Miracle-dz/UniFAR-FTUs huggingface dataset:
Extended Report

Objective It is increasingly being appreciated that multiple autoimmune diseases share common susceptibility genes. The tumour necrosis factor ligand superfamily member 4 gene (TNFSF4, OX40L), which encodes for the T cell costimulatory molecule OX40 ligand, has been identifi ed as a susceptibility gene for the development of systemic lupus erythematosus (SLE). Accordingly, the aim of the current study was to investigate the possible association of the TNFSF4 gene region with systemic sclerosis (SSc), an autoimmune disease that leads to the development of cutaneous and visceral fi brosis. Methods A total of 9 single nucleotide polymorphisms (SNPs) in the TNFSF4 gene region, previously associated with susceptibility to SLE, were tested for association with SSc in a collection of 1059 patients with SSc and 698 controls. Results Case-control comparisons revealed a signifi cant association between susceptibility to The minor allele at rs844644 was protective (OR 0.84, 95% CI 0.70 to 0.97, p FDR =0.038). Analysis of subsets of patients with SSc demonstrated signifi cant associations of the TNFSF4 SNPs with limited and diffuse SSc as well as specifi c SNPs that were associated with SSc-associated autoantibodies. Finally, the analyses suggest a potential interaction between two TNFSF4 SNPs, rs2205960 and rs844648, with regards to SSc susceptibility. Conclusions Polymorphisms in the TNFSF4 gene region are associated with susceptibility to SSc and its clinical and autoantibody subsets. TNFSF4 may be another gene that confers risk to multiple autoimmune diseases.
Spaces of stability conditions

Stability conditions are a mathematical way to understand $\Pi$-stability for D-branes in string theory. Spaces of stability conditions seem to be related to moduli spaces of conformal field theories. This is a survey article describing what is currently known about spaces of stability conditions, and giving some pointers for future research.
β2-Microglobulin Deficient Mice Catabolize IgG More Rapidly Than FcRn-α-Chain Deficient Mice

FcRn, a nonclassical MHC-I protein bound to β2-microglobulin (β2m), diverts IgG and albumin from an intracellular degradative fate, prolonging the half-lives of both. While knockout mouse strains lacking either FcRn-α-chain (AK) or β2m (BK) show much shorter half-lives of IgG and albumin than normal mice, the plasma IgG half-life in the BK and AK strains is different, being shorter in the BK strain. Since β2m does not affect the IgG production rate, we tested whether an additional β2m-associated mechanism protects IgG from catabolism. First, we compared the fractional disappearance rate in plasma of an intravenous dose of radioiodinated IgG in a mouse strain deficient in both FcRn-α-chain and β2m (ABK), in the two parental knockout strains (AK and BK), and in the background wild-type (WT) strain. We found that IgG survived longer in the β2m-expressing AK strain than in the β2m-lacking ABK and BK strains, whereas the IgG half-lives between the ABK and BK strains were identical. Then we compared endogenous concentrations of four typical plasma proteins among the four strains and found that steady-state plasma concentrations of both IgG and albumin were higher in the AK strain than in either the BK or the ABK strain. These results suggest that a β2m-associated effect other than FcRn prolongs the survival of both IgG and albumin, although leaky gene transcription in the AK strain cannot be ruled out.
The influence of intravenous drug use and HIV infection in the transmission of tuberculosis

ObjectiveTo investigate whether smear-positive pulmonary tuberculosis (TB) patients present a different risk of TB transmission according to their HIV status, in an area where the majority of HIV-infected patients studied were intravenous drug users (IVDU). MethodsA case-control study was performed on smear-positive pulmonary TB patients diagnosed between 1990 and 1993 for whom a contact study had been performed. Patients with and without HIV infection were matched by age (±3 years), sex and hospital of diagnosis. A micro-epidemic was defined if two or more secondary cases were detected from the same index case. Data were analysed comparing the percentage of contacts with TB in both groups. ResultsThirty-six secondary cases were detected in 436 contacts of 124 HIV-infected TB patients, whereas only 24 were identified in 624 contacts of 124 HIV-seronegative TB patients [odds ratio (OR), 2.14; 95% confidence interval (CI), 1.22–3.77; P= 0.004], Comparing the contacts of HIV-infected patients, 34 secondary cases of TB were detected in 371 contacts of 97 IVDU, whereas only two cases were detected in 85 contacts of 27 non-IVDU (OR, 4.19; 95% CI, 1.09–15.95). HIV-seropositive index cases were observed to cause more micro-epidemics than seronegative cases (eight versus four), indicating that micro-epidemic cases were more frequent in the contacts of HIV-infected subjects (27 out of 36 versus 10 out of 24; OR, 1.41; 95% CI, 1.41–12.49; P= 0.009). All index cases in eight micro-epidemics were HIV-seropositive IVDU, whereas only four micro-epidemics were generated by HIV-seronegative subjects, none of whom were IVDU. ConclusionsSmear-positive pulmonary TB patients were more likely to transmit TB if they were HIV-infected, as evidenced by the role of IVDU in generating micro-epidemics.
Comparing Completions of a Space at a

There are two practical ways to complete an abelian group A at a prime p. One could complete A with respect to the neighborhood base of zero given by the subgroups p n A. This completion, called p-completion, is lim A=p n A. Or one could complete A with respect to the neighborhood base of zero given by subgroups B A of nite p-power index. This completion, called p-pro-nite completion, is lim A where A runs over the nite p-group quotients of A. They agree for nitely generated groups, but not in general: if V is an F p vector space it is p-complete, but its p-pro-nite completion is the double dual V. Also, the former, p-completion, is easier to deene, but it is neither left nor right exact and the category of p-complete groups is not abelian { it is not closed under cokernels. The latter, p-pro-nite completion, is initially less tractable, but it is right exact and the category of p-pro-nite abelian groups is an abelian category. There are two corresponding completions for topological spaces. The analog of p-completion is Bousseld-Kan completion 3] and the analog of p-pro-nite completion is related to Sullivan's pro-nite completion and has recently been given a homotopical definition by Morel 13]. The purpose of this note is to compare these two completions; in addition, we seek to give Morel's completion the same sort of computational footing that the Bousseld-Kan completion enjoys. To underscore the similarities and diierences, let me make some remarks on how these completions of spaces are constructed.
Quantum dot / optical protein bio-nano hybrid system biosensing

III DEDICATION . IV ACKNOWLEDGEMENTS . V TABLE OF CONTENTS . VII LIST OF FIGURES . XI LIST OF TABLES . XVII ACRONYMS AND ABBREVIATIONS . XVIII CHAPTER 1. I TRODUCTIO . 1 1.1. MOTIVATION . 2 1.2. CURRENT TOXIN DETECTION TECHNIQUES . 3 1.2. 1. Mass Spectrometry . 4 1.2. 2. Immunoassay . 6 1.2. 3. Laser-Based Fluorescence . 7 1.3. BACTERIORHODOPSIN . 8 1.3.1. Production and Purification of bR . 11 1.3.2. Applying bR to Engineered Applications . 12 1.4. QUANTUM DOTS . 19 1.4.1. Quantum Dot Synthesis . 20 1.4.2. Modifying the Quantum Dot Surface Chemistry . 22 1.5. FLUORESCENCE RESONANCE ENERGY TRANSFER . 23 1.5.1. bR as a FRET Acceptor . 25 1.5.2. Quantum Dots as a FRET Donor . 29 1.6. IONIC-SELF ASSEMBLED MONOLAYERS . 33 1.6. 1. bR Ionic-Self Assembled Monolayer Films . 33 viii 1.6. 2. QD Ionic-Self Assembled Monolayer Films . 35 CHAPTER 2. PROTOCOL FOR BR PRODUCTIO . 38 CHAPTER 3. BR-BASED ELECTRODES . 43 3.1 ELECTROPHORETIC DEPOSITION LAYERING/ORIENTATION . 43 3.2 ELECTRICAL MEASUREMENT SETUP . 45 3.3 PHOTOELECTRIC ACTIVITY OF ELECTRODEPOSITED PM FILMS. 46 3.4 TEMPERATURE DEPENDENCE OF BR PHOTOVOLTAIC RESPONSE . 51 CHAPTER 4. QD ACTIVATIO OF BR PHOTOVOLTAIC RESPO SE . 58 4.1 EFFECTS OF CONTINUOUS UV ILLUMINATION ON BR PHOTOVOLTAGE . 59 4.2 BR PHOTOELECTRIC RESPONSE FROM QD ILLUMINATION . 60 4.3 THIN FILM QD ACTIVATION OF BR PHOTORESPONSE . 63 CHAPTER 5. QD-BR HYBRID IO IC-SELF ASSEMBLED MO OLAYERS . 68 5.1 BR IONIC-SELF ASSEMBLED MONOLAYER FILMS . 69 5.1.1 bR Preparation for I-SAM Deposition . 70 5.1.2 bR I-SAM Film Physical Properties . 72 5.1.3 bR I-SAM Film Electrical Activity . 78 5.2 QD IONIC-SELF ASSEMBLED MONOLAYER FILMS . 81 5.2. 1 QD Surface Functionalization . 82 5.2. 2 QD I-SAM Film Physical and Optical Properties. 84 5.3 QD-BR HYBRID IONIC-SELF ASSEMBLED MONOLAYER FILMS . 87 5.3.1 QD-bR Hybrid I-SAM Film Construction . 87 5.3.2 QD-bR Hybrid I-SAM Film Physical Properties . 88 5.3.3 QD-bR Hybrid I-SAM Film Electrical Activity . 91 CHAPTER 6. QD A D BR FRET COUPLI G . 93
UK research staff perspectives on improving recruitment and retention to primary care research; nominal group exercise.

BACKGROUND Primary care studies often encounter recruitment difficulties, but there is little evidence to inform solutions. As part of a National Institute for Health Research School for Primary Care Research and UK Clinical Research Network programme, we elicited research staff perspectives on factors facilitating or obstructing recruitment. OBJECTIVE To identify factors that experienced research staff consider important in successful recruitment and retention and their confidence in achieving them. METHODS An iterative series of three workshops was held. The third used a modified nominal group technique to categorize whether factors related to the 'context' in which the research took place, the 'content' of the study or the recruitment 'process' and to prioritize them by their importance to success. RESULTS Eighteen research staff participated in the prioritization workshop. They prioritized positive attitudes of primary care staff towards research and trust of researchers by potential participants as major contextual factors affecting recruitment. Studies needed to be considered safe and relevant by staff and fit with practice systems. They proposed that researchers strengthen relationships with staff and participants and minimize workload for primary care teams. Although confident in many recruitment processes, respondents remained uncertain how to achieve cultural change so that research became part of normal practice activity and how best to motivate patients to participate. CONCLUSIONS Research workers taking part identified factors which might be important in recruitment, several of which they expressed little confidence in addressing. Understanding how to improve recruitment is crucial if current efforts to strengthen primary care research are to bear fruit.
T lymphocytes and normal tissue responses to radiation

There is compelling evidence that lymphocytes are a recurring feature in radiation damaged normal tissues, but assessing their functional significance has proven difficult. Contradictory roles have been postulated in both tissue pathogenesis and protection, although these are not necessarily mutually exclusive as the immune system can display what may seem to be opposing faces at any one time. While the exact role of T lymphocytes in irradiated normal tissue responses may still be obscure, their accumulation after tissue damage suggests they may be critical targets for radiotherapeutic intervention and worthy of further study. This is accentuated by recent findings that pathologically damaged “self,” such as occurs after exposure to ionizing radiation, can generate danger signals with the ability to activate pathways similar to those that activate adoptive immunity to pathogens. In addition, the demonstration of T cell subsets with their recognition radars tuned to “self” moieties has revolutionized our ideas on how all immune responses are controlled and regulated. New concepts of autoimmunity have resulted based on the dissociation of immune functions between different subsets of immune cells. It is becoming axiomatic that the immune system has the power to regulate radiation-induced tissue damage, from failure of regeneration to fibrosis, to acute and chronic late effects, and even to carcinogenesis. Our understanding of the interplay between T lymphocytes and radiation-damaged tissue may still be rudimentary but this is a good time to re-examine their potential roles, their radiobiological and microenvironmental influences, and the possibilities for therapeutic manipulation. This review will discuss the yin and yang of T cell responses within the context of radiation exposures, how they might drive or protect against normal tissue side effects and what we may be able do about it.
How is the serial order of a verbal sequence coded? Some comparisons between models

Current models of verbal short‐term memory (STM) propose various mechanisms for serial order. These include a gradient of activation over items, associations between items, and associations between items and their positions relative to the start or end of a sequence. We compared models using a variant of Hebb's procedure in which immediate serial recall of a sequence improves if the sequence is presented more than once. However, instead of repeating a complete sequence, we repeated different aspects of serial order information common to training lists and a subsequent test list. In Experiment 1, training lists repeated all the item–item pairings in the test list, with or without the position–item pairings in the test list. Substantial learning relative to a control condition was observed only when training lists repeated item–item pairs with position–item pairs, and position was defined relative to the start rather than end of a sequence. Experiment 2 attempted to analyse the basis of this learning effect further by repeating fragments of the test list during training, where fragments consisted of either isolated position–item pairings or clusters of both position–item and item–item pairings. Repetition of sequence fragments led to only weak learning effects. However, where learning was observed it was for specific position–item pairings. We conclude that positional cues play an important role in the coding of serial order in memory but that the information required to learn a sequence goes beyond position–item associations. We suggest that whereas STM for a novel sequence is based on positional cues, learning a sequence involves the development of some additional representation of the sequence as a whole.
The distribution of corticotectal projection neurons correlates with the interblob compartment in macaque striate cortex

Abstract While much attention has been given to the correlation between cytochrome-oxidase (CO) compartments and patterns of cortico-cortical projections originating from supragranular layers in the striate cortex, little is known in this regard about patterns of cortico-subcortical projections originating from infragranular cortex. We studied the tangential distribution of the striate cortex neurons projecting to the superior colliculus and used two approaches to analyze the relationship of this distribution to the arrangement of CO “blobs. ” First, chi-square analysis indicated that significantly fewer labeled neurons were found within the CO blob compartment than the number expected for a random distribution. Second, spatial cross-correlation analysis – which circumvents the inherent subjectivity of delineating blob boundaries – revealed an area around blob centers in which there was a decreased probability of encountering labeled cells. The size of this area compared well with that of our outlines of CO blobs. We conclude that corticotectal projection neurons in the striate cortex are distributed preferentially within the interblob compartment of the infragranular striate cortex. These results demonstrate that the spatial distribution of cortico-subcortical projection neurons within infragranular cortex can correlate with the CO architecture of the primary visual cortex.
Exact evaluation of Catmull-Clark subdivision surfaces at arbitrary parameter values

In this paper we disprove the belief widespread within the computer graphics community that Catmull-Clark subdivision surfaces cannot be evaluated directly without explicitly subdividing. We show that the surface and all its derivatives can be evaluated in terms of a set of eigenbasis functions which depend only on the subdivision scheme and we derive analytical expressions for these basis functions. In particular, on the regular part of the control mesh where Catmull-Clark surfaces are bi-cubic B-splines, the eigenbasis is equal to the power basis. Also, our technique is both easy to implement and efficient. We have used our implementation to compute high quality curvature plots of subdivision surfaces. The cost of our evaluation scheme is comparable to that of a bi-cubic spline. Therefore, our method allows many algorithms developed for parametric surfaces to be applied to Catmull-Clark subdivision surfaces. This makes subdivision surfaces an even more attractive tool for free-form surface modeling.
Pulmonary hemorrhage: clinical course and outcomes among very low-birth-weight infants.

OBJECTIVE To describe the clinical course, neonatal morbidity, and neurodevelopmental outcomes of very low-birth-weight (<1500 g) children who develop pulmonary hemorrhage. DESIGN A retrospective case-control study in which 58 very low-birth-weight infants who developed pulmonary hemorrhage during 1990 through 1994, of whom 29 survived, were each matched to the next admitted infant who required mechanical ventilation for respiratory distress syndrome and was of the same sex, race, and birth weight (within 250 g). SETTING A regional tertiary neonatal intensive care unit and follow-up clinic for high-risk infants at University Hospitals of Cleveland, Cleveland, Ohio. MAIN OUTCOME MEASURES Survival, neonatal morbidity, and neurodevelopmental outcome at 20 months' corrected age. RESULTS Pulmonary hemorrhage occurred in 5.7% of the total population of very low-birth-weight infants. Despite similar severity of lung disease, significantly more infants who developed pulmonary hemorrhage received surfactant therapy compared with controls (91% vs 69%, P = .005). Infants with pulmonary hemorrhage who died had a lower birth weight and gestational age compared with those who survived (766 g vs 1023 g; 25 weeks vs 28 weeks, P<.001) and more received surfactant therapy (100% vs 83%, P = .05). Survivors with pulmonary hemorrhage did not differ significantly from controls in rates of oxygen dependence at 36 weeks corrected age (52% vs 38%), grade 3 to 4 periventricular hemorrhage (28% vs 17%), or necrotizing enterocolitis (3% vs 7%), but tended to have more seizures (24% vs 3%, P = .05), periventricular leucomalacia (17% vs 0%, P = .06), and patent ductus arteriosus (79% vs 55%, P =.09). There were no significant differences in neurodevelopmental outcomes at 20 months' corrected age, (cerebral palsy, 16% vs 14%; subnormal [<70] Bayley Mental Developmental Index, 59% vs 43%; and deafness, 13% vs 10%). CONCLUSION Although mortality is high, pulmonary hemorrhage does not significantly increase the risk of later pulmonary or neurodevelopmental disabilities among those who survive.
Intraoperative Tight Glucose Control Using Hyperinsulinemic Normoglycemia Increases Delirium after Cardiac Surgery

Background:Postoperative delirium is common in patients recovering from cardiac surgery. Tight glucose control has been shown to reduce mortality and morbidity. Therefore, the authors sought to determine the effect of tight intraoperative glucose control using a hyperinsulinemic–normoglycemic clamp approach on postoperative delirium in patients undergoing cardiac surgery. Methods:The authors enrolled 198 adult patients having cardiac surgery in this randomized, double-blind, single-center trial. Patients were randomly assigned to either tight intraoperative glucose control with a hyperinsulinemic–normoglycemic clamp (target blood glucose, 80 to 110 mg/dl) or standard therapy (conventional insulin administration with blood glucose target, <150 mg/dl). Delirium was assessed using a comprehensive delirium battery. The authors considered patients to have experienced postoperative delirium when Confusion Assessment Method testing was positive at any assessment. A positive Confusion Assessment Method was defined by the presence of features 1 (acute onset and fluctuating course) and 2 (inattention) and either 3 (disorganized thinking) or 4 (altered consciousness). Results:Patients randomized to tight glucose control were more likely to be diagnosed as being delirious than those assigned to routine glucose control (26 of 93 vs. 15 of 105; relative risk, 1.89; 95% CI, 1.06 to 3.37; P = 0.03), after adjusting for preoperative usage of calcium channel blocker and American Society of Anesthesiologist physical status. Delirium severity, among patients with delirium, was comparable with each glucose management strategy. Conclusion:Intraoperative hyperinsulinemic–normoglycemia augments the risk of delirium after cardiac surgery, but not its severity.
Learning to spell in an alphasyllabary: The case of Kannada

We investigated childrens spelling in the alphasyllabic writing system of Kannada, a South Indian language. Kannada represents language at roughly the level of the syllable, but its symbols or akshara can be segmented visually to reveal the consonant and vowel segments within. Having been taught akshara as whole, fourth- and fifth-grade children were poor at constructing complex akshara from their consonant and vowel segments. Analyses of their errors showed confusions between the symbols for phonologically similar consonants, visually based errors, particularly on small diacritic marks, and influences of dialect. Kannada has been considered a transparent writing system, but the challenges that arise in mastering this visuo-spatially complex and extensive orthography suggest that previous studies have missed certain factors that contribute to the ease or difficulty with which a writing system is learned.
The IL-17A G-197A and IL-17F 7488T/C polymorphisms are associated with increased risk of cancer in Asians: a meta-analysis

Background Interleukin-17 (IL-17) is a family of emerged pro-inflammatory cytokines. The IL-17A and IL-17F are two important members of IL-17 family. Previous studies have shown that the functional IL-17A G-197A and IL-17F 7488T/C polymorphisms may contribute to susceptibility to cancer but the results were inconclusive. This meta-analysis was performed to determine the exact association between IL-17 polymorphisms and cancer risk. Methods Online databases were searched to identify eligible case–control studies. Pooled odds ratios (ORs) and confidence intervals (CIs) were calculated by fixed-effect models or random-effect models. Publication bias was detected by Egger’s test and Begg’s test. Results Nine eligible case–control studies of IL-17A G-197A and seven studies of IL-17F 7488T/C, including 3,181 cases and 4,005 controls, were identified. Pooled analysis suggested the variant IL-17A-197A allele was associated with increased risk cancer (GA/AA vs GG, OR =1.27, 95% CI: 1.15, 1.41, Pheterogeneity =0.374; and A vs G, OR =1.30, 95% CI: 1.17, 1.45, Pheterogeneity =0.021). For IL-17F 7488T/C, the homozygote 7488CC genotype significantly increased risk of cancer (CC vs TC/TT, OR =1.36, 95% CI: 0.97, 1.91, Pheterogeneity =0.875; and CC vs TT, OR =1.39, 95% CI: 1.03, 1.88, Pheterogeneity =0.979), especially for gastric cancer. Conclusion The variant IL-17A-197A allele and IL-17F 7488CC genotype were associated with increased risk of cancer, especially for gastric cancer.