Miracle-dz/UniFAR-FTUs huggingface dataset:
IS1403 and IS1404: analysis and distribution of two new insertion sequences in Xanthomonas campestris

A repetitive sequence in Xanthomonas campestris pv. juglandis was identified as a new insertion sequence, IS1403, by nucleotide sequence analysis. A homologous IS, IS1404, was also cloned from X. campestris pv. campestris. Both shared at least 91% identity on a nucleotide level. The sequences had 42-bp terminal inverted repeat sequences with eleven mismatches, and were flanked by 4-bp target site duplications. Comparison of target insertion sites flank- ing IS1403 and IS1404 revealed no similarities, and the G+C content of the flanking sequences of IS1403 was 45%, but that of IS1404 was 74%, indicating the elements transpose quite randomly and do not prefer A-T-rich regions. IS1403 and IS1404 contained two GTG-initiated open reading frames (orfA and orfB), and orfB was in phase -1 relative to orfA. There was an A 6 G motif followed by a potential stem-loop structure between two reading frames, which may have promoted a -1 translational frameshift to produce a transframe protein. The deduced amino acid sequences of orfA and orfB contained a potential α-helix-turn-α-helix DNA-binding motif and a D,D(35)E domain of transposases, respectively. Based on the features discussed, IS1403 and IS1404 were placed among the IS3 family with IS407 from Pseudomonas cepacia, IS476 from X. campestris pv. vesicatoria, IS1222 from Enterobacter agglomerans, and ISR1 from Rhizobium lupini. The insertion sequences were widely distributed and existed in multiple copies in most pathovars of X. campestris, but other plant pathogenic bacteria, such as P. syringae pv. apii, P. syringae pv. tabaci, P. syringae pv. glycinea, P. syringae pv. coronafaciens, Erwinia amylovora, E. carotovora, and E. cypripedii, did not contain this insertion sequence based on Southern hybridization tests.
Antigen requirements for induction of B-memory cells: studies with dinitrophenyl coupled to T-dependent and T-independent carriers

Mice were primed with dinitrophenyl (DNP) (trinitrophenyl, TNP) coupled to thymus-independent (TI) or thymus-dependent (TD) carriers. B cells from these mice were transferred to irradiated recipients with T cells from keyhole limpet hemocyanin (KLH)-primed mice. After secondary immunization with DNP-KLH a significant DNP-specific IgG memory response was produced only by mice which received B cells which had been primed with TD antigens. TI antigens were unable to induce differentiation of B-cell precursors to IgG producing memory B cells but they did not suppress the induction of B-memory cells by TD antigens. The results indicate that TI antigens fail to activate a cell type which is required for the induction of memory B cells.
Restricted Two-Variable FO + MOD Sentences , Circuits and Communication Complexity

We obtain a logical characterization of an important class of regular languages, denoted DO, and of its most important subclasses in terms of two-variable sentences with ordinary and modular quantifiers but in which all modular quantifiers lie outside the scope of ordinary quantifiers. The result stems from a new decomposition of the variety of monoids DO in terms of iterated block products. This decomposition and the ensuing logical characterization allows us to shed new light on recent results on regular languages which are recognized by bounded-depth circuits with a linear number of wires and regular languages with small communication complexity.
Suicide by occupation: Systematic review and meta-analysis

Background Previous research has shown that those employed in certain occupations, such as doctors and farmers, have an elevated risk of suicide, yet little research has sought to synthesise these findings across working-age populations. Aims To summarise published research in this area through systematic review and meta-analysis. Method Random effects meta-analyses were used to calculate a pooled risk of suicide across occupational skill-level groups. Results Thirty-four studies were included in the meta-analysis. Elementary professions (e.g. labourers and cleaners) were at elevated risk compared with the working-age population (rate ratio (RR) = 1.84, 95% CI 1.46–2.33), followed by machine operators and deck crew (RR = 1.78, 95% CI 1.22–2.60) and agricultural workers (RR = 1.64, 95% CI 1.19–2.28). Results suggested a stepwise gradient in risk, with the lowest skilled occupations being at greater risk of suicide than the highest skill-level group. Conclusions This is the first comprehensive meta-analytical review of suicide and occupation. There is a need for future studies to investigate explanations for the observed skill-level differences, particularly in people employed in lower skill-level groups. Declaration on interest None.
Changes in cellular structures revealed by ultra-high resolution retinal imaging in optic neuropathies.

PURPOSE To study the integrity of inner and outer retinal layers in patients with various types of optic neuropathy by using high-resolution imaging modalities. METHODS Three high-resolution imaging systems constructed at the University of California Davis were used to acquire retinal images from patients with optic neuropathy: (1) adaptive optics (AO)-flood-illuminated fundus camera, (2) high-resolution Fourier domain optical coherence tomography (FDOCT), and (3) adaptive optics-Fourier domain optical coherence tomography (AO-FDOCT). The AO fundus camera provides en face images of photoreceptors whereas cross-sectional images (B-scans) of the retina are obtained with both FDOCT and AO-FDOCT. From the volumetric FDOCT data sets, detailed thickness maps of a three-layer complex consisting of the nerve fiber (NF), ganglion cell (GC), and inner plexiform (IP) layers were created. The number of visible cones in the en face images of photoreceptors was then compared with visual sensitivity maps from Humphrey visual field (HVF; Carl Zeiss Meditec, Inc., Dublin, CA) testing, as well as FDOCT and AO-FDOCT images, including the thickness maps of the NF-GC-IP layer complex. Five types of optic neuropathy were studied: (1) optic neuritis with multiple sclerosis (MS), (2) idiopathic intracranial hypertension (pseudotumor cerebri), (3) nonarteritic anterior ischemic optic neuropathy (NAION), (4) optic nerve head drusen with NAION, and (5) systemic lupus erythematosus with MS and arthritis. RESULTS With permanent visual field loss and thinning of the NF-GC-IP layer complex, cone photoreceptors showed structural changes, making them less reflective, which caused the appearance of dark spaces in the en face images (hence, reduced number of visible cones) and indistinct outer retinal layers in OCT images. However, when the visual field loss was only transient, with a normal NF-GC-IP layer complex, there were no detectable abnormalities in cone photoreceptors (i.e., they were densely packed and had distinct photoreceptor layering in the OCT images). CONCLUSIONS Cone photoreceptors show structural changes when there is permanent damage to overlying inner retinal layers. There was a positive relation between the thickness of the three-layer inner retinal complex, visual sensitivity, and integrity of the cone mosaic.
37 Years of Body Mass Index and Dementia: Effect Modification by the APOE Genotype: Observations from the Prospective Population Study of Women in Gothenburg, Sweden.

BACKGROUND Overweight and obesity in mid- and late-life may increase risk for dementia, whereas a decline in body weight or body mass index (BMI) and underweight in years preceding a clinical dementia diagnosis are also associated with dementia. Little is known about the modifying effect of the APOE genotype, a major susceptibility gene for Alzheimer's disease (AD), on the BMI-dementia adult life course trajectory. OBJECTIVE We evaluated the exposure, BMI, in relationship to the outcome, clinical dementia, over 37 years, considering the effect modification of the APOE ɛ4 allele. METHODS The Prospective Population Study of Women (PPSW) in Sweden is a systematic sample of 1462 women born 1908, 1914, 1918, 1922, and 1930 and aged 38-60 years at baseline. Examinations occurred in 1968, 1974, 1980, 1992, 2000, and 2005; 559 women had information on dementia, BMI, and APOE ɛ4 allele status, in addition to covariates. Statistical analyses were conducted using mixed effects regression models. RESULTS Trajectories of BMI over 37 years differed by APOE ɛ4 allele status. While women gained BMI similarly from mid-life to age 70 years, women with at least one APOE ɛ4 allele experienced BMI decline more quickly after age 70 years compared to women without an APOE ɛ4 allele. However, upon stratifying the sample by dementia occurrence, it appeared that dementia drove the overall BMI-trajectory. There was a main effect of age, interactions of age by APOE ɛ4 allele status, and age by presence versus absence of dementia. CONCLUSIONS Women with similar average BMI at mid-life exhibited different BMI trajectories in relation to dementia occurrence. In addition, the pattern of BMI decline in late-life differed on the basis of APOE ɛ4 allele possession. Thus, these data suggest roles for both dementia- and APOE-associated changes in BMI during the adult life course.
L-functions of exponential sums over one-dimensional affinoids: Newton over Hodge

This paper proves a sharp lower bound for Newton polygons of L-functions of exponential sums of one-variable rational functions. Let p be a prime and let F¯p be the algebraic closure of the finite field of p elements. Let f¯(x) be any one-variable rational function over F¯p with l poles of orders d 1 ,…,d l . Suppose p is coprime to d 1 ,…,d l . We prove that there exists a tight lower bound which we call Hodge polygon, depending only on the d j 's, to the Newton polygon of L-function of exponential sums of f¯(x). Moreover, we show that for any f¯(x) these two polygons coincide if and only if p ≡ 1 mod d j for every 1 ≤ j ≤ l. As a corollary, we obtain a tight lower bound for the p-adic Newton polygon of zeta-function of an Artin-Schreier curve given by affine equations yp−y=f¯(x).
Serotonin modulation of cerebral glucose metabolism measured with positron emission tomography (PET) in human subjects

To develop a method to measure the dynamic response of the serotonin system in vivo, the effects of intravenously administered citalopram (the most selective of the serotonin reuptake inhibitors) on cerebral glucose metabolism were evaluated. Cerebral glucose metabolism was measured with positron emission tomography (PET) in 14 normal subjects scanned after administration of saline placebo and citalopram administered on 2 separate days. Citalopram administration resulted in a decrease in metabolism in the right anterior cingulate gyrus (BA 24/32), right superior (BA 9) and right middle frontal gyrus (BA 6), right parietal cortex (precuneus), right superior occipital gyrus, left thalamus, and right cerebellum. Increased metabolism was observed in the left superior temporal gyrus and left occipital cortex. Alterations in metabolism by acute citalopram administration involved the heteromodal association cortices that also show metabolic alterations in patients with geriatric depression and overlap with the regions affected by antidepressant treatment. Future studies will evaluate how the acute metabolic response to citalopram relates to the metabolic response after chronic treatment in patients with geriatric depression. Synapse 45:105–112, 2002. © 2002 Wiley‐Liss, Inc.
Independent Impact of Gout on Mortality and Risk for Coronary Heart Disease

Background— Although gout and hyperuricemia are related to several conditions that are associated with reduced survival, no prospective data are available on the independent impact of gout on mortality. Furthermore, although many studies have suggested that hyperuricemia is associated with cardiovascular disease (CVD), limited data are available on the impact of gout on CVD. Methods and Results— Over a 12-year period, we prospectively examined the relation between a history of gout and the risk of death and myocardial infarction in 51 297 male participants of the Health Professionals Follow-Up Study. During the 12 years of follow-up, we documented 5825 deaths from all causes, which included 2132 deaths from CVD and 1576 deaths from coronary heart disease (CHD). Compared with men without history of gout and CHD at baseline, the multivariate relative risks among men with history of gout were 1.28 (95% confidence interval [CI], 1.15 to 1.41) for total mortality, 1.38 (95% CI, 1.15 to 1.66) for CVD deaths, and 1.55 (95% CI, 1.24 to 1.93) for fatal CHD. The corresponding relative risks among men with preexisting CHD were 1.25 (95% CI, 1.09 to 1.45), 1.26 (95% CI, 1.07 to 1.50), and 1.24 (95% CI, 1.04 to 1.49), respectively. In addition, men with gout had a higher risk of nonfatal myocardial infarction than men without gout (multivariate relative risk, 1.59; 95% CI, 1.04 to 2.41). Conclusions— These prospective data indicate that men with gout have a higher risk of death from all causes. Among men without preexisting CHD, the increased mortality risk is primarily a result of an elevated risk of CVD death, particularly from CHD.
Transient Depletion of CD169+ Cells Contributes to Impaired Early Protection and Effector CD8+ T Cell Recruitment against Mucosal Respiratory Syncytial Virus Infection

Respiratory syncytial virus (RSV) is a major cause of respiratory viral infections in infants and children. Alveolar macrophages (AMs) play a crucial role in combatting airborne pathogens, strongly express CD169, and are localized in the lung alveoli. Therefore, we used CD169-diphtheria toxin receptor (DTR) transgenic mice to explore the roles of CD169+ cells in immune responses to mucosal RSV infection. The administration of diphtheria toxin to CD169-DTR mice induced specific AM depletion and reduced the recruitment of Ly6Chi monocytes. Notably, CD169+ cell depletion reduced levels of innate cytokines, such as interferon-β, IL-6, and TNF-α, in bronchoalveolar lavage fluid during RSV infection without affecting the production of proinflammatory chemokines. Moreover, the depletion of CD169+ cells increased the recruitment of inflammatory cells to the lung during the early stage of RSV infection, although not during the later stages of RSV infection. Furthermore, the depletion of CD169+ cells reduced the recruitment of effector CD8+ T cells to the lungs after RSV mucosal infection. Our findings suggest that modulating the number of CD169+ cells to enhance immune responses to RSV infection may be useful as a new therapeutic strategy.
A Sema3C Mutant Resistant to Cleavage by Furin (FR-Sema3C) Inhibits Choroidal Neovascularization

In age-related macular degeneration (AMD), abnormal sub retinal choroidal neovascularization (CNV) is a major cause of blindness. FR-sema3C is a point mutated form of semaphorin-3C that is resistant to cleavage by furin like pro-protein convertases (FPPC). We have found in previous work that FR-sema3C functions as an anti-angiogenic factor. In this study we investigated the possible use of FR-sema3C as an inhibitor of CNV. FR-sema3C inhibits VEGF as well as PDGF-BB signal transduction in endothelial cells and to less extent bFGF induced signal transduction using a mechanism that does not depend upon the binding of VEGF like the drugs that are currently the mainstay treatment for AMD. CNV was induced in eyes of C57 black mice by laser photocoagulation. Intravitreal injection of FR-Sema3C or aflibercept (VEGF-trap) was then used to inhibit CNV formation. Invading choroidal vessels were visualized a week later by injection of FITC-dextran into the circulation, followed by the measurement of the area of the invading blood vessels. Injection of 0.1 μg FR-Sema3C inhibited CNV by 55% (P<0.01) and was as effective as 5 μg aflibercept. FR-sema3C did not display any adverse effects on retinal function following its injection into eyes of healthy mice as assessed by optokinetic reflex (OKR) and Electro-retinogram (ERG) criteria. Furthermore, FR-sema3C did not induce apoptosis in the retina as determined by TUNEL nor was there any discernable structural damage to the retina as assessed by several immuno-histochemical criteria. Our results suggest that FR-sema3C could perhaps be used for the treatment of AMD, and that it may perhaps be of benefit to patients that do not respond well to current treatments relying on VEGF sequestering agents.
Experimental studies designed to evaluate the management of patients with incurable cancer.

Cancer is a serious problem and every physician and biomedical scientist must surely welcome new ideas, concepts, and approaches that might hasten solution of the problem. The 1976 paper by Cameron and Pauling (1) presented such a new approach. Their 1978 report in this issue (2), however, presents no new ideas, concepts, or approaches. The authors have not used well-established rules for clinical investigation to support their thesis. It would now be appropriate to do the following. (i) Perform prospective instead of retrospective studies, using both a control and a treated group. (ii) Define rigidly their criteria for "untreatability. " (iii) Require random assignment of carefully matched cases to the placebo-treated or the ascorbate-treated group-the assignment to be made by someone not otherwise associated with the study. (iv) Arrange that neither the investigators nor the patients know which patient is in which of the two groups ("doubleblind" study).
The effects of spray-dried blood meal on growth performance of the early-weaned pig.

A total of 1,956 weanling pigs were used in five experiments to evaluate spray-dried blood meal (SDBM) in starter pig diets. In Exp. 1, 432 weanling pigs (initially 6.9 kg BW and 21 d of age) were used to evaluate different protein sources in the d 7 to 28 postweaning diet. Pigs were fed a control diet containing 5% select menhaden fish meal or diets with 3.88% spray-dried porcine plasma, 2.49% SDBM (porcine), 5.74% soy protein concentrate, 5.74% moist extruded soy protein concentrate, or L-lysine.HCl and DL-methionine replacing select menhaden fish meal on an ideal protein basis. Pigs fed diets containing the spray-dried blood products had higher (P < .06) mean ADG than pigs fed the other protein sources. In Exp. 2, 744 weanling pigs (initially 5.8 kg BW and 21 d of age) were used to determine the effects of 0, 1, 2, 3, 4, or 5% SDBM (bovine) in the d 7 to 28 postweaning diet. Pigs fed increasing SDBM had greater (quadratic, P < .01) ADG and improved gain:feed ratio (G/F). Inflection point analysis projected optimum ADG and G/F at 1.9% SDBM. In Exp. 3, 216 weanling pigs (initially 10.9 kg BW and 42 d of age) were used to determine the effects of 0, . 5, 1, 1.5, 2, and 2.5% SDBM (bovine) in the d 21 to 42 postweaning diet. Pigs fed increasing SDBM had decreased (linear, P < .05) ADG and G/F. In Exp. 4 and 5, 144 and 180 weanling pigs (initially 5.3 and 6.2 kg BW and 24 and 21 d of age, respectively) were used to evaluate either 2.5% spray-dried porcine, spray-dried bovine, or flash-dried bovine blood meal (Exp. 4) or 2.5% spray-dried bovine or spray-dried avian blood meal (Exp. 5). Pigs fed diets containing the spray-dried blood meals had improved ADG and G/F (P < .01) compared with pigs fed flash-dried blood meal. However, no differences (P > .10) were observed among treatments when pigs were fed spray-dried blood meals from different species. We conclude that spray-dried bovine, porcine, and avian blood meal are effective protein sources in starter pig diets (d 7 to 28 postweaning). However, SDBM is not necessary in the diets of older pigs (d 21 to 42 postweaning) for maximum growth performance.
A Ten Year Retrospective Study on Adult Tetanus at the Epidemic Disease (ED) Hospital, Mysore in Southern India: A Review of 512 Cases.

BACKGROUND Tetanus still remains a major public health problem in India like in most other developing countries, with a high morbidity and mortality. OBJECTIVES To study the socio-demographic profile and the clinical profile that they presented with, as well as the outcome of the tetanus patients who were admitted to the E.D Hospital, Mysore in India. METHODOLOGY The data of all the patients of tetanus who were above the age of 15 years, who were admitted from January 2001 to December 2010, were collected, compiled and analyzed from the Medical Records Department of the Hospital. RESULTS Out of the 512 cases of tetanus, 379 (74%) were males and 133 (26%) were females. Their ages varied from 15 to 81 years, with a mean and a standard deviation respectively of 47.7 and 15.0 years. The overall mortality rate was 42.2%. The most common presenting symptoms were trismus (95.7%), neck stiffness (89.3%), body spasms/stiffness (73%) and dysphagia (38.9%). The ages of the patients and the presence of complications had a statistically significant relationship with respect to the outcome (survival versus death).
Adult-onset alcohol consumption induces osteopenia in female rats.

BACKGROUND Alcohol is a known risk factor for osteopenia and fracture in humans, and its effects on the skeleton have been studied extensively in animal models. Almost all studies of rats, however, have begun rats on alcohol diets while the animals were young and still growing. The purpose of the current study was to examine the effects of alcohol consumption on rats that began drinking alcohol as adults, so that the confounding effects of growth might be minimized. METHODS Nine-month-old female Sprague-Dawley rats were studied for two durations (8 and 14 weeks). The following diet groups were used for both durations: alcohol (n = 7), in which rats were fed a liquid diet containing ethanol (8.1% v/v; Lieber-DeCarli method); pair-fed (n = 7), in which rats were fed a caloric-equivalent liquid diet matched to the alcohol-fed animals; and pellet (n = 6), in which rats consumed standard rat chow and water. A cessation protocol was also used in which alcohol- and pair-fed groups were fed liquid diets for 8 weeks and then given pellet chow and water for 6 weeks, with pair feeding maintained during the cessation period. RESULTS Only minor effects developed in the rats in the 8-week group, but after 14 weeks, the cancellous bone of the proximal tibia was severely osteopenic in the alcohol-fed animals. The bone volume and trabecular number were both significantly lower in the alcohol-fed animals than in the pair-fed and pellet-fed control animals and also lower than in the alcohol-fed animals in the 8-week group. Mechanical properties of the cancellous bone in the distal femur also were significantly diminished in the 14-week alcohol-fed group. Composition and mechanical properties of the cortical bone in the femur diaphysis were largely unaffected, but the yield stress was significantly lower in the 14-week alcohol-fed group than in the 8-week alcohol-fed group. No significant effects were found in the cessation groups with regard to almost all parameters measured. CONCLUSIONS Our study results demonstrate that chronic adult-onset alcohol consumption leads to significantly diminished cancellous bone properties and that these effects depend on the duration of alcohol use.
Airborne Emissions Assessment of Hot Asphalt Mixing

ABSTRACT Hot mix asphalt industries are required to meet airborne emissions thresholds, yet only a few types of emission measurements are available. This study is therefore aimed at evaluating the influence of operating parameters on airborne emissions at the plant stack, especially Gaseous Organic Compounds (GOC), in addition to identifying both the best mixing conditions and bitumen influence through laboratory testing. Emission measurements have been performed for a given set of production conditions, and results highlight significant changes in emission flows. CO2, SO2, NOx and GOC all seem to be correlated with combustion intensity and energy consumption, whereas CO tends instead to be associated with combustion efficiency. Laboratory GOC variations exhibit monotonic increases with temperature; at the plant level, these effects are concealed by combustion scattering due to burner adjustment. Flow assessment is provided at the plant for each pollutant along with its dispersion.