Miracle-dz/UniFAR-FTUs huggingface dataset:
An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

Accurate annotation of all protein-coding sequences (CDSs) is an essential prerequisite to fully exploit the rapidly growing repertoire of completely sequenced prokaryotic genomes. However, large discrepancies among the number of CDSs annotated by different resources, missed functional short open reading frames (sORFs), and overprediction of spurious ORFs represent serious limitations. Our strategy towards accurate and complete genome annotation consolidates CDSs from multiple reference annotation resources, ab initio gene prediction algorithms and in silico ORFs in an integrated proteogenomics database (iPtgxDB) that covers the entire protein-coding potential of a prokaryotic genome. By extending the PeptideClassifier concept of unambiguous peptides for prokaryotes, close to 95% of the identifiable peptides imply one distinct protein, largely simplifying downstream analysis. Searching a comprehensive Bartonella henselae proteomics dataset against such an iPtgxDB allowed us to unambiguously identify novel ORFs uniquely predicted by each resource, including lipoproteins, differentially expressed and membrane-localized proteins, novel start sites and wrongly annotated pseudogenes. Most novelties were confirmed by targeted, parallel reaction monitoring mass spectrometry, including unique ORFs and variants identified in a re-sequenced laboratory strain that are not present in its reference genome. We demonstrate the general applicability of our strategy for genomes with varying GC content and distinct taxonomic origin, and release iPtgxDBs for B. henselae, Bradyrhozibium diazoefficiens and Escherichia coli as well as the software to generate such proteogenomics search databases for any prokaryote.
Preliminary evaluation of the immunoenhancement potential of Newcastle disease vaccine formulated as a cationic liposome

This study evaluates the enhancement of immune response of birds to Newcastle disease (ND) vaccine encapsulated in 1,2-dioleoyl-3-trimethylammonium propane (DOTAP)-based liposomes. The vesicles of the liposomal ND vaccine were physically characterized for shape, particle size and zeta potential. The results of the analyses showed that vesicles of the liposomal ND vaccine were spherical and tightly packed. The mean size distribution was below 100 nm. The mean zeta potential was 24 mV. Sixty experimental birds were then divided into an unvaccinated group, a liposomal ND vaccine group and a live La Sota® vaccine group. Both the liposomal ND vaccine and live La Sota® vaccine groups were vaccinated orally at 3 and 6 weeks of age. The mean antibody titres, total and differential white blood cell count, and blood chemistry, respectively, were assessed. Ten birds from each group were challenged by oral administration of 0.2 ml virulent Herts 33 strain at 9 weeks of age. The log2 mean antibody titre induced by the liposomal ND vaccine after secondary immunization of the birds was 9.60±0.95 while that of the live La Sota ® vaccine was 6.00±0.63. Nine of the 10 challenged birds in the unvaccinated group died while none died from the liposomal ND vaccine group or the live La Sota® vaccine group. After the boost vaccination, the chickens vaccinated with the liposomal ND vaccine had a higher mean antibody titre, indicating that encapsulating ND vaccine in DOTAP-based liposome induced significantly higher immunity than the live La Sota® vaccine.
Occipital bunning among later Pleistocene Hominids.

Occipital bunning is a posterior projection of the occipital squama, which occurs in varying frequencies in samples of archaic Homo sapiens, Upper Pleistocene anatomically modern humans, and recent humans. It can be best interpreted as a product of the timing of posterior cerebral growth relative to the growth of the cranial vault bones. It is not a feature that was unique to the Neandertals.
Endothelial Dimethylarginine Dimethylaminohydrolase 1 Is an Important Regulator of Angiogenesis but Does Not Regulate Vascular Reactivity or Hemodynamic Homeostasis

Background— Asymmetrical dimethylarginine (ADMA) is an endogenous inhibitor of nitric oxide synthesis and a risk factor for cardiovascular disease. Dimethylarginine dimethylaminohydrolase (DDAH) enzymes are responsible for ADMA breakdown. It has been reported that endothelial DDAH1 accounts for the majority of ADMA metabolism. However, we and others have shown strong DDAH1 expression in a range of nonendothelial cell types, suggesting that the endothelium is not the only site of metabolism. We have developed a new endothelium-specific DDAH1 knockout mouse (DDAH1En−/−) to investigate the significance of endothelial ADMA in cardiovascular homeostasis. Methods and Results— DDAH1 deletion in the DDAH1En−/− mouse was mediated by Tie-2 driven Cre expression. DDAH1 deletion was confirmed through immunocytochemistry, whereas Western blotting showed that DDAH1 remained in the kidney and liver, confirming expression in nonendothelial cells. Plasma ADMA was unchanged in DDAH1En−/− mice, and cultured aortas released amounts of ADMA to similar to controls. Consistent with these observations, vasoreactivity ex vivo and hemodynamics in vivo were unaltered in DDAH1En−/− mice. In contrast, we observed significantly impaired angiogenic responses both ex vivo and in vivo. Conclusions— We demonstrate that endothelial DDAH1 is not a critical determinant of plasma ADMA, vascular reactivity, or hemodynamic homeostasis. DDAH1 is widely expressed in a range of vascular and nonvascular cell types; therefore, the additive effect of DDAH1 expression in multiple organ systems determines plasma ADMA concentrations. Endothelial deletion of DDAH1 profoundly impairs the angiogenic capacity of endothelial cells, indicating that intracellular ADMA is a critical determinant of endothelial cell response.
Oxidative DNA Damage and Antioxidant Defense After Reperfusion in Acute Myocardial Infarction

Purpose Myocardial damage mediated by oxidative stress during acute myocardial infarction (MI) has been suggested as an obstructive factor on recovery after an MI. 8-Hydroxydeoxyguanosine (8-OHdG) is a marker for oxidative DNA damage; superoxide dismutase (SOD) and glutathione peroxidase (G-Px) are major antioxidant enzymes. We determined changes in the plasma level of 8-OHdG and activities of SOD and G-Px in patients with MI and examined the relations between those changes and other cardiac markers. Methods Blood samples were taken at the beginning of the therapy, on the third day of hospitalization, and on the day patients were discharged home. Plasma level of 8-OHdG and SOD and G-Px activities were measured by enzyme-linked immunosorbent assay and spectrophotometric kits, respectively. Results 8-Hydroxydeoxyguanosine level at the beginning of the therapy was found to be decreased on the third day of therapy and on the day patients were discharged home. With respect to the treatment way, 8-OHdG level was found to be slightly decreased on the third day of therapy and then remained stable in the group treated with thrombolytic agents. However, 8-OHdG level was found to be sharply decreased on the third day of therapy in the group that underwent primary percutaneous transluminal coronary angioplasty. No significant relations were determined between those measured parameters and serum levels of cardiac markers. Conclusion Although not correlated with other cardiac markers, plasma level of 8-OHdG shows a decrease after reperfusion therapy in patients with MI, and primary percutaneous transluminal coronary angioplasty seems much more effective than thrombolytic therapy for providing a low level of 8-OHdG.
Quality of Life in Adolescents With Treated Coeliac Disease: Influence of Compliance and Age at Diagnosis

Objective: To assess the influence of gluten-free diet (GFD) compliance on the quality of life (QOL) of adolescents with coeliac disease (CD), and the impact of patient's age at time of diagnosis. Study design: Participants included 365 subjects: 283 adolescents (10–20 years old) with biopsy-proven CD and 82 adolescents without a chronic condition matched for age, sex, education, and social status. Their subjective QOL—comprising physical, mental, and social dimensions as defined by the World Health Organization—was measured and has been analyzed according to compliance status and age at CD diagnosis. Results: Adolescents noncompliant with GFD reported a lower general QOL, more physical problems, a higher burden of illness, more family problems, and more problems in leisure time than adolescents who are compliant with GFD. More frequent GFD transgressions were associated with poorer QOL. Higher problem anticipation and higher feelings of “ill-being” were found in the noncompliant group. No differences between compliant patients with CD and adolescents without any chronic condition were found in all QOL aspects. Adolescents with a late CD diagnosis showed more problems at school and in social contact with peers, as well as worse physical health and higher CD-associated burden. Conclusions: Compliance with GFD is an essential factor to obtain optimal QOL. Psychosocial and educational support should be provided for patients having difficulties strictly adhering to GFD. Early CD onset and diagnosis is associated with better physical health, lower CD-associated burden and fewer social problems, indicating the importance of the earliest CD diagnosis possible.
Animal Genetic Models for Complex Traits of Physical Capacity

BRITTON, S.L. , and L.G. KOCH. Animal genetic models for complex traits of physical capacity. Exerc. Sport Sci. Rev., Vol. 29, No. 1, pp 7–14, 2001. Understanding the genetic basis for variance in complex physical traits such as aerobic capacity has become an attainable goal. A starting point is the development or identification of animal genetic models that contrast the low and high values for the trait of interest. Genes that cause natural trait variation can ultimately be determined from animal models via genetic linkage.
Classical conditioning modifies cytochrome oxidase activity in the auditory system

The effects of excitatory classical conditioning on cytochrome oxidase activity in the central auditory system were investigated using quantitative histochemistry. Rats in the conditioned group were trained with consistent pairings of a compound conditional stimulus (a tone and a light) with a mild footshock, to elicit conditioned suppression of drinking. Rats in the pseudorandom group were exposed to pseudorandom presentations of the same tone, light and shock stimuli without consistent pairings. Untrained rats in a naive group did not receive presentations of the experimental stimuli.
Fractures following electroshock therapy.

The increasing use of convulsive therapy in various psychoses and allied disorders makes it necessary for the radiologist to be familiar with the roentgen changes that may be found in the complications associated with this form of treatment. The present study was undertaken in order to evaluate the traumatic complications (fractures) incident to electroshock therapy in a group of patients treated at the McLean Hospital. It is intended to emphasize the ways in which the radiologist can be of the greatest assistance to the psychiatrist and orthopedist. The therapeutic value of the treatment as it applies to the same group will not be discussed since it has been adequately presented elsewhere (8, 9). Since 1935, when Sakel in Vienna first reported insulin shock therapy for psychosis, the value of convulsive treatment has been more and more widely recognized, and the methods of producing shock have been investigated and expanded. Contraindications for and complications from this form of treatment were soon re.
Monitoring of Argatroban in ARG310 Study: Potential Recommendations for its Use in Interventional Cardiology

Argatroban is a peptidomimetic synthetic direct thrombin inhibitor with reversible and specific properties resulting in predictable anticoagulant effects. Usually, argatroban therapy is monitored by the activated clotting time (ACT) or activated partial thromboplastin time (aPTT). While other global clotting tests for the monitoring of anticoagulants are useful, their applicability to antithrombin agents (particularly of argatroban at higher dosages) is rather questionable. In this study, we sought to compare the argatroban anticoagulant levels in patients undergoing percutaneous transluminal angioplasty (PTCA) and stenting procedures, utilizing both functional and absolute quantitation methods. Argatroban produced a comparable increase of ACT and HMT, 5 to 10 minutes after administration. The level of anticoagulation achieved (400-450 seconds with ACT and HMT) following a slow bolus of argatroban (350 aglkg) was maintained throughout the procedure using 25 jtg/kg/min infusion. Following discontinuation of argatroban at the end of the procedure, the ACTs and HMTs showed a comparable progressive reduction in the anticoagulant response, which reflected the elimination of argatroban 2 to 3 hours after the procedure. No significant differences between the three methods (Hemotec, Hemochron, and HMT) were noted at any given sampling time. Argatroban dosage at 350 Ag/kg intravenous slow bolus followed by 25 Ag/kg/min infusion was adequate to perform PTCA and stenting procedures. There was no incidence of bleeding complications. Absolute quantitation of argatroban levels in patient plasmas by a newly developed HPLC method was found to be quite comparable with the ecarin clotting time (ECT) results. The ECT system was found to be less sensitive when compared to other tests, and therefore, could be used as a point-of-care test during the PTCA/stenting procedures to monitor argatroban.
Building an English-Chinese Parallel Corpus Annotated with Sub-sentential Translation Techniques

Human translators often resort to different non-literal translation techniques besides the literal translation, such as idiom equivalence, generalization, particularization, semantic modulation, etc., especially when the source and target languages have different and distant origins. Translation techniques constitute an important subject in translation studies, which help researchers to understand and analyse translated texts. However, they receive less attention in developing Natural Language Processing (NLP) applications. To fill this gap, one of our long term objectives is to have a better semantic control of extracting paraphrases from bilingual parallel corpora. Based on this goal, we suggest this hypothesis: it is possible to automatically recognize different sub-sentential translation techniques. For this original task, since there is no dedicated data set for English-Chinese, we manually annotated a parallel corpus of eleven genres. Fifty sentence pairs for each genre have been annotated in order to consolidate our annotation guidelines. Based on this data set, we conducted an experiment to classify between literal and non-literal translations. The preliminary results confirm our hypothesis. The corpus and code are available. We hope that this annotated corpus will be useful for linguistic contrastive studies and for fine-grained evaluation of NLP tasks, such as automatic word alignment and machine translation.
Must Children be Vaccinated or not? Annotating Modal Verbs in the Vaccination Debate

In this paper we analyze the use of modal verbs in a corpus of texts related to the vaccination debate. Broadly speaking, the vaccination debate centers around whether vaccination is safe, and whether it is morally acceptable to enforce mandatory vaccination. In order to successfully intervene and curb the spread of preventable diseases due to low vaccination rates, health practitioners need to be adequately informed on public perception of the safety and necessity of vaccines. Public perception can relate to the strength of conviction that an individual may have towards a proposition (e.g. ‘one must vaccinate’ versus ‘one should vaccinate’), as well as qualify the type of proposition, be it related to morality (‘government should not interfere in my personal choice’) or related to possibility (‘too many vaccines at once could hurt my child’). Text mining and analysis of modal auxiliaries are economically viable means of gaining insights into these perspectives, particularly on a large scale due to the widespread use of social media and blogs as vehicles of communication.
Antitumor activity of chloroform fraction of Scutellaria barbata and its active constituents

Scutellaria barbata (SB) is widely used as an antitumor agent in China, but the antitumor components of SB are still unclear. The antitumor activity of various fractions of an ethanol extract of SB was studied in six human malignant cell lines. Bio‐based assays showed that non‐polar and low‐polar solvent fractions of SB had dose‐dependent cytotoxicities on six cancer cell lines. The IC50 values of these fractions on the cancer cell lines tested ranged from 16 to 70 µg/mL after 48 h of treatment. Among them, the chloroform fraction (CE‐SB) had the strongest cytotoxicity on cancer cell lines with a lower cytotoxic effect on a normal liver cell line. Bel‐7402 cell apoptosis induced by CE‐SB was examined using Hoechst 33258 staining, agarose gel electrophoresis and flow cytometry. CE‐SB dose‐dependently decreased the S phase content. Treatment with CE‐SB caused cytochrome c release and activation of caspase‐9. The antitumor activity of CE‐SB in vivo was also evaluated. At 60 mg/kg/day, CE‐SB significantly inhibited the solid tumor proliferation and increased the life span of ascites tumor bearing mice (p < 0.01). CE‐SB was subjected to bioassay‐guided isolation of the active compounds by chromatography on silica gel and Sephadex LH‐20. Phytol, wogonin, luteolin and hispidulin were obtained as cytotoxic constituents. Copyright © 2007 John Wiley & Sons, Ltd.
Factors influencing breath ammonia determination

Amongst volatile compounds (VCs) present in exhaled breath, ammonia has held great promise and yet it has confounded researchers due to its inherent reactivity. Herein we have evaluated various factors in both breath instrumentation and the breath collection process in an effort to reduce variability. We found that the temperature of breath sampler and breath sensor, mouth rinse pH, and mode of breathing to be important factors. The influence of the rinses is heavily dependent upon the pH of the rinse. The basic rinse (pH 8.0) caused a mean increase of the ammonia concentration by 410 ± 221 ppb. The neutral rinse (pH 7.0), slightly acidic rinse (pH 5.8), and acidic rinse (pH 2.5) caused a mean decrease of the ammonia concentration by 498 ± 355 ppb, 527 ± 198 ppb, and 596 ± 385 ppb, respectively. Mode of breathing (mouth-open versus mouth-closed) demonstrated itself to have a large impact on the rate of recovery of breath ammonia after a water rinse. Within 30 min, breath ammonia returned to 98 ± 16% that of the baseline with mouth open breathing, while mouth closed breathing allowed breath ammonia to return to 53 ± 14% of baseline. These results contribute to a growing body of literature that will improve reproducibly in ammonia and other VCs.
Low Risk for Hepatitis C Seroconversion in Methadone Maintenance Treatment

Objectives:To study the risk factors for seroconversion to hepatitis C virus (HCV) infection since admission to methadone maintenance treatment (MMT) and to characterize the seronegative admitted group. Methods:All 657 patients admitted to our MMT clinic in Tel Aviv, Israel, between 1993 and 2008 were prospectively followed up. Those who were HCV negative (n = 271) with >1 HCV tests (n = 207) were included for seroconversion analyses. Results:Proportions of ever drug injectors, benzodiazepine abuse, and former USSR immigrants were higher among HCV sera-positive versus sera-negative patients on admission to MMT. The incidence of HCV seroconversion in MMT was 2/100 person years [py] (25 seroconversions, 1133.9 py). Seroconversion rates were higher among 44 younger patients (<30 years: 9.6/100 vs 1.4/100 py, P < 0.0005), among 103 patients with positive urine results to benzodiazepines (3.6/100 vs 1/100 py, P = 0.005), among 118 patients who injected the drugs (3.9/100 vs 1/100 py, P = 0.003), and among 43 patients who dropped out and were readmitted to the MMT (4.3/100 vs 1.7/100 py, P = 0.04). There was a trend of higher seroconversion among 61 females (P = 0.1), among 62 patients with no children (P = 0.1), and among those having hepatitis B antigen (n = 7; P = 0.09). Variables that predicted seroconversion were drug injection, benzodiazepine abuse, and being younger at admission to MMT. Being a former USSR immigrant did not predict seroconversion. Conclusions:The HCV seroconversion rate of patients in MMT is low, also, for former USSR immigrants. The predictors for seroconversion were only admission variables (younger age at admission to MMT, ever drug injector, and having positive urine to benzodiazepines at MMT admission). Specific intervention to eliminate seroconversion is needed for these high-risk groups.
Estrogen and the prefrontal cortex: Towards a new understanding of estrogen's effects on executive functions in the menopause transition

Midlife decline in cognition, specifically in areas of executive functioning, is a frequent concern for which menopausal women seek clinical intervention. The dependence of executive processes on prefrontal cortex function suggests estrogen effects on this brain region may be key in identifying the sources of this decline. Recent evidence from rodent, nonhuman primate, and human subject studies indicates the importance of considering interactions of estrogen with neurotransmitter systems, stress, genotype, and individual life events when determining the cognitive effects of menopause and estrogen therapy. Hum Brain Mapp 35:847–865, 2014. © 2012 Wiley Periodicals, Inc.
Biochemical properties of RuvBD113N: a mutation in helicase motif II of the RuvB hexamer affects DNA binding and ATPase activities.

Many DNA helicases utilise the energy derived from nucleoside triphosphate hydrolysis to fuel their actions as molecular motors in a variety of biological processes. In association with RuvA, the E. coli RuvB protein (a hexameric ring helicase), promotes the branch migration of Holliday junctions during genetic recombination and DNA repair. To analyse the relationship between ATP-dependent DNA helicase activity and branch migration, a site-directed mutation was introduced into the helicase II motif of RuvB. Over-expression of RuvBD113N in wild-type E. coli resulted in a dominant negative UVs phenotype. The biochemical properties of RuvBD113N were examined and compared with wild-type RuvB in vitro. The single amino acid substitution resulted in major alterations to the biochemical activities of RuvB, such that RuvBD113N was defective in DNA binding and ATP hydrolysis, while retaining the ability to form hexameric rings and interact with RuvA. RuvBD113N formed heterohexamers with wild-type RuvB, and could inhibit RuvB function by affecting its ability to bind DNA. However, heterohexamers exhibited an ability to promote branch migration in vitro indicating that not all subunits of the ring need to be catalytically competent.