Miracle-dz/UniFAR-FTUs huggingface dataset:
Feature extraction and quantification for mass spectrometry in biomedical applications using the mean spectrum

MOTIVATION Mass spectrometry yields complex functional data for which the features of scientific interest are peaks. A common two-step approach to analyzing these data involves first extracting and quantifying the peaks, then analyzing the resulting matrix of peak quantifications. Feature extraction and quantification involves a number of interrelated steps. It is important to perform these steps well, since subsequent analyses condition on these determinations. Also, it is difficult to compare the performance of competing methods for analyzing mass spectrometry data since the true expression levels of the proteins in the population are generally not known. RESULTS In this paper, we introduce a new method for feature extraction in mass spectrometry data that uses translation-invariant wavelet transforms and performs peak detection using the mean spectrum. We examine the method's performance through examples and simulation, and demonstrate the advantages of using the mean spectrum to detect peaks. We also describe a new physics-based computer model of mass spectrometry and demonstrate how one may design simulation studies based on this tool to systematically compare competing methods. AVAILABILITY MATLAB scripts to implement the methods described in this paper and R code for the virtual mass spectrometer are available at http://bioinformatics.mdanderson. org/software.html SUPPLEMENTARY INFORMATION http://bioinformatics.mdanderson. org/supplements.html.
Preparation of specific polyclonal antibodies to a C‐C chemokine receptor, CCR1, and determination of CCR1 expression on various types of leukocytes

cDNA cloning has revealed the presence of at least three distinct human receptors for macrophage inflammatory protein‐1α (MIP‐1α) and RANTES: C‐C chemokine receptor (CCR) 1, 4, and 5. To clarify the physiological role of CCR1, we prepared specific antibodies to CCR1 by immunizing rabbits with recombinant glutathione‐S‐transferase (GST) fused with its NH2‐terminal portion. The resultant antibodies stained positively 293 cells transfected with CCR1 cDNA but neither parental cells nor cells transfected with CXCR1 [interleukin‐8 (IL‐8) receptor type A] cDNA, confirming its specificity. Immunofluorescence analysis revealed that peripheral blood lymphocytes and monocytes but not neutrophils express CCR1. Positive staining of transfectants, monocytes, and lymphocytes was inhibited by the GST protein fused with the NH2‐terminal portion of CCR1, further indicating that this antibody recognized the NH2‐terminal portion of CC CKR1. A majority of CD3+, CD4+, CD8+, or CD16+ peripheral blood lymphocytes but not CD19+ lymphocytes expressed CCR1. Among CD4+ peripheral blood lymphocytes, CD45RO+ cells expressed a larger number of CCR1 compared with CD45RO‐. Moreover, CD34+ cells in human bone marrow as well as cord blood were uniformly stained with this antibody. Furthermore, the antibody inhibited calcium mobilization in CCR1 transfectants stimulated with human rMIP‐1α, suggesting that its NH2‐terminal portion is critically involved in ligand binding or signaling. Finally, the antibody partially inhibited monocyte chemotactic activities of human rMIP‐1α, suggesting that CCR1 is a functional receptor for MIP‐1α on human peripheral blood monocytes. J. Leukoc. Biol. 60: 658–666; 1996.
Forensic Issues in Autism Spectrum Disorder: Learning from Court Decisions

Utilising a series of recent Australian decisions, this paper reviews contemporary approaches of the courts in relation to the relevance of Autism Spectrum Disorder (ASD) to criminal responsibility and culpability. It employs the definition of the disorder expected to be em‐ ployed in DSM-V (American Psychiatric Association, 26 January 2011), recognising that the new formulation is broad-brush and does not avail itself of the nomenclature or separate diagnostic criteria for Asperger’s Disorder.
Neural Degeneration in the Retina of the Streptozotocin-Induced Type 1 Diabetes Model

Diabetic retinopathy, a vision-threatening disease, has been regarded as a vascular disorder. However, impaired oscillatory potentials (OPs) in the electroretinogram (ERG) and visual dysfunction are recorded before severe vascular lesions appear. Here, we review the molecular mechanisms underlying the retinal neural degeneration observed in the streptozotocin-(STZ-) induced type 1 diabetes model. The renin-angiotensin system (RAS) and reactive oxygen species (ROS) both cause OP impairment and reduced levels of synaptophysin, a synaptic vesicle protein for neurotransmitter release, most likely through excessive protein degradation by the ubiquitin-proteasome system. ROS also decrease brain-derived neurotrophic factor (BDNF) and inner retinal neuronal cells. The influence of both RAS and ROS on synaptophysin suggests that RAS-ROS crosstalk occurs in the diabetic retina. Therefore, suppressors of RAS or ROS, such as angiotensin II type 1 receptor blockers or the antioxidant lutein, respectively, are potential candidates for neuroprotective and preventive therapies to improve the visual prognosis.
Prognostic factors in renal cell carcinoma: analysis of 227 patients treated at the Brazilian National Cancer Institute.

PURPOSE We evaluated the role of several prognostic factors in predicting death and/or progressive disease in patients with renal cell carcinoma. MATERIALS AND METHODS Between 2004 and 2010, 227 consecutive patients with renal cell carcinoma underwent radical nephrectomy at our Institute. All histological specimens were examined by the same pathologist. We considered certain histological parameters, including histological subtype, conventional Fuhrman grade, presence of sarcomatoid features, adrenal gland infiltration, invasion of the perinephric fat, vascular embolization, collecting system invasion, presence or absence of tumour necrosis (0 %, 1 % to 49 %, or 50 % or greater) and regional lymph node metastasis. RESULTS Variables significantly associated with death and/or progressive disease on univariate analysis were histological subtype (p = 0.006), Fuhrman grade (p < 0.0001), tumor necrosis (p = 0.009), perinephric fat invasion (p = 0.002), vascular embolization (p = 0.0002), presence of lymph node involvement (p < 0.002), tumor size (p = 0.0006), TNM stage (p < 0.00001) and presence of metastasis (p < 0.00001). In the multivariable model histological subtype, tumor necrosis, lymph node involvement and presence of metastasis were independent risk factors for disease-free survival (p = 0.011, 0.042, 0.025 and p < 0.0001, respectively). CONCLUSION Histological subtype, tumor necrosis, lymph node involvement and presence of metastasis proved to be independent prognostic factors for disease-free survival. Therefore, the presence and rate of tumor necrosis should always be informed by the pathologist and lymphadenectomy should be performed in all patients.
An optimization-based approach to estimate the range of consistency in hesitant fuzzy linguistic preference relations

The study of consistency is a very important problem in decision making using preference relations. This paper focuses on measuring the consistency of hesitant fuzzy linguistic preference relations (HFLPRs). In this paper we propose the optimization-based approach to estimate the range of consistency degree in a HFLPR. The underlying idea of the proposed approach consists in measuring the pessimistic consistency index (PCI) of HFLPRs, and also the optimistic consistency index (OCI) of HFLPRs. The PCI of HFLPRs is determined by its linguistic preference relation with the worst consistency degree, and the OCI of HFLPRs is determined by its linguistic preference relation with the best consistency degree. Furthermore, numerical examples are provided to show the use of the proposed consistency measure.
Recombinant human epoetin beta in the treatment of chemotherapy-related anemia

Anemia is a common complication of systemic anti-cancer treatment. In this context epoetin beta, like other erythropoiesis-stimulating agents (ESAs), has demonstrable efficacy in raising Hb concentration and reducing the requirement for red cell transfusion. Consequently ESA therapy has gained increasing prominence in the management of chemotherapy-related anemia. However, recent trial data have suggested a higher rate of thromboembolic events, enhanced tumor progression and reduced survival in some patients with cancer who receive ESA therapy. In response, regulatory authorities have mandated increasingly restrictive label changes. In light of these new developments we consider the current role of epoetin beta in the management of chemotherapy-related anemia.
Optimal Power Control over Fading Cognitive Radio Channel by Exploiting Primary User CSI

This paper is concerned with spectrum sharing for wireless communication, where a secondary or cognitive radio (CR) link communicates over the same bandwidth that has been assigned to an existing primary radio (PR) link. It is assumed that the CR transmitter has perfect channel state information (CSI) on the channels from it to both the PR and CR receivers (as usually assumed in the literature), as well as the channel from the PR transmitter to PR receiver (a new assumption made). With known PR CSI, we study the optimal power control for the CR fading channel to maximize its ergodic capacity subject to the CR's transmit power constraint as well as the constraint on the maximum ergodic capacity loss of the PR link due to the CR transmission. It is shown that the new power-control policy performs better than the conventional one that does not depend on the primary user CSI, but is based on the average interference-power constraint at the PR receiver, in terms of both the PR and CR channel ergodic capacities.
Acute Targeting of General Transcription Factor IIB Restricts Cardiac Hypertrophy via Selective Inhibition of Gene Transcription

Background—We previously reported that specialized and housekeeping genes are differentially regulated via de novo recruitment and pause-release of RNA polymerase II, respectively, during cardiac hypertrophy. However, the significance of this finding remains to be examined. Therefore, the purpose of this study was to determine the mechanisms that differentially regulate these gene groups and exploit them for therapeutic targeting. Methods and Results—Here, we show that general transcription factor IIB (TFIIB) and cyclin-dependent kinase 9 are upregulated during hypertrophy, both targeted by microRNA-1, and play preferential roles in regulating those 2 groups of genes. Chromatin immunoprecipitation-sequencing reveals that TFIIB is constitutively bound to all paused, housekeeping, promoters, whereas de novo recruitment of TFIIB and polymerase II is required for specialized genes that are induced during hypertrophy. We exploited this dichotomy to acutely inhibit induction of the latter set, which encompasses cardiomyopathy, immune reaction, and extracellular matrix genes, using locked nucleic acid–modified antisense TFIIB oligonucleotide treatment. This resulted in suppression of all specialized genes, while sparing the housekeeping ones, and, thus, attenuated pathological hypertrophy. Conclusions—The data for the first time reveal distinct general TFIIB dynamics that regulate specialized versus housekeeping genes during cardiac hypertrophy. Thus, by acutely targeting TFIIB, we were able to inhibit selectively the former set of genes and ameliorate pressure overload hypertrophy. We also demonstrate the feasibility of acutely and reversibly targeting cardiac mRNA for therapeutic purposes using locked nucleic acid–modified antisense oligonucleotides.
Dynamical Principles of Emotion-Cognition Interaction: Mathematical Images of Mental Disorders

The key contribution of this work is to introduce a mathematical framework to understand self-organized dynamics in the brain that can explain certain aspects of itinerant behavior. Specifically, we introduce a model based upon the coupling of generalized Lotka-Volterra systems. This coupling is based upon competition for common resources. The system can be regarded as a normal or canonical form for any distributed system that shows self-organized dynamics that entail winnerless competition. Crucially, we will show that some of the fundamental instabilities that arise in these coupled systems are remarkably similar to endogenous activity seen in the brain (using EEG and fMRI). Furthermore, by changing a small subset of the system's parameters we can produce bifurcations and metastable sequential dynamics changing, which bear a remarkable similarity to pathological brain states seen in psychiatry. In what follows, we will consider the coupling of two macroscopic modes of brain activity, which, in a purely descriptive fashion, we will label as cognitive and emotional modes. Our aim is to examine the dynamical structures that emerge when coupling these two modes and relate them tentatively to brain activity in normal and non-normal states.
Is Intravenous Administration of Branched Chain Amino Acids Effective in the Treatment of Hepatic Encephalopathy? A Multicenter Study

The influence of intravenous infusion of branched‐chain amino acids (BCAAs) on brain function in patients with liver cirrhosis and acute hepatic encephalopathy was examined using a double‐blind, randomized study design. Five medical centers in France and Sweden participated, and 50 patients were studied. The patients received either BCAAs (40 gm per day) in 5% glucose or 5% glucose alone (placebo) for 5 days or until “wake up”. Nutritional support was provided with equal proportions of carbohydrate and fat. During BCAA adminstration, plasma concentrations of aromatic amino acids and methionine fell (20 to 40%, p < 0.05 to 0.01), and the ratio of BCAAs to aromatic amino acid concentrations increased significantly. Clinical improvement was seen in 14 of 25 BCAA‐treated patients and in 12 of 25 patients receiving placebo (N.S.). EEG responses were similar in the two groups during treatment. In the BCAA group, 10 of 25 patients died in the course of the study, compared to 5 of 25 in the placebo group (N.S.); six patients died from encephalopathy in the BCAA group as compared to three among placebo‐treated patients. It is concluded that BCAA adminstration, in the dose and composition employed in the present study, reduces the concentrations of aromatic amino acids but neither improves cerebral function nor decreases mortality in patients with hepatic encephalopathy.
Sexual Coercion, Drinking to Cope Motives, and Alcohol-Related Consequences among Self-Identified Bisexual Women

ABSTRACT Background: Given higher sexual victimization and greater alcohol use among bisexual women, a critical public health challenge is to understand within-group variation that may heighten or explain these associations in bisexual women. Objectives: The present study tested a moderated-mediation model in which sexual coercion was hypothesized to be associated with alcohol-related consequences via drinking to cope motives in self-identified bisexual women who reported at least occasional binge drinking. Negative affect was hypothesized to moderate the sexual coercion-drinking to cope motives association. Methods: Participants were a community sample of 107 self-identified bisexual women (age M = 20.97, SD = 2.11) who completed an online survey and reported at least one binge drinking episode as well as engaging in sexual activity in the past 30 days. Results: Of these participants, 57 (53.3%) reported one or more experiences of sexual coercion in the past 30 days. Sexual coercion was associated with negative alcohol-related consequences via drinking to cope motives. Negative affect moderated the association between sexual coercion and drinking to cope motives such that the association was stronger among women with greater negative affect. Conclusions/Importance: Methods of addressing vulnerability to sexual coercion and educating young bisexual women about the association between sexual coercion and potentially problematic affective coping through alcohol use are needed.
An improved single-disk method for testing the antibiotic susceptibility of rapidly-growing pathogens.

The Kirby-Bauer method of disk antibiotic-susceptibility tests is well standardized and accurate, but the method for standardizing the inoculum is rather time-consuming and is often impractical for routine use. This report describes a somewhat more practical, efficient method for inoculating the test plates. A calibrated inoculum obtained from a small volume of broth culture is spread over the agar surface with a seeded agar overlay. Comparison of this new method with the standardized Kirby-Bauer method shows that the zones of inhibition are nearly identical in size, and thus the same zone standards for interpretation can be applied to both methods. Because the inhibitory zone edges were better defined on plates inoculated with the agar-overlay method, there was a slightly better correlation between zone diameters and minimal inhibitory concentrations, especially with bacteriostatic drugs. Tests with swarming Proteus mirabilis were much more satisfactory with the agar-overlay method. The new technic is recommended as a routine method for testing the common Enterobacteriaceae, P. aeruginosa and S. aureus .
Adequacy of Lymph Node Examination in Colorectal Surgery: Contribution of the Hospital Versus the Surgeon

Background:Examination of at least 12 lymph nodes (LNs) in the staging of colon cancer (CC) was recommended by the National Comprehensive Cancer Network in 2000; however, rates of an adequate examination remain low. This study compares the impact of the hospital contextual variance against that of the operating surgeon on delivery of an adequate LN examination. Study Design:Retrospective analysis of California Cancer Registry data for all CC operations (2001–2006). Hierarchical models predicted the adequacy of LN examination as a function of patient, surgeon, and hospital characteristics. Models were created using penalized quasi-likelihood approximation with second order Taylor linearization as implemented in MLwiN 2.15. Results:A total of 25,606 resections involving 3376 surgeons operating in 346 hospitals were analyzed. Half of cases had an adequate examination. Hierarchical models showed the median odds of an adequate examination associated with the hospital context [(MORhosp 2.05; 95% confidence interval, 1.9–2.2) was much higher than that associated with the surgeon (MORsurg 1.34; 95% confidence interval, 1.2–1.4)]. Hospital characteristics teaching and high volume predicted higher odds of an adequate examination. There was no association with hospital revenue. Conclusions:Approximately half of patients undergoing surgery for CC received an adequate LN examination. Hospital contextual factors had a stronger association with receipt of an adequate examination than surgeon factors. Our results suggest that quality improvement initiatives and incentives should be targeted at the hospital level to achieve the highest impact. Furthermore, we have identified nonteaching and low volume settings as rational targets for these efforts.
Platelet-derived growth factor expression and function in idiopathic pulmonary arterial hypertension.

RATIONALE Platelet-derived growth factor (PDGF) promotes the proliferation and migration of pulmonary artery smooth muscle cells (PASMCs), and may play a role in the progression of pulmonary arterial hypertension (PAH), a condition characterized by proliferation of PASMCs resulting in the obstruction of small pulmonary arteries. OBJECTIVES To analyze the expression and pathogenic role of PDGF in idiopathic PAH. METHODS PDGF and PDGF receptor mRNA expression was studied by real-time reverse transcription-polymerase chain reaction performed on laser capture microdissected pulmonary arteries from patients undergoing lung transplantation for idiopathic PAH. Immunohistochemistry was used to localize PDGF, PDGF receptors, and phosphorylated PDGFR-beta. The effects of imatinib on PDGF-B-induced proliferation and chemotaxis were tested on human PASMCs. MEASUREMENTS AND MAIN RESULTS PDGF-A, PDGF-B, PDGFR-alpha, and PDGFR-beta mRNA expression was increased in small pulmonary arteries from patients displaying idiopathic PAH, as compared with control subjects. Western blot analysis revealed a significant increase in protein expression of PDGFR-beta in PAH lungs, as compared with control lungs. In small remodeled pulmonary arteries, PDGF-A and PDGF-B mainly localized to PASMCs and endothelial cells (perivascular inflammatory infiltrates, when present, showed intensive staining), PDGFR-alpha and PDGFR-beta mainly stained PASMCs and to a lesser extent endothelial cells. Proliferating pulmonary vascular lesions stained phosphorylated PDGFR-beta. PDGF-BB-induced proliferation and migration of PASMCs were inhibited by imatinib. This effect was not due to PASMC apoptosis. CONCLUSIONS PDGF may play an important role in human PAH. Novel therapeutic strategies targeting the PDGF pathway should be tested in clinical trials.
Reproductive risk factors for cardiovascular disease mortality among postmenopausal women in Korea: the Kangwha Cohort Study, 1985-2005

Objective:The relationship between reproductive factors and the risk of mortality from cardiovascular disease in postmenopausal women is unclear. In this study, we aimed to investigate this relationship in Korean postmenopausal women. Methods:Subcohort analysis was carried out using the data of 3,257 postmenopausal women (age, ≥55 y at study entry) from the Kangwha Cohort Study who were followed up from 1985 until 2005. Cox proportional hazards models were used to evaluate the associations between reproductive factors and cardiovascular disease mortality. Results:The risk of cardiovascular mortality in women who were 20 to 22 years old at first childbirth was 26% lower (95% CI, 0.60-0.92) than that in women younger than 20 years at first childbirth, after adjustment for age at entry, body mass index, hypertension, drinking, smoking, education, and occupation. Early first childbirth was associated with increased cardiovascular disease mortality (P trend = 0.036). The risk of coronary heart disease mortality was 51% lower in women who were 17 to 18 years old at menarche (95% CI, 0.25-0.95) than that in women who were younger than 17 years at menarche. Conclusions:An inverse relationship between age at first childbirth and the risk of cardiovascular disease mortality exists. In addition, early menarche may be a reproductive risk factor for coronary heart disease mortality.