Miracle-dz/UniFAR-FTUs huggingface dataset:
Glucose harmonization: the role of accurate calibrators.

To the Editor. —The article by Miller et al in the May issue of the Archives of Pathology & Laboratory Medicine contains critical data pertaining to the trueness of calibrators for glucose assays.1 As shown in their Figure 3, the mean concentration of glucose reported by 23 of 31 peer groups for sample C-02 was less than 1 mg/dL away from the reference target, but 9 of the remaining peer groups reported mean concentrations of glucose that were more than 2 mg/dL greater than target. The deviant results are not surprising. During the past 10 years, my associates and I at Quest Diagnostics Inc (Madison, NJ) have detected 4 glucose calibrator problems upon receipt of new lots of calibrators. In each case, we changed the assigned glucose set point based on a rigorous internal validation protocol that uses NIST SRM (National Institute of Standards and Technology Standard Reference Materials) and the distribution of glucose concentrations of tens of thousands of patient samples. The deviation of vendor-assigned calibrator values from truth was always positive and ranged from 1.8% to 5.2%. Falsely assigned high values for calibrators lead to falsely high results for patient samples. It is clear from the analysis of the survey data for C-02 that variation in glucose results is caused by variation from instrument type to instrument type and not by variation from reagent type to reagent type. The instrument to instrument variation is driven primarily by variation in the accuracy of the set points for the calibrators. The survey data and our experience point to the need for a program to harmonize glucose calibrators and patient results similar to that established for the National Glycohemoglobin Standardization Program.2 Finally, the need for tight control of glucose calibration is supported by the recent discovery that variation in fasting plasma glucose concentrations within the normal range is highly informative.3
Evolution of Enzymes for the Metabolism of New Chemical Inputs into the Environment*

For all of the biological growth in the world, there is a corre- sponding amount of biodegradation. Together, biosynthesis and biodegradation underlie much of the global carbon cycle. The bio- logical cycling of carbon is largely dependent on microbial enzymes because they are the most abundant and functionally divergent of biocatalysts (1). It is well documented that microbial catabolic enzymes biodegrade: ( a ) natural products, ( b ) compounds gener- ated by humans, and ( c ) compounds derived from abiotic reactions. As of the latter, a structurally of aromatic hydrocarbons is generated abiotically in sediments by diagenesis slow burning Aromatic hydrocarbons in and to in top abiotic, more 65,000 of are thought to be biodegradable
Adipocytokines levels at delivery, functional variation of TFAP2β, and maternal and neonatal anthropometric parameters

Adipocytokines participate in the regulation of glucose metabolism and fetal development. The transcription factor activating protein 2B (TFAP2β) has been associated with adipocytokine regulation, and gene variations with type 2 diabetes and obesity. This study investigated associations between maternal TFAP2B variation, adipocytokine levels, and maternal and neonatal anthropometric characteristics.
HIGH-REDSHIFT METALS. II. PROBING REIONIZATION GALAXIES WITH LOW-IONIZATION ABSORPTION LINES AT REDSHIFT SIX

We present a survey for low-ionization metal absorption line systems toward 17 QSOs at redshifts zem = 5.8–6.4. Nine of our objects were observed at high resolution with either Keck/HIRES or Magellan/MIKE, and the remainder at moderate resolution with Keck/ESI. The survey spans 5.3 < zabs < 6.4 and has a path length interval ΔX = 39.5 or Δz = 8.0. In total we detect ten systems, five of which are new discoveries. The line-of-sight number density, ℓ(X) = 0.25+0.21− 0.13 (95% confidence), is consistent with the combined number density at z ∼ 3 of damped Lyα systems (DLAs) and sub-DLAs, which comprise the main population of low-ionization systems at lower redshifts. This apparent lack of evolution may occur because low-ionization systems are hosted by lower-mass halos at higher redshifts, or because the mean cross section of low-ionization gas at a given halo mass increases with redshift due to the higher densities and lower ionizing background. The roughly constant number density notably contrasts with the sharp decline at z > 5.3 in the number density of highly ionized systems traced by C iv. The low-ionization systems at z ∼ 6 span a similar range of velocity widths as lower-redshift sub-DLAs but have significantly weaker lines at a given width. This may imply that the mass–metallicity relation of the host galaxies evolves toward lower metallicities at higher redshifts. These systems lack strong Si iv and C iv, which are common among lower-redshift DLAs and sub-DLAs. This is consistent, however, with a similar decrease in the metallicity of the low- and high-ionization phases, and does not necessarily indicate a lack of nearby, highly ionized gas. The high number density of low-ionization systems at z ∼ 6 suggests that we may be detecting galaxies below the current limits of i-dropout and Lyα emission galaxy surveys. These systems may therefore be the first direct probes of the “typical” galaxies responsible for hydrogen reionization.
Excision of C-4′-oxidized Deoxyribose Lesions from Double-stranded DNA by Human Apurinic/Apyrimidinic Endonuclease (Ape1 Protein) and DNA Polymerase β*

Oxidative damage to DNA deoxyribose generates oxidized abasic sites (OAS) that may constitute one-third of ionizing radiation damage. The antitumor drug bleomycin produces exclusively OAS in the form of C-4-keto-C-1-aldehydes in unbroken DNA strands and 3′-phosphoglycolate esters terminating strand breaks. We investigated whether two human DNA repair enzymes can mediate OAS excision in vitro: Ape1 protein (the main human abasic endonuclease (also called Hap1, Apex, or Ref1)) and DNA polymerase β, which carries out both the abasic excision and the resynthesis steps. We used a duplex oligonucleotide substrate with one main target for bleomycin-induced damage. Ape1 catalyzed effective incision at the C-4-keto-C-1-aldehyde sites at a rate that may be only a few-fold lower than incision of hydrolytic abasic sites at the same location. Consistent with several previous studies, Ape1 hydrolyzed 3′-phosphoglycolates 25-fold more slowly than C-4-keto-C-1-aldehydes. DNA polymerase β excised the 5′-terminal OAS formed by Ape1 incision at a rate similar to its removal of unmodified abasic residues. Polymerase β-mediated excision of 5′-terminal OAS was stimulated by Ape1 as it is for unmodified abasic sites. Escherichia coli Fpg (MutM) protein also excised 5′-terminal OAS, but in our hands, the RecJ protein did not. These observations help define mammalian pathways of OAS repair, point to interactions that might coordinate functional steps, and suggest that still unknown factors may contribute to removal of 3′-phosphoglycolate esters.
Transport Distraction Osteogenesis With Recombinant Human Bone Morphogenic Protein-2 for Large Calvarial Defect Reconstruction

BackgroundTransport distraction osteogenesis (TDO) has been used in attempts to treat large calvarial defects but has, until now, lacked consistency and reliability. To achieve sufficient bone formation, the effect of TDO was compared to the effect of TDO combined with recombinant human bone morphogenic protein-2 (rhBMP-2). MethodsFourteen dogs were divided into 2 groups; 6 animals in the control group received TDO only, and 8 received TDO combined with rhBMP-2. A calvarial defect 33 × 35 mm in size was generated, and the drug-delivering internal distractor was applied. After a 5-day latency period, distraction with rhBMP-2 at 10 &mgr;g/day was initiated at a rate of 2 mm/day. This was followed by a consolidation period of 3 months, after which areas of osteogenesis and strength were measured and histologic examinations were conducted. ResultsThe average area of osteogenesis was higher in the experimental group (P < 0.01). Regenerated bone of the experimental group showed increased strength (P < 0.05). Histological examination showed typical mature bone in the experimental group. Prominent osteoblastic rimming was observed in the bone marrow of the experimental group. ConclusionsTDO with an internal distraction device delivering rhBMP-2 can enhance bone regeneration of large calvarial defects in a dog model. These results suggest the potential for human clinical testing of TDO combined with rhBMP-2.
Cholesterol and neuropathologic markers of AD

Objective: To examine the association of plasma cholesterol (total and high-density [HDL] and low-density lipoprotein) levels with neuritic plaques (NP) and neurofibrillary tangles (NFT) in a population-based autopsy series of 218 Japanese American men followed as a part of the Honolulu–Asia Aging Study. Methods: Cholesterol levels were measured in late life (average age at death 84.6 years) in all subjects (n = 218) and in midlife (20 years before late life) in a subsample (n = 89); for the analyses, levels were categorized into quintiles, with the lowest quintile serving as the reference. Tissue from four areas of neocortex and two areas of hippocampus was prepared with Bielschowsky silver-stained sections and evaluated by one of three neuropathologists who were blinded to clinical information. Diffuse and neuritic plaques and NFT were counted in field areas standardized to 1 mm2. Fields were selected from areas with the highest numbers of lesions, and the field with the highest count was taken to represent the brain area. Results: After adjusting for age at death, education, APOE allele, dementia, neuropathologic infarction, and blood pressure, a strong linear association was found for increasing late-life HDL cholesterol (HDL-C) levels and an increasing number of neocortical NP (5th versus 1st quintile: count ratio [95% CI] 2.30 [1.05 to 5.06]) and hippocampal (2.63 [1.25 to 5.50]) and neocortical (4.20 [1.73 to 10.16]) NFT. Trends were similar for the midlife HDL-C levels. Conclusions: The constituents of HDL-C may play a role in the formation of AD pathology, and these processes are reflected in peripheral measures.
Effect of the acute and chronic administration of the putative atypical antipsychotic drug Y‐931 (8‐fluoro‐12‐ (4‐methylpiperazin‐1‐yl)‐6H‐[1]benzothieno[2,3b][1,5] benzodiazepine maleate) on spontaneously active rat midbrain dopamine neurons: An in vivo electrophysiological study

This study examined the effect of the p.o. administration of the putative atypical antipsychotic drug Y‐931 (8‐fluoro‐12‐(4‐methylpiperazin‐1‐yl)‐6H‐[1]benzothieno[2,3b][1,5] benzodiazepine maleate) on the activity of spontaneously active dopamine (DA) neurons in the ventral tegmental area (VTA) and substantia nigra pars compacta (SNC) in anesthetized male Sprague‐Dawley rats. This was accomplished using in vivo electrophysiology. The acute p.o. administration of Y‐931 did not significantly alter the number of spontaneously active SNC DA neurons compared to vehicle‐treated animals. A single p.o. administration of 3 and 10 mg/kg of Y‐931 significantly increased and decreased, respectively, the number of spontaneously active VTA DA neurons compared to vehicle‐treated animals. The acute administration of 3 mg/kg of Y‐931 significantly altered the firing pattern parameters for all spontaneously active SNC DA. The 3 and 10 mg/kg doses of Y‐931 significantly increased the degree of bursting and irregular activity of spontaneously active VTA and SNC DA neurons firing in a bursting pattern. The repeated p.o. administration (21 days) of 1, 3, or 10 mg/kg of Y‐931 significantly decreased the number of spontaneously active VTA DA neurons but had no significant effect on SNC DA neurons compared to vehicle‐treated animals. The repeated administration of Y‐931 did not significantly alter the firing pattern of all spontaneously active SNC or VTA DA neurons. Our findings indicate that the acute and chronic administration of Y‐931 significantly alters the activity of midbrain DA neurons in rats and the electrophysiological profile of chronic Y‐931 resembles that of atypical antipsychotic agents. Synapse 51:19–26, 2004. © 2003 Wiley‐Liss, Inc.
Modeling X Chromosome Data Using Random Forests: Conquering Sex Bias

Machine learning methods, including Random Forests (RF), are increasingly used for genetic data analysis. However, the standard RF algorithm does not correctly model the effects of X chromosome single nucleotide polymorphisms (SNPs), leading to biased estimates of variable importance. We propose extensions of RF to correctly model X SNPs, including a stratified approach and an approach based on the process of X chromosome inactivation. We applied the new and standard RF approaches to case‐control alcohol dependence data from the Study of Addiction: Genes and Environment (SAGE), and compared the performance of the alternative approaches via a simulation study. Standard RF applied to a case‐control study of alcohol dependence yielded inflated variable importance estimates for X SNPs, even when sex was included as a variable, but the results of the new RF methods were consistent with univariate regression‐based approaches that correctly model X chromosome data. Simulations showed that the new RF methods eliminate the bias in standard RF variable importance for X SNPs when sex is associated with the trait, and are able to detect causal autosomal and X SNPs. Even in the absence of sex effects, the new extensions perform similarly to standard RF. Thus, we provide a powerful multimarker approach for genetic analysis that accommodates X chromosome data in an unbiased way. This method is implemented in the freely available R package “snpRF” (http://www.cran.r‐project.org/web/packages/snpRF/).
Arab Conference on Information Technology ( ACIT ' 2016 ) Improved Hierarchical Classifiers for MultiWay Sentiment Analysis

Sentiment Analysis (SA) is a computational study of the sentiments expressed in text toward entities (such as news, products, services, organizations, events, etc.) using NLP tools. The conveyed sentiments can be quantified using a simple positive/negative model. A more fine-grained approach known as Multi-Way SA (MWSA) uses a ranking system like the 5-star ranking system. Since in such systems, rankings close to each other can be confusing, it has been suggested that Hierarchical Classifiers (HCs) can outperform traditional Flat Classifier (FCs) for MWSA. Unlike FCs which try to address the entire classification problem at once, HCs utilizes tree structures where the nodes are simple classifiers customized to address a subset of the classification problem. This study aims to explore extensively the use of HCs to address MWSA by studying six different hierarchies. We compare these hierarchies with four well-known classifiers (SVM, Decision Tree, Naive Bayes, and KNN) using many measures such as Precision, Recall, F1, Accuracy and Mean Square Error (MSE). The experiments are conducted on the LABR dataset consisting of 63K book reviews in Arabic. The results show that using some of the proposed HCs yield a significant improvement in accuracy. Specifically, while the best Accuracy and MSE for FC are 45.77% and 1.61, respectively, the best accuracy and MSE for an HC are 72.64% and 0.53, respectively. Also, the results show that, in general, KNN benefitted the most from using hierarchical classification.
An Assessment of Social Support in People With Inflammatory Bowel Disease

The purpose of this descriptive study was to assess the perceived level of social support in a sample of people with inflammatory bowel disease. This assessment was to serve as the basis for the development and evaluation of a program of social support. The Personal Resource Questionnaire (PRQ-85), which measures perceived level of social support, was mailed to all members (n = 300) of the Northwestern Society for Intestinal Research. Adults who met the eligibility criteria were invited to participate. Questionnaires and consent forms were completed and returned by 97 subjects. Results indicated that subjects would use a variety of resources if confronted with situations that required social support. The perceived level of social support was high, with mean scores for this inflammatory bowel disease sample reported at 143.86 of a possible 175. A two-tailed t-test suggests there is no significant difference in perceived level of social support between those subjects with Crohn disease and those with ulcerative colitis at the 0.05 level of significance. Because the level of social support was so high in this sample, plans to develop a program of support were abandoned. The meaning of these results including an analysis of the scores and a critique of the questionnaire are discussed.
Studies on variation in Coxsackie A-9 virus.

After 6 to 14 serial passages of Coxsackie A-9 virus in x-irradiated patas cultures, a strain was obtained which a) multiplied in patas cultures, b) was reduced in virulence for new born mice, and c) produced only small plaques (5 mm at 7 days) on both rhesus and patas monolayers. A single passage of the adapted virus either in mice or in rhesus cultures (both in fluid medium and under agar), shifted the virus population toward the original large plaque type and tissue culture host range. Reversion to the large plaque type was observed after 4–8 hr growth (single growth cycle) when the adapted virus at limiting dilutions was transferred to rhesus cultures. However, if harvests were made after 24–48 hr a mixed plaque size population was obtained. This was attributed to a slower growth rate in the adapted virus.
Vitamin D status and its relationship with bone mineral density and parathyroid hormone in Southeast Asian adults with low bone density.

OBJECTIVE To investigate the vitamin D sufficiency status and the relationships among serum 25-hydroxyvitamin D [25(OH)D] levels, intact parathyroid hormone (iPTH) levels, and bone mineral density (BMD) in patients attending an osteoporosis clinic in Singapore. METHODS In total, 193 adults with or without prevalent fragility fractures and with low BMD at the femoral neck, total hip, or lumbar spine underwent assessment. Multivariate regression models were used to investigate the relationships among serum 25(OH)D, iPTH, and BMD. RESULTS The mean values (standard deviation) for age of the patients and serum 25(OH)D level were 61 (14) years and 26.05 (7.97) ng/mL, respectively. In 72% of patients, serum 25(OH)D levels were below 30 ng/mL. There was no association between 25(OH)D levels and BMD at the femoral neck, total hip, or lumbar spine (P = .568, .461, and .312, respectively). Serum iPTH levels were negatively associated with BMD at the total hip (P = .035) and the lumbar spine (P = .019). At levels <30 ng/mL, 25(OH)D was negatively associated with iPTH (P = .036). CONCLUSION Among this Southeast Asian population of patients with low BMD, no direct relationship between serum 25(OH)D levels and BMD was observed. A negative correlation existed, however, between iPTH and 25(OH)D at serum 25(OH)D concentrations <30 ng/mL, and serum iPTH levels showed a significant negative association with BMD at the total hip and lumbar spine. These significant negative associations between iPTH levels and BMD at the total hip and lumbar spine underscore the critical role of this hormone in bone metabolism and health.
The significance of adenosine cyclic 3′,5′‐monophosphate for the contraction of smooth muscle

1. The influence of adenosine cyclic 3′,5′‐monophosphate (3′,5′‐AMP) and of drugs believed to increase or decrease its concentration in the tissues has been determined on the response of vascular and uterine smooth muscles to catecholamines. Generally, drugs believed to increase tissue content of 3′,5′‐AMP potentiated the responses and those believed to decrease it depressed them.
Clinical relevance of HER2 overexpression/amplification in patients with small tumor size and node-negative breast cancer.

PURPOSE To assess the prognostic role of HER2 overexpression/amplification in patients with node-negative, pT1a-b breast cancers. PATIENTS AND METHODS All patients with HER2-positive breast cancer were identified among a population of 2,130 patients whose diseases were staged as pT1a-b, pN0 and who underwent surgery at the European Institute of Oncology from 1999 to 2006. A matched cohort was selected by using variables of hormone receptor status, age, and year of surgery. We estimated rates of local and distant recurrence, disease-free survival (DFS), and overall survival (OS) in the two groups. RESULTS We identified 150 consecutive patients with pT1a-b, pN0, HER2-positive tumors. No patient received adjuvant trastuzumab. The median follow-up was 4.6 years (range, 1.0 to 9.0 years). In the hormone receptor-positive group, 5-year DFS rates were 99% (95% CI, 96% to 100%) for HER2-negative disease and 92% (95% CI, 86% to 99%) for HER2-positive disease. In the hormone receptor-negative group, 5-year DFS rates were 92% (95% CI, 84% to 100%) for HER2-negative disease and 91% (95% CI, 84% to 99%) for HER2-positive disease. Overall, the hazard ratio (HR) associated with HER2 overexpression was 2.4 (95% CI, 0.9 to 6.5; P = .09). After analysis was adjusted for pT1 stage, hormone receptor-positive disease with HER2-positive status was associated with a worse prognosis (HR, 5.1; 95% CI, 1.0 to 25.7). OS in HER2-positive, pT1a-b, pN0 breast cancer was similar irrespective of the hormone receptor status (P = .93). CONCLUSION Patients with node-negative, HER2 positive, pT1a-b breast cancer have a low risk of recurrence at 5 years of follow-up. In patients with hormone receptor-positive disease and pT1a-b, N0 tumors, HER2 overexpression was associated with a worse DFS.
Maturity-related Variability of the Thymus in Cynomolgus Monkeys (Macaca fascicularis)

Terminal body weights (TBWs), thymus weight parameters, and thymus morphology were retrospectively evaluated in 453 cynomolgus monkeys assigned to control groups on nonclinical toxicity studies. Morphology of bone, ovary, and testis/epididymis were used to determine maturity status of individual animals. There was no correlation between TBW and thymus weight (absolute and/or relative to TBW or brain weight). Thymus weight parameters and grades of decreased lymphocytes in the thymus were highly variable in immature animals compared to mature animals. There was also high (up to 11-fold) variability of thymus weight parameters within a given control group on the same study (generally 3 or 4 animals per sex). Several parameters evaluated had more pronounced age-related changes in males when compared to females. Our results demonstrate the inherent variability of thymus weight parameters and morphologic observations for cynomolgus monkeys on toxicology studies. Changes in thymus parameters in cynomolgus monkeys are unreliable indicators of immunomodulation or immunotoxicity in the absence of other relevant findings. Therefore, the thymus parameters commonly evaluated in preclinical safety assessments should not be the primary data set used to determine the presence of a direct test article–related effect on the immune system.
Nutritional and therapeutic importance of Daucus carota- A review

Phytochemical analysis showed that the root of Daucus carota contained alkaloids, carbohydrates, chlorogenic acid, flavonoids, phenols, essential oil, terpenoid and coumarin. The nutritional analysis of carrot juice showed that the juice contained: protein 1.067 ± 0.058%, crude fat 0.367 ± 0.089%, crude fibre 1.167 ± 0.153%, carbohydrates 6.100 ± 0.346%, many vitamins and minerals. The pharmacological studies revealed that the plant possessed cytotoxic, antioxidant, antidiabetic, antimicrobial, smooth muscle relaxant, hypotensive effect and decrease intraocular pressure, gastro-protective, nephro-protective, hepato-protective, cardioprotective antidepressant memory enhancement, anti-inflammatory, reproductive, wound healing and hear induction and many other effects. The current review highlights the chemical constituents, nutritional and pharmacological effects of Daucus carota.