Miracle-dz/UniFAR-FTUs huggingface dataset:
Results of open carpal tunnel release: a comprehensive, retrospective study of 188 hands.

BACKGROUND Many recent reports of the results of decompression of the median nerve in the carpal tunnel have concentrated on only one aspect of recovery (numbness, grip etc.), and there are no reports of a comprehensive study of outcome. The aim of the present study was to review comprehensively the results of the direct visualization method of decompression of the carpal tunnel and to compare them with the published results of endoscopic release. METHODS Patients' perceptions of the severity of pain, numbness and paraesthesiae due to carpal tunnel syndrome (CTS), before and after open carpal tunnel release (CTR) in 188 hands were reviewed retrospectively at a minimum time of follow-up of 18 months. Motor and sensory testing, provocation testing and measurement of scar tenderness in 135 hands were performed at a clinical review. RESULTS Subjective results showed that 70% experienced a reduction in the severity of pain after CTR, 78% of hands experienced a reduction in the severity of paraesthesiae and 77% experienced a reduction in the severity of numbness. A total of 49% had improvements in all three symptoms after CTR. At the clinical review, sensory testing revealed that 59% of hands had normal or slightly diminished light touch, 35% had normal static two-point discrimination and 61% had normal dynamic two-point discrimination. Results for Tinel's test, Phalen's test and pressure provocation testing were positive in 10% of hands. There was no scar tenderness in 38%, no persisting thenar atrophy in 90%. Normal grip strength was found in 93% and 91% had normal pinch strength. CONCLUSIONS It was concluded that open carpal tunnel release remains a safe and reliable treatment for carpal tunnel syndrome. The very low incidence of serious complications from the open technique of CTR, when compared with endoscopic CTR as published by different authors in the literature, and the comparable clinical results, appears to make the open technique a safer and preferable option. However, a properly controlled trial of both techniques is necessary to compare them.
Genetics and Evolution of the Salmonella Galactose-Initiated Set of O Antigens

This paper covers eight Salmonella serogroups, that are defined by O antigens with related structures and gene clusters. They include the serovars that are now most frequently isolated. Serogroups A, B1, B2, C2-C3, D1, D2, D3 and E have O antigens that are distinguished by having galactose as first sugar, and not N-acetyl glucosamine or N-acetyl galactosamine as in the other 38 serogroups, and indeed in most Enterobacteriaceae. The gene clusters for these galactose-initiated appear to have entered S. enterica since its divergence from E. coli, but sequence comparisons show that much of the diversification occurred long before this. We conclude that the gene clusters must have entered S. enterica in a series of parallel events. The individual gene clusters are discussed, followed by analysis of the divergence for those genes shared by two or more gene clusters, and a putative phylogenic tree for the gene clusters is presented. This set of O antigens provides a rare case where it is possible to examine in detail the relationships of a significant number of O antigens. In contrast the more common pattern of O-antigen diversity within a species is for there to be only a few cases of strains having related gene clusters, suggesting that diversity arose through gain of individual O-antigen gene clusters by lateral gene transfer, and under these circumstances the evolution of the diversity is not accessible. This paper on the galactose-initiated set of gene clusters gives new insights into the origins of O-antigen diversity generally.
High-Grade Mixed Adenoneuroendocrine Carcinoma in the Cecum: A Case Report

Gastrointestinal neoplasms with an exocrine and a neuroendocrine component are rare. Such neoplasms are called “mixed adenoneuroendocrine carcinomas” (MANECs) according to the most recent World Health Organization classification of gastrointestinal tract neoplasms. MANECs have no specific findings that distinguish them from pure adenocarcinomas. In addition, the optimal management strategy of MANECs is largely unknown. We describe the case of a 32-year-old man with dizziness and abdominal bloating. A cecal mass was suspected based on an image study done at a local clinic. We evaluated the cecal mass by using colonoscopy, contrast enhanced computed tomography of the abdomen, positron emission tomography-computed tomography, and laboratory studies. The patient underwent a right hemicolectomy and adjuvant chemotherapy. The final histopathological diagnosis was a high-grade MANEC of the ascending colon, tumor stage T3N2M0.
An International Comparison of Technology Adoption and Efficiency: A Dynamic Panel Model

We propose a dynamic model that estends the neoclassical growth model by including technology diffusion and possible inefficiency caused by institutional rigidities. We use alternative panel data methods to estimate the model for three regions: Europe, Latin America and East Asia. Our results strongly indicate that the technology gap to the leader nation is a significant source of growth, but that regions differ in their absorption capability. In addition, countries show large heterogeneity. When combining the country-specific effects with regional absorption capabilities, we obtain robust "efficiency" results for each country. The estimated efficiency levels are consistent with common beliefs and significantly explained by institutional variables such as bureaucratic efficiency and political and civil rights.
Bootstrapping Regression Models

Bootstrapping is a general approach to statistical inference based on building a sampling distribution for a statistic by resampling from the data at hand. The term ‘bootstrapping,’ due to Efron (1979), is an allusion to the expression ‘pulling oneself up by one’s bootstraps’ – in this case, using the sample data as a population from which repeated samples are drawn. At first blush, the approach seems circular, but has been shown to be sound. Two S libraries for bootstrapping are associated with extensive treatments of the subject: Efron and Tibshirani’s (1993) bootstrap library, and Davison and Hinkley’s (1997) boot library. Of the two, boot, programmed by A. J. Canty, is somewhat more capable, and will be used for the examples in this appendix. There are several forms of the bootstrap, and, additionally, several other resampling methods that are related to it, such as jackknifing, cross-validation, randomization tests, and permutation tests. I will stress the nonparametric bootstrap. Suppose that we draw a sample S = {X1,X2, . ,Xn} from a population P = {x1, x2, . , xN}; imagine further, at least for the time being, that N is very much larger than n, and that S is either a simple random sample or an independent random sample from P;1 I will briefly consider other sampling schemes at the end of the appendix. It will also help initially to think of the elements of the population (and, hence, of the sample) as scalar values, but they could just as easily be vectors (i.e., multivariate). Now suppose that we are interested in some statistic T = t(S) as an estimate of the corresponding population parameter θ = t(P). Again, θ could be a vector of parameters and T the corresponding vector of estimates, but for simplicity assume that θ is a scalar. A traditional approach to statistical inference is to make assumptions about the structure of the population (e.g., an assumption of normality), and, along with the stipulation of random sampling, to use these assumptions to derive the sampling distribution of T , on which classical inference is based. In certain instances, the exact distribution of T may be intractable, and so we instead derive its asymptotic distribution. This familiar approach has two potentially important deficiencies:
Epstein-Barr virus-negative lymphoproliferate disorders in long-term survivors after heart, kidney, and liver transplant.

BACKGROUND Solid organ transplant patients undergoing long-term immunosuppression have high risk of developing lymphomas. The pathogenesis of the late-occurring posttransplantation lymphoproliferative disorders (PTLD) have not yet been extensively investigated. METHODS We studied 15 patients who developed PTLD after a median of 79 months (range 22-156 months) after organ transplant. Clonality, presence of Epstein-Barr virus (EBV) genome, and genetic lesions were evaluated by Southern blot analysis or polymerase chain reaction. RESULTS All monomorphic PTLD and two of three polymorphic PTLD showed a monoclonal pattern. Overall, 44% of samples demonstrated the presence of the EBV genome. Within monomorphic PTLD, the EBV-positive lymphomas were even lower (31%). A c-myc gene rearrangement was found in two cases (13%), whereas none of the 15 samples so far investigated showed bcl-1, bcl-2, or bcl-6 rearrangement. The modulation of immunosuppression was ineffective in all patients with monomorphic PTLD independent of the presence of the EBV genome. The clinical outcome after chemotherapy was poor because of infectious complications and resistant disease. With a median follow-up of 4 months, the median survival time of these patients was 7 months. CONCLUSIONS Late occurring lymphomas could be considered an entity distinct from PTLD, occurring within 1 year of transplant, because they show a histological and clinical presentation similar to lymphomas of immunocompetent subjects, are frequently negative for the EBV genome, are invariably clonal, and may rearrange the c-myc oncogene. New therapeutic strategies are required to reduce the mortality rate, and new modalities of long-lasting immunosuppression are called for.
The Dynamics of Naturally Acquired Immune Responses to Plasmodium falciparum Sexual Stage Antigens Pfs230 & Pfs48/45 in a Low Endemic Area in Tanzania

Background Naturally acquired immune responses against sexual stages of P. falciparum can reduce the transmission of malaria from humans to mosquitoes. These antigens are candidate transmission-blocking vaccines but little is known about the acquisition of sexual stage immunity after exposure to gametocytes, or their longevity and functionality. We conducted a longitudinal study on functional sexual stage immune responses. Methodology/Principal Findings Parasitaemic individuals (n = 116) were recruited at a health centre in Lower Moshi, Tanzania. Patients presented with gametocytes (n = 16), developed circulating gametocytes by day 7 (n = 69) or between day 7 and 14 (n = 10) after treatment or did not develop gametocytes (n = 21). Serum samples were collected on the first day of gametocytaemia and 28 and 84 days post-enrolment (or d7, 28, 84 after enrolment from gametocyte-negative individuals). Antibody responses to sexual stage antigens Pfs230 and Pfs48/45 were detected in 20.7% (72/348) and 15.2% (53/348) of the samples, respectively, and were less prevalent than antibodies against asexual stage antigens MSP-119 (48.1%; 137/285) and AMA-1 (52.4%; 129/246)(p<0.001). The prevalence of anti-Pfs230 (p = 0.026) and anti-Pfs48/45 antibodies (p = 0.017) increased with longer duration of gametocyte exposure and had an estimated half-life of approximately 3 months. Membrane feeding experiments demonstrated a strong association between the prevalence and concentration of Pfs230 and Pfs48/45 antibodies and transmission reducing activity (TRA, p<0.01). Conclusions/Significance In a longitudinal study, anti-Pfs230 and Pf48/45 antibodies developed rapidly after exposure to gametocytes and were strongly associated with transmission-reducing activity. Our data indicate that the extent of antigen exposure is important in eliciting functional transmission-reducing immune responses.
Prevalence of ESBL, AmpC β-lactamases and MRSA among uropathogens and its antibiogram

Urinary tract infections (UTIs) are one of the most common bacterial infections in humans. Current knowledge on antimicrobial susceptibility pattern is essential for appropriate therapy. Therefore the aim of the present study was to determine the distribution and antibiotic susceptibility pattern of bacterial strains, with special reference to ESBL, AmpC β-lactamase and MRSA production. A total of 325 clinical isolates were collected from UTI patients from various tertiary care hospitals over a period of 6 months (June 2011 to December 2011). The antimicrobial susceptibility to various drugs was studied by the disc diffusion method as guided by CLSI guidelines. Confirmation of the extended spectrum β-lactamase (ESBL), AmpC β-lactamase and methicillin resistant Staphylococcus aureus (MRSA) production was done by an E-test respectively. Of the 325 isolates, 225 were characterized as gram negative and 77 isolates as S. aureus isolates. The majority (69.3 %) of the isolates were from females compared to males (30.7 %). Prevalence of ESBL and AmpC β-lactamase and the coexistence of the phenotype (ESBL+ AmpC β-lactamase) and MRSA in the urinary isolates were found to be 48.9 %, 20.4 %, 6.2 % and 27.5 % respectively. Ampicillin/sulbactam, norfloxacin should be no longer considered as first line of drugs for UTI, because of high resistance. Parentral drugs such as aminoglycosides, carbapenems and piperacillin/tazobactum can be the alternative choice for complicated UTI. Also, control measures such as judicious use of antibiotics, formulation of infection committee may control the spread of resistance.
mTOR is required for asymmetric division through small GTPases in mouse oocytes

Mammalian target of rapamycin (mTOR) is central to the control of cell proliferation, growth, and survival in mammalian cells. Prolonged treatment with rapamycin inhibits mTOR complex 2 (mTORC2) activity, and both the mTORC1‐mediated S6K1 and 4E‐BP1/eIF4E pathways are essential for TORC2‐mediated RhoA, Cdc42, and Rac1 expression during cell motility and F‐actin reorganization. The functions of mTOR in the mouse oocyte remain unclear, however. The present study shows that rapamycin affects mTOR expression and cytoskeleton reorganization during meiotic maturation of mouse oocytes. mTOR mRNA was expressed in germinal vesicles (GV) until metaphase I (MI), and increased during metaphase II (MII). Immunostaining showed that mTOR localized around the spindle and in the cytoplasm of oocytes. Treatment of oocytes with rapamycin decreased mTOR at the RNA and protein level, and altered asymmetric division. Formation of the actin cap and the cortical granule‐free domain were also disrupted after rapamycin treatment, indicating the failure of spindle migration. Injection of an anti‐mTOR antibody yielded results consistent with those obtained for rapamycin treatment, further confirming the involvement of mTOR in oocyte polarity. Furthermore, rapamycin treatment reduced the mRNA expression of small GTPases (RhoA, Cdc42, and Rac1), which are crucial regulatory factors for cytoskeleton reorganization. Taken together, these results suggest that rapamycin inhibits spindle migration and asymmetric division during mouse oocyte maturation via mTOR‐mediated small GTPase signaling pathways. Mol. Reprod. Dev. 79: 356–366, 2012. © 2012 Wiley Periodicals, Inc.
Convergence Rates of Active Learning for Maximum Likelihood Estimation

An active learner is given a class of models, a large set of unlabeled examples, and the ability to interactively query labels of a subset of these examples; the goal of the learner is to learn a model in the class that fits the data well. Previous theoretical work has rigorously characterized label complexity of active learning, but most of this work has focused on the PAC or the agnostic PAC model. In this paper, we shift our attention to a more general setting - maximum likelihood estimation. Provided certain conditions hold on the model class, we provide a two-stage active learning algorithm for this problem. The conditions we require are fairly general, and cover the widely popular class of Generalized Linear Models, which in turn, include models for binary and multi-class classification, regression, and conditional random fields. We provide an upper bound on the label requirement of our algorithm, and a lower bound that matches it up to lower order terms. Our analysis shows that unlike binary classification in the realizable case, just a single extra round of interaction is sufficient to achieve near-optimal performance in maximum likelihood estimation. On the empirical side, the recent work in [12] and [13] (on active linear and logistic regression) shows the promise of this approach.
Theoretical model of human apolipoprotein B100 tertiary structure

Low density lipoprotein (LDL) particles are the main cholesterol carriers in human plasma. The organization of the particle, composed of apolar lipids and phospholipid monolayer stabilized by apolipoprotein B100 (apoB), is highly complex and still unknown. ApoB is an extremely large protein (4563 amino acids) and very little is known about its structure. A 3D model of the N‐terminal region has been recently proposed and has provided interesting insights about the physico‐chemical properties of the protein and putative interaction zones with lipids. In the present article, we propose the first tentative 3D modelling for most remaining residues. All predicted features emerging from the models are confronted with agreement to experimental data available. Using different up‐to‐date prediction methods, we decomposed the protein into eight domains and predicted 3D structure for each of them. The analysis of hydrophobic patches, polar regions, coupled with functional predictions based on the 3D models, gives new clues to understanding of the functional role of apoB. We suggest precise regions putatively involved in the lipid interactions, and discuss the position of apoB on the LDL particle. Finally, we propose relative organization of the domains, providing a shape quite compatible with the low resolution electron microscopy map. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Perspectives on Hydrate Thermal Conductivity

In this review, the intriguing, anomalous behaviour of hydrate thermal conductivity will be described, and progress in performing experimental measurements will be described briefly. However particular attention shall be devoted to recent advances in the development of detailed theoretical understandings of mechanisms of thermal conduction in clathrate hydrates, and on how information gleaned from molecular simulation has contributed to mechanistic theoretical models.
A generalization of a theorem of Rankin and Swinnerton-Dyer on zeros of modular forms

Rankin and Swinnerton-Dyer (1970) prove that all zeros of the Eisenstein series E k in the standard fundamental domain for Γ lie on A:= {e iθ : π/2 ≤ θ ≤ 2π/3). In this paper we generalize their theorem, providing conditions under which the zeros of other modular forms lie only on the arc A. Using this result we prove a speculation of Ono, namely that the zeros of the unique gap function in M k , the modular form with the maximal number of consecutive zero coefficients in its q-expansion following the constant 1, has zeros only on A. In addition, we show that the j-invariant maps these zeros to totally real algebraic integers of degree bounded by a simple function of weight k.
DNA Methylation of IGF2DMR and H19 Is Associated with Fetal and Infant Growth: The Generation R Study

Changes in epigenetic programming of embryonic growth genes during pregnancy seem to affect fetal growth. Therefore, in a population-based prospective birth cohort in the Netherlands, we examined associations between fetal and infant growth and DNA methylation of IGF2DMR, H19 and MTHFR. For this study, we selected 69 case children born small-for-gestational age (SGA, birth weight <-2SDS) and 471 control children. Fetal growth was assessed with serial ultrasound measurements. Information on birth outcomes was retrieved from medical records. Infant weight was assessed at three and six months. Methylation was assessed in DNA extracted from umbilical cord white blood cells. Analyses were performed using linear mixed models with DNA methylation as dependent variable. The DNA methylation levels of IGF2DMR and H19 in the control group were, median (90% range), 53.6% (44.5–61.6) and 30.0% (25.6–34.2) and in the SGA group 52.0% (43.9–60.9) and 30.5% (23.9–32.9), respectively. The MTHFR region was found to be hypomethylated with limited variability in the control and SGA group, 2.5% (1.4–4.0) and 2.4% (1.5–3.8), respectively. SGA was associated with lower IGF2DMR DNA methylation (β = −1.07, 95% CI −1.93; −0.21, P-value = 0.015), but not with H19 methylation. A weight gain in the first three months after birth was associated with lower IGF2DMR DNA methylation (β = −0.53, 95% CI −0.91; −0.16, P-value = 0.005). Genetic variants in the IGF2/H19 locus were associated with IGF2DMR DNA methylation (P-value<0.05), but not with H19 methylation. Furthermore, our results suggest a possibility of mediation of DNA methylation in the association between the genetic variants and SGA. To conclude, IGF2DMR and H19 DNA methylation is associated with fetal and infant growth.
Cadmium Accumulation in Soil and in Some Vegetable Crops induced by Phosphate Fertilizer

To evaluate the impact of four levels of phosphorus fertilizer on cadmium (Cd) accumulation in soil and in the vegetative parts of tomato (Lycopersicum esculentum L.), lettuce (Lactuca sativa L.) and radish (Raphanus sativus L.), three field experiments using loamy sandy soil, in West Al-Nubaria area, Abu-El-Atta Village, were conducted in 2004 and 2005 winter seasons. The levels of triple superphosphate fertilizer (45-47% P2O5) used were 0, 100, 200, and 300 kg P2O5/fed (fed = fedan =4200 m ). Different rates of triple super-phosphate had significant effects on Cd concentration in the plant tissues of the three studied crops. Phosphate increased Cd accumulation in plant parts, with more evident effect with the highest rate. The range of Cd concentration in tomato fruit juice (0.08-0.12 mg kg) was higher than that in tomato fruit flesh (0.009-0.020 mg kg). Cd concentration in radish ranged between 0.65-0.76 mg kg which was higher than that in lettuce 0.12 0.24 mg kg or in tomato fruits ( 0.100 – 0.176 mg kg) at the applied levels of phosphate fertilizer. In lettuce plants, the Cd concentration in root was higher than that of shoots while the opposite was found in radish plants. Soil available cadmium and phosphorus levels after harvest increased significantly with increasing application rates of phosphorus in the three experiments.
ENC-1: A Novel MammalianKelch-Related Gene Specifically Expressed in the Nervous System Encodes an Actin-Binding Protein

We have identified and characterized a novel murine gene,Ectoderm-Neural Cortex-1 (ENC-1), that is an early and highly specific marker of neural induction in vertebrates.ENC-1, which encodes a kelch family related protein, is expressed during early gastrulation in the prospective neuroectodermal region of the epiblast and later in development throughout the nervous system (NS). ENC-1 expression is highly dynamic and, after neurulation, preferentially defines prospective cortical areas. The only apparent expression of ENC-1 outside the NS is restricted to the rostral-most somitomere of the presomitic mesoderm, at the times corresponding to the epithelialization that precedes somite formation. Cellular expression of epitope-tagged ENC-1 shows extensive co-localization of ENC-1 with the actin cytoskeleton, and immunoprecipitation studies demonstrate a physical association between ENC-1 and actin. ENC-1 functions as an actin-binding protein that may be important in the organization of the actin cytoskeleton during neural fate specification and development of the NS.