Miracle-dz/UniFAR-FTUs huggingface dataset:
ICT: isotope correction toolbox

SUMMARY Isotope tracer experiments are an invaluable technique to analyze and study the metabolism of biological systems. However, isotope labeling experiments are often affected by naturally abundant isotopes especially in cases where mass spectrometric methods make use of derivatization. The correction of these additive interferences--in particular for complex isotopic systems--is numerically challenging and still an emerging field of research. When positional information is generated via collision-induced dissociation, even more complex calculations for isotopic interference correction are necessary. So far, no freely available tools can handle tandem mass spectrometry data. We present isotope correction toolbox, a program that corrects tandem mass isotopomer data from tandem mass spectrometry experiments. Isotope correction toolbox is written in the multi-platform programming language Perl and, therefore, can be used on all commonly available computer platforms. AVAILABILITY AND IMPLEMENTATION Source code and documentation can be freely obtained under the Artistic License or the GNU General Public License from: https://github.com/jungreuc/isotope_correction_toolbox/ CONTACT {christian.jungreuthmayer@boku.ac. at,juergen.zanghellini@boku.ac. at} SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Serum Osteocalcin Concentration in Treadmill-Trained Adult Male Wistar Rats

Serum Osteocalcin Concentration in Treadmill-Trained Adult Male Wistar Rats Mechanical stress is considered to be essential for the regulation of bone mass. The purpose of this study was to determine whether treadmill exercise at moderate intensity induces alterations in blood osteocalcin concentration in rats. Male Wistar rats, aged 5 months, were divided randomly into two groups: trained animals (n = 6) and controls (n = 7). Trained rats were exercised 5 days/week for 4 weeks on a motor-driven treadmill. Each exercise session lasted 60 minutes and the average locomotion speed was 16.2 m/min. After completion of the training period, a blood sample was taken for osteocalcin measurement and the hindlimbs medial gastrocnemius muscles were excised and weighed. Comparative analysis showed significantly lower circulating osteocalcin levels in the exercised rats in comparison to control animals. It is possible that the observed decreased blood osteocalcin concentration is transient in nature. Factors including stress may also influenced the results. Serum osteocalcin concentration in treadmill-trained rats
Validation of a generic quantitative (1)H NMR method for natural products analysis.

INTRODUCTION Nuclear magnetic resonance (NMR) spectroscopy is increasingly employed in the quantitative analysis and quality control (QC) of natural products (NP) including botanical dietary supplements (BDS). The establishment of QC protocols based on quantitative (1) H NMR (qHNMR) requires method validation. OBJECTIVE Develop and validate a generic qHNMR method. Optimize acquisition and processing parameters, with specific attention to the requirements for the analysis of complex NP samples, including botanicals and purity assessment of NP isolates. METHODS In order to establish the validated qHNMR method, samples containing two highly pure reference materials were used. The influence of acquisition and processing parameters on the method validation was examined, and general aspects of method validation of qHNMR methods discussed. Subsequently, the method established was applied to the analysis of two NP samples: a purified reference compound and a crude mixture. RESULTS The accuracy and precision of qHNMR using internal or external calibration were compared, using a validated method suitable for complex samples. The impact of post-acquisition processing on method validation was examined using three software packages: TopSpin, Mnova and NUTS. The dynamic range of the qHNMR method developed was 5000:1 with a limit of detection (LOD) of better than 10 µm. The limit of quantification (LOQ) depends on the desired level of accuracy and experiment time spent. CONCLUSION This study revealed that acquisition parameters, processing parameters and processing software all contribute to qHNMR method validation. A validated method with a high dynamic range and general workflow for qHNMR analysis of NP is proposed.
Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function[OPEN]

Plants have many, highly variable resistance (R) gene loci, which provide resistance to a variety of pathogens. The first R gene to be cloned, maize (Zea mays) Hm1, was published over 25 years ago, and since then, many different R genes have been identified and isolated. The encoded proteins have provided clues to the diverse molecular mechanisms underlying immunity. Here, we present a meta-analysis of 314 cloned R genes. The majority of R genes encode cell surface or intracellular receptors, and we distinguish nine molecular mechanisms by which R proteins can elevate or trigger disease resistance: direct (1) or indirect (2) perception of pathogen-derived molecules on the cell surface by receptor-like proteins and receptor-like kinases; direct (3) or indirect (4) intracellular detection of pathogen-derived molecules by nucleotide binding, leucine-rich repeat receptors, or detection through integrated domains (5); perception of transcription activator-like effectors through activation of executor genes (6); and active (7), passive (8), or host reprogramming-mediated (9) loss of susceptibility. Although the molecular mechanisms underlying the functions of R genes are only understood for a small proportion of known R genes, a clearer understanding of mechanisms is emerging and will be crucial for rational engineering and deployment of novel R genes.
B-BOX DOMAIN PROTEIN28 Negatively Regulates Photomorphogenesis by Repressing the Activity of Transcription Factor HY5 and Undergoes COP1-Mediated Degradation

The B-box protein BBX28 negatively regulates photomorphogenic development by functioning as a key factor in the CONSTITUTIVELY PHOTOMORPHOGENIC1-HY5 regulatory hub. Plants have evolved a delicate molecular system to fine-tune their growth and development in response to dynamically changing light environments. In this study, we found that BBX28, a B-box domain protein, negatively regulates photomorphogenic development in a dose-dependent manner in Arabidopsis thaliana. BBX28 interferes with the binding of transcription factor HY5 to the promoters of its target genes through physical interactions, thereby repressing its activity and negatively affecting HY5-regulated gene expression. In darkness, BBX28 associates with CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and undergoes COP1-mediated degradation via the 26S proteasome system. Collectively, these results demonstrate that BBX28 acts as a key factor in the COP1-HY5 regulatory hub by maintaining proper HY5 activity to ensure normal photomorphogenic development in plants.
Transplantation of kidneys from hepatitis C‐positive donors into hepatitis C virus‐infected recipients followed by early initiation of direct acting antiviral therapy: a single‐center retrospective study

The availability of direct acting antiviral agents (DAA) has transformed the treatment of hepatitis C virus (HCV) infection. The current study is a case series that reports the outcomes from a cohort of twenty‐five HCV‐infected ESRD patients who received a kidney from an anti‐HCV‐positive deceased organ donor followed by treatment with DAAs in the early post‐transplant period. Time to transplantation and the efficacy of DAA therapy as measured by sustained viral response at 12 weeks were assessed. The median waiting time from original date of activation on the United Network Organ Sharing (UNOS) waiting list until transplantation was 427 days; however, the median time from entering the patient into UNetsm for a HCV‐positive offer until transplantation was only 58 days. The 25 patients were started on antiviral treatment early post‐transplant (median 125 days) and 24 of 25 (96%) achieved a sustained virologic response at 12 weeks. Tacrolimus dose adjustments were required during antiviral treatment in 13 patients to maintain therapeutic levels. Accepting a kidney from an anti‐HCV‐positive deceased donor shortened the waiting time for HCV‐infected kidney transplant candidates. We recommend that kidneys from anti‐HCV‐positive donors should be considered for transplant into HCV‐infected recipients followed by early post‐transplant treatment with DAA agents.
Underlying Host Risk Factors for Nontuberculous Mycobacterial Lung Disease

Abstract Nontuberculous mycobacteria (NTM) are environmental microbes that cause a variety of human diseases, particularly chronic lung infections. Despite the fact that NTM are widespread in the environment, relatively few people develop NTM lung disease, suggesting intrinsic vulnerability in some individuals. This paper reviews the evidence that underlying disorders predispose to NTM lung disease, in particular primary conditions that result in bronchiectasis, chronic obstructive pulmonary disease, α-1-antitrypsin anomalies, pneumoconiosis, pulmonary alveolar proteinosis, and frank immunosuppressive states such as that associated with the use of anti–tumor necrosis factor-α biologics, posttransplantation immunosuppression, and HIV infection. Over the past several decades, NTM lung disease has been increasingly identified in postmenopausal women with slender body habitus. Thus we will also review the clinical and experimental evidence which supports the observation that such individuals are predisposed to NTM lung disease.
Small-angle neutron scattering of aggregated whey protein colloids with an exocellular polysaccharide

We have investigated the scattering properties of mixtures of aggregated-whey-protein colloid (AWC) particles and an exocellular polysaccharide (EPS) from a lactic acid bacterium. Exceeding a certain concentration leads to a phase separation, which can be explained by an effective depletion attraction between the AWCs due to non-adsorbing EPS. The measured scattering intensity of a AWC/EPS mixture shows that the structure factor of the AWC particles increases at low wave vectors with increasing EPS concentration. The measurements can be described qualitatively in terms of the structure factor, calculated using integral theory including an expression for the depletion interaction potential.
Multilevel biological characterization of exomic variants at the protein level significantly improves the identification of their deleterious effects

MOTIVATION There are now many predictors capable of identifying the likely phenotypic effects of single nucleotide variants (SNVs) or short in-frame Insertions or Deletions (INDELs) on the increasing amount of genome sequence data. Most of these predictors focus on SNVs and use a combination of features related to sequence conservation, biophysical, and/or structural properties to link the observed variant to either neutral or disease phenotype. Despite notable successes, the mapping between genetic variants and their phenotypic effects is riddled with levels of complexity that are not yet fully understood and that are often not taken into account in the predictions, despite their promise of significantly improving the prediction of deleterious mutants. RESULTS We present DEOGEN, a novel variant effect predictor that can handle both missense SNVs and in-frame INDELs. By integrating information from different biological scales and mimicking the complex mixture of effects that lead from the variant to the phenotype, we obtain significant improvements in the variant-effect prediction results. Next to the typical variant-oriented features based on the evolutionary conservation of the mutated positions, we added a collection of protein-oriented features that are based on functional aspects of the gene affected. We cross-validated DEOGEN on 36 825 polymorphisms, 20 821 deleterious SNVs, and 1038 INDELs from SwissProt. The multilevel contextualization of each (variant, protein) pair in DEOGEN provides a 10% improvement of MCC with respect to current state-of-the-art tools. AVAILABILITY AND IMPLEMENTATION The software and the data presented here is publicly available at http://ibsquare.be/deogen CONTACT : wvranken@vub.ac. be SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
A Smile Radiates Outwards and Biases the Eye Expression

Abstract This study investigated how extrafoveally seen smiles influence the viewers’ perception of non-happy eyes in a face. A smiling mouth appeared in composite faces with incongruent (angry, fearful, neutral, etc.) eyes, thus producing blended expressions, or they appeared in intact faces with genuine expressions. Overt attention to the eye region was spatially cued, foveal vision of the mouth was blocked by gaze-contingent masking, and the distance between the eyes and the mouth was varied. Participants evaluated whether the eyes were happy or not. Results indicated that the same non-happy eyes were more likely to be judged as happy, and more slowly to be judged as not happy, in presence more than in absence of a smile. As (a) the smiling mouth was highly salient regardless of type of eyes, (b) the influence on the eyes increased gradually as a function of eye-mouth proximity, and (c) the effect occurred in the absence of fixations on the mouth, we conclude that a salient smile radiates outwards to other face regions through a projection mechanism, thus making the eye expression look happy.
Older people in A&E: Literature review and implications for British policy and practice

As the proportion of older people in the population rises, health services must continue to develop to meet their special needs. This includes accident and emergency (A&E) services which work at the interface between primary and secondary health care for individuals of all ages. This literature review aimed to answer the following questions: 1) What are the characteristics and special needs of older people in A&E? 2) Which of the current literature describes, evaluates or advocates service initiatives aimed at meeting the needs of older people in A&E? 3) What are the policy implications of the literature reviewed for British A&E services?
2,4-Bis[1-(4-hydroxyphenyl)-1-methylethyl]phenol: a three-dimensional framework built from O-H...O hydrogen bonds.

In the crystal structure of the title compound, C(24)H(26)O(3), (I), there are three different O-H.O hydrogen bonds, which individually form chains of C(10), C(12) and C(16) types. The combined effect of all these hydrogen bonds is the formation of a three-dimensional network, which is additionally stabilized by a single intermolecular C-H.pi interaction. The significance of this study lies in the comparison drawn between the molecular structure of (I) and those of several of its analogues, which shows a close similarity in the almost perpendicular orientation of the benzene rings.
RANKS: a flexible tool for node label ranking and classification in biological networks

UNLABELLED RANKS is a flexible software package that can be easily applied to any bioinformatics task formalizable as ranking of nodes with respect to a property given as a label, such as automated protein function prediction, gene disease prioritization and drug repositioning. To this end RANKS provides an efficient and easy-to-use implementation of kernelized score functions, a semi-supervised algorithmic scheme embedding both local and global learning strategies for the analysis of biomolecular networks. To facilitate comparative assessment, baseline network-based methods, e.g. label propagation and random walk algorithms, have also been implemented. AVAILABILITY AND IMPLEMENTATION The package is available from CRAN: https://cran.r-project.org/ The package is written in R, except for the most computationally intensive functionalities which are implemented in C. CONTACT valentini@di.unimi. it SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Renal volume assessed by magnetic resonance imaging volumetry correlates with renal function in living kidney donors pre‐ and postdonation: a retrospective cohort study

Renal function of potential living kidney donors is routinely assessed with scintigraphy. Kidney anatomy is evaluated by imaging techniques such as magnetic resonance imaging (MRI). We evaluated if a MRI‐based renal volumetry is a good predictor of kidney function pre‐ and postdonation. We retrospectively analyzed the renal volume (RV) in a MRI of 100 living kidney donors. RV was correlated with the tubular excretion rate (TER) of MAG3‐scintigraphy, a measured creatinine clearance (CrCl), and the estimated glomerular filtration rate (eGFR) by Cockcroft‐Gault (CG), CKD‐EPI, and modification of diet in renal disease (MDRD) formula pre‐ and postdonation during a follow‐up of 3 years. RV correlated significantly with the TER (total: r = 0.6735, P < 0.0001). Correlation between RV and renal function was the highest for eGFR by CG (r = 0.5595, P < 0.0001), in comparison with CrCl, MDRD‐GFR, and CKD‐EPI‐GFR predonation. RV significantly correlated with CG‐GFR postdonation and predicted CG‐GFR until 3 years after donation. MRI renal volumetry might be an alternative technique for the evaluation of split renal function and prediction of renal function postdonation in living kidney donors.
Evaluation of an oscillometric blood pressure monitor for use in anesthetized sheep.

OBJECTIVE To determine the accuracy of an oscillometric blood pressure monitor in anesthetized sheep. STUDY DESIGN Prospective study. ANIMALS Twenty healthy adult sheep, 11 males and nine females, weighing 63.6 ± 8.6 kg. METHODS After premedication with buprenorphine or transdermal fentanyl, anesthesia was induced with ketamine-midazolam and maintained with isoflurane and ketamine, 1.2 mg kg(-1) hour(-1), ± lidocaine, 3 mg kg(-1) hour(-1). Invasive blood pressure measurements were obtained from an auricular arterial catheter and noninvasive measurements were from a cuff on the metatarsus or antebrachium. Simultaneous invasive and noninvasive measurements were recorded over a range (55-111 mmHg) of mean arterial pressures (MAP). Isoflurane concentration was increased to decrease MAP and decreasing the isoflurane concentration and infusing dobutamine achieved higher pressures. Invasive and noninvasive measurements were compared. RESULTS Correlation (R(2)) was good between the two methods of measurement (average of three consecutive readings) for systolic (SAP) (0.87), diastolic (DAP) (0.86), and mean (0.90) arterial pressures (p < 0.001). Bias ± SD between noninvasive and invasive measurements for SAP was 3 ± 8 mmHg, for DAP was -10 ± 7 mmHg, and MAP was -7 ± 6 mmHg. There was no significant difference between the average of three measurements and use of the first measurement. Correlations using the first measurement were SAP (0.82), DAP (0.84), and MAP (0.89). Bias ± SD for SAP was 3 ±10 mmHg, for DAP was -11 ± 7 mmHg, and MAP was -7 ± 6 mmHg. The oscillometric monitor slightly overestimated SAP and underestimated DAP and MAP for both average values and the first reading. CONCLUSIONS AND CLINICAL RELEVANCE This oscillometric model provided MAP measurements that were acceptable by ACVIM standards. MAP measurements with this monitor were lower than those found with the invasive technique so a clinical diagnosis of hypotension may be made in sheep that are not hypotensive.
Perceptions and Practices of Therapeutic Hypothermia in American Neonatal Intensive Care Units

Abstract Objective In 2005, therapeutic hypothermia (TH) was used in few American neonatal intensive care units (NICUs) with great variability in practices. We hypothesized that TH would be used with greater frequency and uniformity today. Study Design We surveyed directors of 797 NICUs queried in our prior study to determine attitudes toward and practices of TH. Results Of the 781 participants with valid addresses, we received completed surveys from 330 (42.3%). There was an increase in the number of respondents who believed that TH is effective (85% versus 31%, p < 0.0001). More NICUs used TH (50% versus 6%, p < 0.0001) and nearly all not offering TH transferred eligible neonates to centers that did (97% versus 29%, p < 0.0001). There has been increased standardization of TH practices with regard to enrollment criteria, duration, and methods of monitoring. Conclusion TH has become standard of care for the treatment of HIE in the United States. Most NICUs that use TH adhere to protocols, but variation still exists in TH practices.
Catecholaminergic Polymorphic Ventricular Tachycardia in Children

Purpose:Catecholaminergic polymorphic ventricular tachycardia (CPVT) is the disease entity of adrenergic dependent, potentially lethal tachyarrhythmia in a child with no structural heart disease, which manifest itself as a syncope or sudden death. The objective of this study is to present our experiences on this important, although rare, disease. Methods:Retrospective analysis of 5 patients with episodes of syncope related to exercise, who were referred to our hospital from January 1985 to December 1998. Results:All patients were male and the mean age at the time of the first syncopal episode was 5.1±3.2 years (range 1.3 to 10 years). There were no structural cardiac abnormalities in clinical and laboratory evaluations. In all, polymorphic ventricular tachycardia showing the characteristic pattern of CPVT in which, as the heart became stimulated adrenergically, isolated ventricular premature beats appeared, increased with rate, became polymorphic, finally formed burst with bidirectional salvoes and disappeared in resting state was induced during exercise test and/or isoproterenol infusion test. During the mean follow up period of 3.75±3.1 years (range 1 month to 7.3 years), one died suddenly. In this case, low dose of β-blocker was administered because of associated sinus bradycardia resulting in incomplete control of the syncopal episodes. The other 4 cases were alive and asymptomatic by means of adequate modification of β-blocker dosage and method of administration. Conclusions:This study emphasizes that CPVT is an important, although rare, cause of exercise related syncope in children and can be diagnosed by means of exercise test and/or isoproterenol infusion. β-blockers were very effective in all cases, even though increasing amount of β-blocker was frequently necessary to control ventricular arrhythmia in some cases. (Korean Circulation J 2000;30(2):191-197)
NET-GE: a web-server for NETwork-based human gene enrichment

MOTIVATION Gene enrichment is a requisite for the interpretation of biological complexity related to specific molecular pathways and biological processes. Furthermore, when interpreting NGS data and human variations, including those related to pathologies, gene enrichment allows the inclusion of other genes that in the human interactome space may also play important key roles in the emergency of the phenotype. Here, we describe NET-GE, a web server for associating biological processes and pathways to sets of human proteins involved in the same phenotype RESULTS: NET-GE is based on protein-protein interaction networks, following the notion that for a set of proteins, the context of their specific interactions can better define their function and the processes they can be related to in the biological complexity of the cell. Our method is suited to extract statistically validated enriched terms from Gene Ontology, KEGG and REACTOME annotation databases. Furthermore, NET-GE is effective even when the number of input proteins is small. AVAILABILITY AND IMPLEMENTATION NET-GE web server is publicly available and accessible at http://net-ge.biocomp.unibo.it/enrich CONTACT: gigi@biocomp.unibo.itSupplementary information: Supplementary data are available at Bioinformatics online.