Miracle-dz/UniFAR-FTUs huggingface dataset:
A novel integrative and conjugative element (ICE) of Escherichia coli: the putative progenitor of the Yersinia high‐pathogenicity island

Diversification of bacterial species and pathotypes is largely caused by horizontal transfer of diverse DNA elements such as plasmids, phages and genomic islands (e.g. pathogenicity islands, PAIs). A PAI called high‐pathogenicity island (HPI) carrying genes involved in siderophore‐mediated iron acquisition (yersiniabactin system) has previously been identified in Yersinia pestis, Y. pseudotuberculosis and Y. enterocolitica IB strains, and has been characterized as an essential virulence factor in these species. Strikingly, an orthologous HPI is a widely distributed virulence determinant among Escherichia coli and other Enterobacteriaceae which cause extraintestinal infections. Here we report on the HPI of E. coli strain ECOR31 which is distinct from all other HPIs described to date because the ECOR31 HPI comprises an additional 35 kb fragment at the right border compared to the HPI of other E. coli and Yersinia species. This part encodes for both a functional mating pair formation system and a DNA‐processing region related to plasmid CloDF13 of Enterobacter cloacae. Upon induction of the P4‐like integrase, the entire HPI of ECOR31 is precisely excised and circularised. The HPI of ECOR31 presented here resembles integrative and conjugative elements termed ICE. It may represent the progenitor of the HPI found in Y. pestis and E. coli, revealing a missing link in the horizontal transfer of an element that contributes to microbial pathogenicity upon acquisition.
Response of Soil Microbial Properties to Long-Term Application of Organic and Inorganic Amendments in a Tropical Soil (Saria, Burkina Faso)

Soil microbial biomass carbon (MBC), β-glucosidase, acid phosphatase and fluorescein diacetate (FDA) activities and bacterial community structure were assessed in a long-term (26 years) experiment, at physiological stages of sorghum growth, comparing different management methods for organic (manure, straw residues) and inorganic (urea) amendments at the INERA field station in Saria (Burkina Faso). Annual application of manure led to the highest soil microbial biomass and enzyme activities. Investigations indicated that only microbial biomass and β-glucosidase activities were affected during the cropping season. Phosphatase and FDA enzyme activities did not depend on the crop development stages. The application of N fertilizer modified phosphatase and FDA enzyme activities, the activities being higher in soils amended with N fertilizer. The bacterial community structure was analyzed by PCR-denaturing gradient gel electrophoresis (PCR-DGGE) targeting the eubacterial 16S rRNA gene. Cluster analysis of PCR-DGGE patterns showed two major clusters, the first containing the mineral fertilization and straw treatments and the second, the straw + urea, manure and manure + urea treatments. Sorghum grain yields were the highest for manure treatments. In this long-term experiment, applying straw did not produce a better grain yield than that obtained in the un-amended plot.
Cellular Expression of Gut Chitinase mRNA in the Gastrointestinal Tract of Mice and Chickens

Recently, the second mammalian chitinase, designated acidic mammalian chitinase (AMCase), has been identified in human, mouse, and cow. In contrast to the earlier identified macrophage-derived chitinase (chitotriosidase), this chitinase is richly expressed in the gastrointestinal (GI) tract, suggesting its role in digestion of chitin-containing foods as well as defense against chitin-coated microorganisms and parasites. This in situ hybridization study first revealed cellular localization of the gut-type chitinase in the mouse and chicken. In adult mice, the parotid gland, von Ebner's gland, and gastric chief cells, all of which are exocrine cells of the serous type, expressed the gut chitinase mRNA. In the chicken, oxyntico-peptic cells in glandular stomach (proventriculus) and hepatocytes expressed the chitinase mRNA. Because cattle produce the gut chitinase (chitin-binding protein b04) only in the liver, the gut chitinases in mammals and birds have three major sources of production, i.e., the salivary gland, stomach, and liver. During ontogenetic development, the expression level in the parotid gland and stomach of mice increased to the adult level before weaning, whereas in the stomach of chickens intense signals were detectable in embryos from incubation day 7.
Brain-Mind States: Reciprocal Variation in Thoughts and Hallucinations

The exclusion of thinking from recent studies of sleep mentation has hindered a full appreciation of how cognitive activity differs across the states of waking and sleep. To overcome this limitation, this study investigated thoughts and hallucinations using experience sampling, home-based sleep-wake monitoring, and formal analyses of the psychological data. The prevalence of thoughts decreased gradually from waking through sleep onset and non-REM sleep, to reach its nadir in REM sleep, whereas hallucinations increased sharply across these states. Furthermore, multiple occurrences of hallucinations but not of thoughts increased significantly from sleep onset through non-REM sleep, to a peak in REM sleep. This reciprocity in thoughts and hallucinations might reflect a progressive shift from high to low aminergic-to-cholinergic neuromodulatory ratios across wake-sleep states, accompanied by an array of changes in the regional activation patterns of the brain.
A Narrative Enquiry of Experienced Family Carers of People with Dementia Volunteering in a Carer Supporter Programme

Whilst positive and negative aspects of general volunteering have been noted in the literature, little is known about the experience of volunteering to provide peer support to carers of people with dementia. The present study explored the impact of participating in a carer supporter programme in the context of previous caring experiences. Eight carer supporters, who had participated in the programme for at least 5 months, took part in semi-structured interviews to elicit rich, extended narratives of their experiences. Narrative analysis of the interview transcripts covered structural, thematic and wider socio-cultural components. The results indicated that most carer supporters naturally reflected on the positive impact of having shared experiences with the newer carers. Emotional and practical gains from participating in the programme were highlighted, as well as a greater sense of connection with others, extending to a wider social and organisational network. However, carer supporters also reflected on the negative emotions that could be evoked. The findings of the study indicate that the carer supporter role has potential to facilitate new roles, activities and social identities, but participation needs to be considered in relation to potentially stressful transitional points throughout the caring career. Role definition issues also need further consideration. Copyright © 2014 John Wiley & Sons, Ltd.
Characterization of ionic currents of circular smooth muscle cells of the canine pyloric sphincter.

1. The ionic currents of circular muscle cells from canine pyloric sphincter were characterized using the whole‐cell patch clamp technique. 2. Subpopulations of circular muscle cells from the myenteric and submucosal halves of the circular layer were isolated and studied separately to determine whether differences in the currents expressed by these cells could explain differences in electrical behaviour observed in situ. 3. Resting potentials of isolated cells were about 20 mV positive to cells in intact muscles. Polarization under current clamp to the level of tissue resting potentials caused spontaneous discharge of action potentials in many cells. 4. Outward current measured under voltage clamp could be divided into a voltage‐dependent component and a voltage‐ and Ca(2+)‐dependent component. The latter was affected by manipulations of external [Ca2+], nifedipine and dialysis of cells with EGTA. 5. A few cells exhibited a channel that was activated with hyperpolarization. These channels produced inward current at potentials positive to the potassium reversal potential, EK, and reversed at ‐13 mV. 6. Inward currents, recorded from Cs(+)‐loaded cells, were characterized by a transient phase and a sustained phase that persisted throughout the test depolarization. The inward current was reduced by nifedipine but in some cells a nifedipine‐resistant component was observed. 7. There were no fundamental differences in the ionic currents recorded from circular muscle cells from the myenteric and submucosal regions, suggesting that the electrical activity of the tissue must be dependent upon structural characteristics (i.e. electrical coupling, fibre bundle dimensions, etc.) of the tissue. 8. The ionic conductance characterized can be related to many of the excitable events recorded from pyloric muscles.
Validation of the comprehensive ICF Core Set for rheumatoid arthritis: the perspective of physicians.

OBJECTIVE The "Comprehensive ICF Core Set for rheumatoid arthritis" represents the typical spectrum of problems in functioning of patients with rheumatoid arthritis according to the International Classification of Functioning, Disability and Health (ICF). The objective of this study was to validate this ICF Core Set from the perspective of physicians. METHODS Physicians experienced in rheumatoid arthritis treatment were asked about the problems they commonly treat in patients with rheumatoid arthritis in a 3-round survey using the Delphi technique. Responses were linked to the ICF. RESULTS Seventy-nine physicians in 41 countries named 512 patients' problems. Two hundred and 27 ICF categories were linked to these answers. Twenty-six ICF categories were not represented in the Comprehensive ICF Core Set for rheumatoid arthritis and 19 aspects were not covered by the ICF. CONCLUSION The content validity of 3 ICF components was well supported. However, several body functions were identified that are not covered and need to be investigated further.
The dorsal motor nucleus of the vagus and regulation of pancreatic secretory function

• What is the Topic of this review? This review describes new evidence for the control of pancreatic exocrine and endocrine secretion by the dorsal motor nucleus of the vagus. It describes the effects of several gastrointestinal peptides on pancreatic secretion and considers their sites of action in the vago‐vagal reflex pathway. • What advances does it highlight? This review draws together recent electrophysiological, anatomical and pharmacological studies to provide a state‐of‐art view of the parasympathetic control of the exocrine and endocrine pancreas.
How Physicians Cope With Stillbirth or Neonatal Death: A National Survey of Obstetricians

OBJECTIVE: To identify U.S. obstetricians’ experiences and attitudes about perinatal death, their coping strategies, and their beliefs about the adequacy of their training on this topic. METHODS: A total of 1,500 randomly selected U.S. obstetricians were mailed a self-administered survey about their experiences and attitudes in dealing with perinatal death. Physicians received up to three copies of the survey, a reminder card, and a $2 cash incentive. Eight hundred four physicians (54%) completed the entire survey. RESULTS: Seventy-five percent of respondents reported that caring for a patient with a stillbirth took a large emotional toll on them personally, and nearly one in 10 obstetricians reported they had considered giving up obstetric practice because of the emotional difficulty in caring for a patient with a stillbirth. Talking informally with colleagues (87%) or friends and family (56%) were the most common strategies used by physicians to personally cope with these situations. CONCLUSION: Perinatal death has a profound effect on the delivering obstetrician, and a significant number of participants in our study have even considered giving up obstetrics altogether. Improved bereavement training may help obstetricians care for grieving families but also cope with their own emotions after this devastating event. LEVEL OF EVIDENCE: II
Clinical Criteria for Airway Assessment: Correlations with Laryngoscopy and Endotracheal Intubation Conditions

Difficult intubation, inadequate ventilation and esophageal intubation are the principal causes of death or brain damage related to airway manipulation. The objective of this cross-sectional study was to correlate a preanesthetic evaluation that may be capable of predicting a difficult intubation with the conditions encountered at laryngoscopy and endotracheal intubation. Eighty-one patients submitted to general anesthesia were evaluated at a preanesthetic consultation according to the modified Mallampati classification, the Wilson score and the American Society of Anesthesiologists (ASA) difficult airway algorithm. Findings were then correlated with the Cormack-Lehane classification and with the number of attempts at endotracheal intubation. No statistically significant correlations were found between the patients’ Mallampati classification and their Cormack-Lehane grade or between the Mallampati classification and the number of attempts required to achieve endotracheal intubation. Laryngoscopy proved difficult in four patients and in all of these cases the Wilson score had been indicative of a possibly difficult airway, highlighting its good predicting sensitivity. However, the specificity of this test was low, since another 24 patients had the same Wilson score but were classified as Cormack-Lehane I/II. Moreover, two patients who had a Wilson score ≥ 4 were also classified as Cormack-Lehane grade I/II. The study concluded that the Wilson score, although seldom used in clinical practice, is a highly sensitive predictor of a difficult airway; its specificity, however, is low.
Strong interaction shift and width of the 1s level in pionic hydrogen.

The 3{ital p}{minus}1{ital s} x-ray line of pionic hydrogen was measured with a reflecting bent crystal spectrometer. The strong interaction energy level shift and the total decay width of the 1{ital s} state, obtained from the transition energy and the linewidth, are {var_epsilon}{sub 1{ital s}}={minus}7.127{plus_minus}0.028(stat){plus_minus}0.036(syst)eV (attractive) and {Gamma}{sub 1{ital s}}=0.97{plus_minus}0.10(stat){plus_minus}0.05(syst)eV. The corresponding hadronic {pi}{ital N} {ital s}-wave scattering lengths for elastic scattering and single charge exchange are {ital a}{sub {pi}{sup {minus}}{ital p}{r_arrow}{pi}{sup {minus}}{ital p}}{sup {ital h}}=0.0885{plus_minus}0.0009{ital m}{sub {pi}}{sup {minus}1} and {ital a}{sub {pi}{sup {minus}}{ital p}{r_arrow}{pi}{sup 0}{ital n}}{sup {ital h}}={minus}0.136{plus_minus}0.010{ital m}{sub {pi}}{sup {minus}1}. {copyright} {ital 1995} {ital The} {ital American} {ital Physical} {ital Society}.
Structure and Function of the XpsE N-Terminal Domain, an Essential Component of the Xanthomonas campestris Type II Secretion System*

Secretion of fully folded extracellular proteins across the outer membrane of Gram-negative bacteria is mainly assisted by the ATP-dependent type II secretion system (T2SS). Depending on species, 12-15 proteins are usually required for the function of T2SS by forming a trans-envelope multiprotein secretion complex. Here we report crystal structures of an essential component of the Xanthomonas campestris T2SS, the 21-kDa N-terminal domain of cytosolic secretion ATPase XpsE (XpsEN), in two conformational states. By mediating interaction between XpsE and the cytoplasmic membrane protein XpsL, XpsEN anchors XpsE to the membrane-associated secretion complex to allow the coupling between ATP utilization and exoprotein secretion. The structure of XpsEN observed in crystal form P43212 is composed of a 90-residue α/β sandwich core domain capped by a 62-residue N-terminal helical region. The core domain exhibits structural similarity with the NifU-like domain, suggesting that XpsEN may be involved in the regulation of XpsE ATPase activity. Surprisingly, although a similar core domain structure was observed in crystal form I4122, the N-terminal 36 residues of the helical region undergo a large structural rearrangement. Deletion analysis indicates that these residues are required for exoprotein secretion by mediating the XpsE/XpsL interaction. Site-directed mutagenesis study further suggests the more compact conformation observed in the P43212 crystal likely represents the XpsL binding-competent state. Based on these findings, we speculate that XpsE might function in T2SS by cycling between two conformational states. As a closely related protein to XpsE, secretion ATPase PilB may function similarly in the type IV pilus assembly.
Skip-Gram − Zipf + Uniform = Vector Additivity

In recent years word-embedding models have gained great popularity due to their remarkable performance on several tasks, including word analogy questions and caption generation. An unexpected “side-effect” of such models is that their vectors often exhibit compositionality, i.e., adding two word-vectors results in a vector that is only a small angle away from the vector of a word representing the semantic composite of the original words, e.g., “man” + “royal” = “king”. This work provides a theoretical justification for the presence of additive compositionality in word vectors learned using the Skip-Gram model. In particular, it shows that additive compositionality holds in an even stricter sense (small distance rather than small angle) under certain assumptions on the process generating the corpus. As a corollary, it explains the success of vector calculus in solving word analogies. When these assumptions do not hold, this work describes the correct non-linear composition operator. Finally, this work establishes a connection between the Skip-Gram model and the Sufficient Dimensionality Reduction (SDR) framework of Globerson and Tishby: the parameters of SDR models can be obtained from those of Skip-Gram models simply by adding information on symbol frequencies. This shows that Skip-Gram embeddings are optimal in the sense of Globerson and Tishby and, further, implies that the heuristics commonly used to approximately fit Skip-Gram models can be used to fit SDR models.
Cluster Headache and “Dynamite Headache”: Blood Flow Velocities in the Middle Cerebral Artery

Nitroglycerin (NG) induces in cluster headache patients and controls an increase in systemic diastolic blood pressure and/or heart rate and a decrease in blood flow velocity in the middle cerebral artery (VMCA). Termination of NG induced cluster headache-like attack was correlated to an increase of VMCA compared to the VMCA before NG administration (p < 0.01). This increase was not found in patients without attack or in controls. The NG induced “dynamite headache” in the controls subsided when blood pressure and heart rate were normalized, but the decrease of VMCA still prevailed. Orbital phlebograms have shown pathologic changes in cluster headache and in Tolosa-Hunt syndrome but not in controls. Ocular sympathetic nerves are involved in cluster headache but seldom in Tolosa-Hunt syndrome. It is suggested that the start of a cluster headache attack is due to an increase and the termination of the attack to a decrease of blood flow to the sympathoplegic phlebopathic cavernous sinus.
The influence of seasons on blood constituents of dromedary camel (Camelus dromedarius).

This study was carried out in White Nile State, Sudan for a period of one year, and was designed to investigate the effect of seasons on the blood constituents of dromadery camel (Camelus dromedarius). One hundred and four Samples different sex and age were collected in July (Rainy Season), September (Rainy hot summer), October (Dry wet winter) and April (Dry hot summer). The effect of season on some blood hematology, metabolites, enzymes and minerals profile was studied. The results showed higher significant level were: Monocytes, total protein and GlutamicOxaloacetic Transaminase (GPT) during rainy season, while MCV, MCH, lymphocytes, Eosinophils and Basophils in rainy hot summer, whereas within dry wet winter were: glucose, albumin and k, even in dry hot summer were: MCHC, total white blood cells, neutrophils, uric acid, creatinine, Serum Glutamic-Oxaloacetic Transaminase (GOT) and Ca. The results also indicate that the fluctuations of seasons were observed in red blood cells, hematocrit (PCV) and E.S. R as lower level. Therefore, it could be valuable to provide that the dromedary camels adapted to tropical conditions.
Ionic conductances contributing to spike repolarization and after‐potentials in rat medial vestibular nucleus neurones.

1. Intracellular recordings were made from 123 tonically active medial vestibular nucleus (MVN) neurones in a horizontal slice preparation of the dorsal brainstem of the rat. On the basis of their averaged action potential shapes, the cells were classified as either type A, having a single deep after‐hyperpolarization (AHP; 40/123 cells, 33%), or type B, having an early fast AHP and a delayed slow AHP (83/123 cells, 67%). The two cell types were distributed throughout the rostrocaudal extent of the MVN. 2. In type A cells TEA reduced the single deep AHP and decreased the rate of spike repolarization. Depolarizing current pulses from a hyperpolarized membrane potential elicited spikes with short plateau potentials in TEA. These persisted in Ca(2+)‐free medium but were abolished along with the spontaneous activity in TTX. Ca(2+)‐free medium did not affect the initial rate of repolarization but reduced the deep AHP. Apamin and carbachol had little effect. 4‐Aminopyridine (4‐AP) slowed spike repolarization and the AHP amplitude by a small amount. Thus, in type A cells spike repolarization and AHP appear to be mediated largely by a TEA‐sensitive potassium current (presumably IK) and an apamin‐insensitive Ca(2+)‐activated potassium current (presumably IC). 3. The early fast AHP in type B cells was readily abolished in TEA. In seven of ten type B cells tested, the spontaneous spikes developed plateau potentials of 100‐120 ms duration in 10 mM TEA, which then became 7‐9 s long in Ca(2+)‐free medium. In the remaining three cells, the spontaneous plateaux were 1.75‐2 s long in TEA, and were reduced to 30‐100 ms in Ca(2+)‐free medium. TTX abolished the spontaneous spikes and plateaux. The delayed AHP was abolished by apamin, which induced irregular firing. 4‐AP slowed spike repolarization and abolished the fast AHP, but did not induce plateaux. Thus, in type B cells spike repolarization involves a TEA‐sensitive current (presumably IK) as well as IC and the 4‐AP‐sensitive potassium current IA, while the apamin‐sensitive potassium current IAHP is responsible for the delayed AHP. 4. The tonic activity in type B cells appears to be regulated mainly by interactions between a persistent Na+ current, which in most cells is large enough to generate plateaux when repolarization is impeded in TEA, and the hyperpolarization mediated by IAHP. About 30% of type B cells have an additional inward Ca2+ current. (ABSTRACT TRUNCATED AT 400 WORDS)
Definability of types, and pairs of O-minimal structures

Abstract Let T be a complete O-minimal theory in a language L. We first give an elementary proof of the result (due to Marker and Steinhorn) that all types over Dedekind complete models of T are definable. Let L* be L together with a unary predicate P. Let T* be the L*-theory of all pairs (N, M), where M is a Dedekind complete model of T and N is an ⅼMⅼ+-saturated elementary extension of N (and M is the interpretation of P). Using the definability of types result, we show that T* is complete and we give a simple set of axioms for T*. We also show that for every L*-formula ϕ(x) there is an L-formula ψ(x) such that T* ⊢ (∀x)(P(x) → (ϕ(x) ↔ ψ(x)). This yields the following result: Let M be a Dedekind complete model of T. Let ϕ(x, y) be an L-formula where l(y) – k. Let X = {X ⊂ Mk: for some a in an elementary extension N of M, X = ϕ(a, y)N ∩ Mk}. Then there is a formula ψ(y, z) of L such that X = {ψ(y, b)M: b in M}.