence of spatial autocorrelation in the values of GDP per capita, we address the question of convergence in terms of both classic and spatial regression models, thus filling a gap in the Romanian literature on this topic. The empirical results seem to provide support for both absolute and relative beta divergence in GDP/capita, as well as sigma divergence among Romanian counties on the long run. This is the consequence of the two-speed regional development, with the capital region and some large cities thriving by attracting human capital and FDIs, while the lagging regions are systematically left behind. Failing to validate the neoclassical approach on convergence, our results rather support the new divergence theory based on polarization and centre-periphery inequality.
La contagion de la crise asiatique : dynamiques de court terme et de long terme

In this paper, we test the presence of the contagion during the Asian financial crisis. We propose a new procedure which consists in testing the non-linearity of the propagation mechanisms of the shocks, estimated with a model of long term interdependence. We apply this methodology to the markets of the sovereign debts (spreads) which measure the risk perception. Our results prove that Malaysia and the Philippines have been contaminated by contagion.
Characterization of nuclear proteins that bind the EFII enhancer sequence in the Rous sarcoma virus long terminal repeat

The EFII cis element is a 38-bp sequence at the 5' end of the Rous sarcoma virus long terminal repeat, extending from nucleotides -229 to -192 (with respect to the viral transcription start site), which is recognized by sequence-specific DNA-binding proteins in avian fibroblast nuclear extracts (L. Sealy and R. Chalkley, Mol. Cell. Biol. 7:787-798, 1987). We demonstrate that multiple copies of the EFII cis element strongly activate transcription of a reporter gene in vivo. We correlate the region of the EFII cis element which activates transcription in vivo with the in vitro binding site for three nuclear factors, EFIIa, EFIIb, and EFIIc. The sequence motif recognized by EFIIa, -b, and -c is also found in consensus binding sites for members of a rapidly growing family of transcription factors related to the CCAAT/enhancer-binding protein (C/EBP). EFIIa, -b, and -c are present in fibroblast and epithelial cell lines from various species but are much less abundant in differentiated rat liver and kidney cells. The EFIIa binding activity is particularly abundant in an avian B-cell lymphoma line. As judged from molecular weight analysis, cell type distribution, and sequence recognition properties, the EFII factors under study appear to differ from most of the previously described C/EBP-related factors and thus may expand the diversity of the C/EBP family.
Rare and spatially segregated release sites mediate a synaptic interaction between two identified network neurons.

Laser-scanning confocal microscopy (LSCM), electron microcopy (EM), and cellular electrophysiology were used in combination to study the structural basis of an inhibitory synapse between two identified neurons of the same network. To achieve this, we examined the chemical inhibitory synapse between identified neurons belonging to the lobster (Homarus gammarus) pyloric network: the pyloric dilator (PD) and the lateral pyloric (LP) neurons. In order to visualize simultaneously these two neurons, we used intrasomatic injection of Lucifer Yellow (LY) in one and rhodamine/horseradish peroxydase (HRP) in the other. Under LSCM, we found only two zones of close apposition in a restricted part of the neuritic tree of the two network neurons. Then, within these two zones, the synaptic release sites were searched using EM. To this end, photoconversion of LY with immunogold and development of HRP with DAB were performed on the previously observed preparations. Structural evidence was found for only one release site per zone. To confirm this result, and because the zones of contact were always segregated in a restricted part of the dendrites, we used laser photoablation to selectively delete, either pre- or postsynaptically, the branches on which the release sites were located. In both cases, such restrictive ablation completely abolished the functional interaction between these neurons. Our results therefore demonstrate that an inhibitory synapse that is essential for the operation of a neural network relies on only very few sites of contact localized in a highly restricted part of each neuron's dendritic arbor.
Outcomes of chronic subdural hematoma drainage in nonagenarians and centenarians: a multicenter study.

OBJECTIVE Chronic subdural hemorrhage (SDH) or hematoma is a condition that affects elderly individuals. With advances in medical care, the number of nonagenarians and centenarians will increase. However, surgical treatments in this age group are associated with high rates of morbidity and mortality. Because no data are available on the rates of survival among elderly patients with chronic SDHs who undergo surgical drainage or receive only conservative care, the goal of this study was to determine survival rates in patients 90 years of age or older with symptomatic chronic SDHs. METHODS The authors conducted a retrospective analysis of patient data that were collected at 3 hospitals over a 13-year period (from January 2001 to June 2013). The data from patients 90 years or older with symptomatic chronic SDHs and who were offered surgical treatment were included in the analysis. Patients who underwent surgical treatment were included in the surgical group and patients who declined an operation were included in the conservative care group. The patients' Charlson Comorbidity Index score, Karnofsky Performance Scale score, dates of death, presenting symptoms, Glasgow Coma Scale score, length of stay in the hospital, discharge location, side of the SDH, and neurological improvements at 30-day and 6-month follow-ups were recorded. Data were statistically analyzed with Fisher exact test, Kaplan-Meier curves, and logistic regression. RESULTS In total, 101 patients met the inclusion criteria of this study; 70 of these patients underwent surgical drainage, and 31 received conservative care. Patients in the surgical group had statistically significantly (p < 0.001) higher survival at both the 30-day and 6-month follow-ups, with 92.9% and 81.4% of the patients in this group surviving for at least 30 days and 6 months, respectively, versus 58.1% and 41.9%, respectively, in the conservative care group. Moreover, the mean overall length of survival of 34.4 ± 28.7 months was longer in the surgical group than it was in the conservative care group (11.3 ± 16.6 months). Overall, 95.7% of patients in the surgical group exhibited an improvement in neurological status after the SDH drainage, whereas none of the patients in the conservative care group showed any neurological improvement during their hospital stay. The surgical complication rate was 11.4%, and the overall rate of chronic SDH recurrence after surgery was 12.9%. CONCLUSIONS Surgical drainage of chronic SDHs in nonagenarians and centenarians is associated with lower incidence of inpatient death and higher 30-day and 6-month survival rates.
Transverse Cervical Artery Perforator Flap: Standardized Surgical Technique and Multiple Reconstructive Opportunity in Head and Neck Surgery

Abstract The main purpose of head and neck reconstructive surgery is to provide anatomic restoration of the demolited region and to provide preservation and recovery of function. The anatomical investigations conducted over the years has enabled a detailed knowledge of human body vascularization, giving the opportunity to design and harvest more and more versatile and refined flaps, with increasingly satisfactory results. Even if in the last 2 decades free flaps have been considered a reconstructive criterion standard, they still determine a great physical impact for the patient and require a certain surgical experience. In particular, perforator flaps (based on vessels that, emerging from the main deep axis, supply superficial myofascial cutaneous tissues) represent the new reconstructive frontier, of which a wide variety of types has been described. Our purpose is to illustrate the preparation and harvesting of the transverse cervical artery perforator flap and the variety of its utilization in head and neck reconstruction. From February 2005 to May 2015, 41 reconstructions were performed, and not only for oncologic reasons. Thanks to its anatomical features, reduced donor site morbidity and rapid preparation, this flap is a safe and feasible alternative to most famous free and locoregional flaps. Because our outcomes in functional and aesthetic terms were mostly satisfying, we can assert that the transverse cervical artery perforator flap has an important role in an appropriate reconstructive strategy for head, neck, and oropharyngolaryngeal region.
Gastrointestinal stromal tumors in a cohort of Chinese patients in Hong Kong.

AIM To investigate the prevalence and clinical pattern of gastrointestinal stromal tumors (GISTs) in Hong Kong Chinese, and to assess the impact of introduction of CD117 on the disease incidence. METHODS From the database of the Department of Pathology of Yan Chai Hospital, 47 patients, with GISTs from September 1995 to December 2003 were included in this study. Ten GISTs were diagnosed before the introduction of CD117. The clinical features, tumor characteristics, and treatment were analyzed. Factors predicting tumor related death or recurrence were studied with Cox proportional hazard model. RESULTS The patients included 26 males and 21 females, with a mean age of 66.6 years (SD 13.1, range 29-87 years). The estimated prevalence of GISTs was 13.4-15.6 per 100,000 people, with an annual incidence of 1.68-1.96 per 100,000 people. The annual incidence of GISTs before and after the introduction of CD117 was 1.1 per 100,000 people and 2.1 per 100,000 people respectively. Stomach (34 patients, 72.3%) was the most common location for the tumor, followed by the small intestine (8 patients, 17.0%), esophagus (2 patients, 4.3%), omentum (2 patients, 4.3%) and colon (1 patient, 2.1%). Thirty-one patients (66%) had complete tumor resection. Eleven out of 16 deaths (23%) were tumor-related. The median survival time was 26 mo. Five-year survival rate was 61.3%. The significant factors associated with tumor-related death or recurrence were incomplete resection, tumor size 5 cm or above, invasion to the adjacent organ or presence of metastasis. CONCLUSION The incidence of GIST in Hong Kong is comparable to that in the United States but lower than that in Finland. The true incidence of GISTs could be underestimated before the introduction of CD117. Incomplete resection, tumor size 5 cm or above, invasion to the adjacent organ or presence of metastasis are factors predicting tumor-related death or recurrence.
Estimating the Allele Frequency of Autosomal Recessive Disorders through Mutational Records and Consanguinity: The Homozygosity Index (HI)

In principle mutational records make it possible to estimate frequencies of disease alleles (q) for autosomal recessive disorders using a novel approach based on the calculation of the Homozygosity Index (HI), i.e., the proportion of homozygous patients, which is complementary to the proportion of compound heterozygous patients P(CH). In other words, the rarer the disorder, the higher will be the HI and the lower will be the P(CH). To test this hypothesis we used mutational records of individuals affected with Familial Mediterranean Fever (FMF) and Phenylketonuria (PKU), born to either consanguineous or apparently unrelated parents from six population samples of the Mediterranean region. Despite the unavailability of precise values of the inbreeding coefficient for the general population, which are needed in the case of apparently unrelated parents, our estimates of q are very similar to those of previous descriptive epidemiological studies. Finally, we inferred from simulation studies that the minimum sample size needed to use this approach is 25 patients either with unrelated or first cousin parents. These results show that the HI can be used to produce a ranking order of allele frequencies of autosomal recessive disorders, especially in populations with high rates of consanguineous marriages.
Long‐term tobramycin aerosol therapy in cystic fibrosis

The long‐term efficacy and safety of aminoglycoside aerosol therapy for Pseudomonas aeruginosa colonization/infection in cystic fibrosis has not been fully investigated. In the present study, 14 patients with cystic fibrosis, ages 8–19 years (mean: 13.3 years), received tobramycin aerosol therapy for a mean duration of 20 months. Eighty milligrams of a tobramycin solution were inhaled twice daily after physiotherapy via a jet nebulizer. After 1 year, weight for height increased significantly by 2.9% of the predicted normal, and the Kraemer clinical score increased by 2.1 points (P <0.05). The frequency of hospital admissions decreased from 2.0 to 1.3 per patient, respectively, during the years before and after the study onset. The antibody response to P. aeruginosa elastase, exotoxin A, and alkaline phosphatase showed a reduction in serum titers against one or more enzymes in eight patients. The best long‐term results after 12–38 months of treatment were obtained in moderately ill children. No evidence of ototoxicity or renal damage was observed. Although intermittent bacterial resistance occurred in five patients after 10–21 months of tobramycin inhalation, this was not associated with clinical deterioration. The study demonstrates the safety and clinical efficacy of long‐term tobramycin aerosol therapy. Double‐blind studies with larger patient cohorts are required to determine the value of aminoglycoside inhalation as an adjunct to the established therapeutic regimens.
Effects of Growth Temperature on the Responses of Ribulose-1,5-Biphosphate Carboxylase, Electron Transport Components, and Sucrose Synthesis Enzymes to Leaf Nitrogen in Rice, and Their Relationships to Photosynthesis

Effects of growth temperature on the photosynthetic gas-exchange rates and their underlying biochemical properties were examined in young, fully expanded leaves of rice (Oryza sativa L.). The plants were grown hydroponically under day/night temperature regimes of 18/15[deg]C, 23/18[deg]C, and 30/23[deg]C and all photosynthetic measurements were made at a leaf temperature of 25[deg]C and an irradiance of 1800 [mu]mol quanta m-2 s-1. Growth temperature affected the photosynthetic CO2 response curve. The relative ratio of the initial slope to the CO2-saturated photosynthesis increased with rising growth temperature. This was caused mainly by an increase in CO2-limited photosynthesis for a given leaf nitrogen content with rising growth temperature. However, there was no difference in ribulose-1,5-bisphosphate carboxylase (Rubisco) content at any given leaf nitrogen content among temperature treatments. In addition, the activation state and catalytic turnover rate of Rubisco were not affected by growth temperature. The increase in CO2-limited photosynthesis with rising growth temperature was the result of an increase in the CO2 transfer conductance between the intercellular airspaces and the carboxylation sites. The amounts of total chlorophyll and light-harvesting chlorophyll a/b protein II increased for the same leaf nitrogen content with rising growth temperature, but the amounts of cytochrome f and coupling factor 1 and the activities of cytosolic fructose-1,6-bisphosphatase and sucrose-phosphate synthase were the same between plants grown at 23/18[deg]C and those grown at 30/23[deg]C. Similarly, CO2-saturated photosynthesis was not different for the same leaf nitrogen content between these treatments. For the 18/15[deg]C-grown plants, a slight decrease in the amounts of cytochrome f and coupling factor 1 and an increase in the activities of cytosolic fructose-1,6-bisphosphatase and sucrose-phosphate synthase were found, but these were not reflected in CO2-saturated photosynthesis.
Event-based optimization for the continuous-time Markov systems

Performance optimization plays an important role in both applied and theoretical research. Recent research provides a unified view, with which the main results in many different areas can be derived or explained using two foundational sensitivities equations. With this approach, event-based optimization has been proposed to overcome the difficulties that the traditional approaches could not solve. However, most of the previous results are on discrete-time Markov systems. In the real world, many practical problems require the model of the continuous-time Markov systems. This paper focuses on extending the event-based optimization approach to the continuous-time Markov systems. As any Markov process can be viewed as a GSMP, we first give a standard description on the GSMP model and then slightly modify it to fit our problem setting. Compared with the event-based optimization with the discrete-time model, in the continuous-time case, in addition to control the probabilities of the controllable events, we need also control the rates of the triggerable events. The final result keeps as intuitive as that for the discrete-time Markov systems, and provides a natural framework for studying the event-based optimization problems.
Corporate social responsibility (CSR) practices by SIN firms

Purpose The purpose of this paper is to examine corporate social responsibility (CSR) practices of SIN firms. SIN firms are firms from controversial sectors such as tobacco, alcohol, gambling and firearms. Design/methodology/approach This paper explains contrasts CSR practices of SIN firms with similar size and industry non-SIN counterparts. Findings This paper shows that SIN firms conduct more CSR practices than non-SIN firms. This paper also finds that CSR practices of SIN firms are value relevant only when these firms are performing below their peers. Originality/value The motivation for SIN firms to engage in higher CSR is the competitive advantage hypothesis and not moral rebalancing.
Predicting ribosomal frameshifting efficiency

Many retroviruses use −1 ribosomal frameshifting as part of the mechanism in translational control of viral protein synthesis. Quantitative prediction of the efficiency of −1 frameshifting is crucial for understanding the viral gene expression. Here we investigate the free energy landscape for a minimal −1 programmed ribosomal frameshifting machinery, including the codon–anticodon base pairs at the slippery site, the downstream messenger RNA structure and the spacer between the slippery site and the downstream structure. The free energy landscape analysis leads to a quantitative relationship between the frameshifting efficiency and the tension force generated during the movement of codon–anticodon complexes, which may occur in the A/T to A/A accommodation process or the translocation process. The analysis shows no consistent correlation between frameshifting efficiency and global stability of the downstream mRNA structure.
Involvement of nicotinic receptors in alcohol self-administration.

BACKGROUND Alcohol and nicotine, in the form of tobacco, are commonly co-abused. Nicotinic receptors also have been implicated in alcohol action. We designed the present study to examine the possible involvement of nicotinic receptors in alcohol self-administration. METHODS AND RESULTS Pretreatment with lower doses (0.1-0.4 mg/kg) of nicotine, administered acutely or chronically, did not affect alcohol consumption, whereas a higher dose (0.8 mg/kg) initially suppressed alcohol consumption but stimulated alcohol consumption on repeated treatment. We observed the same pattern of nicotine effects on alcohol self-administration using an operant procedure. A dose of 0.8 mg/kg of nicotine initially suppressed operant responding for alcohol. Such suppression of alcohol self-administration was more pronounced during the first 20 min of the 60 min operant session. Responding for alcohol in the nicotine treated group, however, was significantly increased above the saline treated group by the 5th day of treatment. Mecamylamine, a noncompetitive nicotinic receptor antagonist, reduced alcohol consumption, whereas dihydro-beta-erythroidine (DHbetaE), a competitive nicotinic receptor antagonist, did not modify alcohol consumption. CONCLUSIONS The stimulation of alcohol intake induced by nicotine treatment and the suppression of alcohol intake induced by mecamylamine provide evidence for the involvement of nicotinic receptors in alcohol consumption and/or self-administration. The failure of DHbetaE to reduce alcohol consumption, however, suggests that ethanol-nicotine interaction is mediated by other nicotinic receptor subtypes rather than alpha4beta2 receptor subtype, or that mecamylamine acts through a nonnicotinic mechanism.