Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic Laboratory Notebooks Progress and Challenges in Implementation

Electronic laboratory notebooks (ELNs) are increasingly replacing paper notebooks in life science laboratories, including those in industry, academic settings, and hospitals. ELNs offer significant advantages over paper notebooks, but adopting them in a predominantly paper-based environment is usually disruptive. The benefits of ELN increase when they are integrated with other laboratory informatics tools such as laboratory information management systems, chromatography data systems, analytical instrumentation, and scientific data management systems, but there is no well-established path for effective integration of these tools. In this article, we review and evaluate some of the approaches that have been taken thus far and also some radical new methods of integration that are emerging.
Impairment in Pain Perception in Adult Rats Lesioned as Neonates with 5.7-Dihydroxytryptamine.

BACKGROUND Whereas some studies have demonstrated the essential role of 5-hydroxytryptamine (5-HT) in tramadol and acetaminophen analgesia, other research has presented conflicting results. To dispel doubts, some aspects of the involvement of 5-HT in the antinociceptive properties of these drugs remain to be clarified. OBJECTIVES The aim of this study was to determine whether the serotoninergic system dysfunction produced by neonatal 5-HT lesion in rats may affect the antinociceptive effects of tramadol and acetaminophen administered in adulthood. MATERIAL AND METHODS Three days after birth, the control rats were pretreated with desipramine HCl (20 mg/kg i.p.) 30 min before intraventricular saline--vehicle injection. A separate group received 5.7-DHT; 2×35 µg in each lateral ventricle. At the age of 8 weeks, 5-HT and 5-hydroxyidoleaceticacid (5-HIAA) concentrations were determined in the thalamus and spinal cord by an HPLC/ED method. The antinociceptive effects of tramadol (20 mg/kg i.p.) or acetaminophen (100 mg/kg i.p.) were evaluated by a battery of tests. RESULTS 5.7-DHT lesioning was associated with a reduction in 5-HT and 5-HIAA content of the thalamus (>85% and >90%) and spinal cord (>58% and 70%). Neonatal 5.7-DHT treatment produced a significant reduction in the antinociceptive effect of tramadol in the hot plate, tail-immersion, paw withdrawal and writhing tests. In the formalin hind paw test, the results were ambiguous. 5-HT lesion was also associated with a decrease in the analgesic effect of acetaminophen in the hot plate and writhing tests. A similar relationship wasn't found in the other assessments conducted with the use of acetaminophen. CONCLUSIONS The present study provides evidence that (1) an intact serotoninergic system is required for the adequate antinociceptive action of tramadol, and (2) the serotoninergic system exerts a negligible influence on acetaminophen-induced analgesia in rats. We hypothesize that similar abnormalities in nociception may occur in patients with 5-HT dysfunction (e.g. depression), so these results should be complied in analgesic dosage adjustment.
A reduction in Ptprq associated with specific features of the deafness phenotype of the miR-96 mutant mouse diminuendo

miR‐96 is a microRNA, a non‐coding RNA gene which regulates a wide array of downstream genes. The miR‐96 mouse mutant diminuendo exhibits deafness and arrested hair cell functional and morphological differentiation. We have previously shown that several genes are markedly downregulated in the diminuendo organ of Corti; one of these is Ptprq, a gene known to be important for maturation and maintenance of hair cells. In order to study the contribution that downregulation of Ptprq makes to the diminuendo phenotype, we carried out microarrays, scanning electron microscopy and single hair cell electrophysiology to compare diminuendo mutants (heterozygous and homozygous) with mice homozygous for a functional null allele of Ptprq. In terms of both morphology and electrophysiology, the auditory phenotype of mice lacking Ptprq resembles that of diminuendo heterozygotes, while diminuendo homozygotes are more severely affected. A comparison of transcriptomes indicates there is a broad similarity between diminuendo homozygotes and Ptprq‐null mice. The reduction in Ptprq observed in diminuendo mice appears to be a major contributor to the morphological, transcriptional and electrophysiological phenotype, but does not account for the complete diminuendo phenotype.
Identification of differentially expressed microRNAs in metastatic melanoma using next-generation sequencing technology

In this study, we investigated differentially expressed microRNAs (miRNAs or miRs) and their functions in metastatic melanoma using next-generation sequencing technology. The GSE36236 data set was downloaded from the Gene Expression Omnibus (GEO) database and 4 primary cutaneous melanoma samples (used as controls) and 3 metastatic melanoma samples were selected from 31 samples for further analysis. Firstly, the differentially expressed miRNAs were screened by limma package in R language. Secondly, the target genes of the miRNAs were retrieved with TargetScanHuman 6.2, and the interactions among these genes were identified by String and an interaction network was established. Finally, functional and pathway analyses were performed for the genes in the network using Expression Analysis Systematic Explorer (EASE). A total of 4 differentially expressed miRNAs (hsa-miR-146, hsa-miR-27, hsa-miR-877 and hsa-miR-186) were obtained between the metastatic melanoma and primary cutaneous melanoma samples. We predicted 101 high-confidence target genes of hsa-miR-27 and obtained a network with 41 interactions. Finally, functional and pathway analyses revealed that the genes in the network were significantly enriched at the transcriptional level. Differentially expressed miRNAs were identified in the metastatic melanoma compared with the primary cutaneous melanoma samples and the target genes of hsa-miR-27 were found to be significantly enriched at the transcriptional level. The results presented in our study may prove helpful in the diagnosis and treatment of metastatic melanoma.
A committee of neural networks for traffic sign classification

We describe the approach that won the preliminary phase of the German traffic sign recognition benchmark with a better-than-human recognition rate of 98.98%. We obtain an even better recognition rate of 99.15% by further training the nets. Our fast, fully parameterizable GPU implementation of a Convolutional Neural Network does not require careful design of pre-wired feature extractors, which are rather learned in a supervised way. A CNN/MLP committee further boosts recognition performance.
OriginalClinicalScience Performance Characteristics of Galactomannan and bd-Glucan in High-Risk Liver Transplant Recipients

Background.The utility ofAspergillus galactomannan (GM) and β-D-glucan (BG) in liver transplant recipients remains uncertain. Methods.As part of a randomized, double-blind trial of antifungal prophylaxis in liver transplant recipients at risk for invasive fungal infections (IFIs), GM and BG were assessed in 199 patients at baseline (enrollment) and weekly thereafter for the duration of study drug. Receiver operating characteristic (ROC) analysis was used to evaluate the accuracy of these for the diagnosis of IFIs. Results.Overall, 46.4% of the patients at baseline had positive GM (index ≥ 0.5) and 89.6% had BG of 80 pg/mL or greater with BG level of 500 pg/mL or greater in 31.8%. Patients with invasive aspergillosis (IA) (3/3) had positive GM at baseline as did 45.5% of those without IA (P = 0.098); the area under the ROC curve for the diagnosis of IA was 0.77 (fair test, i.e., good sensitivity but poor specificity). Using BG cutoff of 80 pg/mL or higher, 100% (12/12) of the patients with IFI had positive baseline BG and as did 88.9% (160/180) of those without IFI (P = 0.618); the area under the ROC curve for predicting IFIs was 0.56 (poor test). In multivariate analyses, GM positivity was associated with study site (P = 0.041), and BG positivity with renal replacement therapy (P = 0.05) and study site (P = 0.01). The GM and BG levels declined over time; positivity at subsequent time points was lower in comparison with baseline (P < 0.001). Conclusions. The GM and BG tests had significant center variability and limited accuracy for the diagnosis of IFIs in high-risk liver transplant recipients.
Antibody response to Engerix‐B® and Recombivax‐HB® hepatitis B vaccination in end‐stage renal disease

Recombivax‐HB® (REC) and Engerix‐B® (ENG) are FDA‐approved vaccines for hepatitis B virus (HBV) in end‐stage renal disease (ESRD). This study compares antibody response rates between them in routine clinical practice. Patients completing the recommended 40 μg dose of REC (3 doses) or ENG (4 doses) between January 1, 2000 to April 30, 2003 were eligible. Patients with prior positive HBV surface antigen (HBsAg) or antibody (HBsAb) test results were excluded. The conversion rate and persistence of protective titer (HBsAb titer≥10 IU/mL) were tracked for 1 year. A supplemental analysis of a one‐to‐one matched patient sample was also performed. REC patients (N=885) were older, had longer dialysis vintage, and had a larger proportion of whites than ENG patients (N=13,661). Cumulative conversion response was greater in ENG (58%) than REC (40%) at 1 year (p<0.0001). The odds ratio for response to ENG compared with REC was 1.96 (95% limits: 1.56, 2.45; p<0.0001) adjusted for age, gender, race, diabetes, vintage, BSA, hemoglobin, and eKt/V. Persistent protective HBsAb after 1 year was 77% (ENG) vs. 53% (REC). HBsAg was positive in 208 ENG patients (1.5%) with all but 1 because of transient, vaccine‐related antigenemia. The difference in conversion response favoring ENG persisted in a one‐to‐one sample matched for age, gender, race, modality, and dialysis vintage. The study found higher seroconversion response to ENG compared with REC at several time points up to 1 year. Protective HBsAb disappeared in 23–47% of patients 1 year later, validating CDC recommendations to re‐test HBsAb yearly. The observed difference in response rates may be related to the extra ENG dose given at the second month (0, 1, 2, 6 regimen). The study raises a hypothesis that requires confirmation in a prospective clinical trial.
Sex Drugs, Peer Connections, and HIV: Use and Risk Among African-American, Latino, and Multiracial Young Men Who Have Sex with Men in Los Angeles and New York

African-American and Latino young men who have sex with men (YMSM) are at high risk for HIV infection. We administered brief intercept surveys (N = 416) at 18 black and Latino gay pride events in Los Angeles and New York in 2006 and 2007. Ordinal logistic regressions were used to model the effects of substance use during sex, peer connectedness, relationship status, and homelessness on condom use. Alcohol use, crystal use, homelessness, and having a primary relationship partner were negatively associated with condom use, while peer connectedness and marijuana use during sex were positively associated with condom use. Implications for service providers and future research are discussed.
Swelling Properties and Environmental Responsiveness of a Superabsorbent Composite Microsphere Based on Starch-g-Poly(acrylic acid)/Organo-Mordenite

Abstract Starch-g-poly(acrylic acid)/organo-mordenite superabsorbent composite microsphere, was prepared by grafting partially neutralized acrylic acid onto starch in the presence of organo-mordenite as an inorganic component. The morphology was characterized with scanning electron microscope (SEM). The swelling properties of the superabsorbent composite microsphere were evaluated in distilled water, various NaCl solutions, solutions with different pH values, and urea solutions. Swelling kinetics of the superabsorbent composite microsphere in above environments were discussed by means of a Schott's second-order model. The results showed that the incorporation of 10 wt% organo-mordenite enhanced the water absorbency by 144% (from 268 to 655 g · g−1) and possessed the maximum swelling absorbency (75 g · g−1) in the 0.9% NaCl solution and (667 g · g−1) in 0.04 mol · l−1 urea solution. Moreover, swelling of starch-g-poly(acrylic acid)/organo-mordenite (with 10 wt% organo-mordenite) in distilled water and in all other environments followed Schott's second order kinetics. Swelling was extremely environmental-responsive to the concentration of the NaCl solution, the pH values, and urea solutions, respectively. The overall results inferred that the novel superabsorbent composite can be exploited for many potential applications.
Can nature promote development? The role of sustainable tourism for economic growth

In this paper, we analyse whether biodiversity can enhance the developmental process in developing countries (DCs) by increasing tourism receipts in a trade-based endogenous growth framework. The model is based on the underlying assumption that a rich biodiversity provides a comparative advantage in sustainable tourism services. The empirical evidence shows that biodiversity while being significantly and positively correlated with inbound tourism receipts has no significant effect on tourist arrivals (mass tourism). This suggests that the biodiversity endowment of a very country is an important precondition for sustainable tourism. Moreover, we empirically show that specialising in sustainable tourism promotes economic growth. Therefore, a promising development strategy can rests on the investment into biodiversity which attracts high-budget tourists.
An assessment of long-term reaction to rape.

To examine long-term reactions to rape, 27 adult women who had been rape victims were interviewed and their current functioning assessed through a variety of written measures. Victims were significantly more depressed and reported less pleasure in daily activities than matched nonvictim controls. Women who had been victims of sudden violent attacks by complete strangers showed the most severe reactions, being even more depressed, fatigued, and fearful, and getting less satisfaction from activities than victims of other types of assaults.
The Effects of Institutional Investment on CEO Compensation

Institutional investors claim to monitor and influence executive compensation practices in their portfolio companies. Thus, compensation practices are a reasonable place to look to assess the institutions’ effectiveness in achieving their governance objectives. I explore the relationship between institutional ownership and CEO compensation levels and equity performance sensitivity. I address ownership structure endogeneity by using instrumental variables and fixed-effects regression models with S&P 500 index inclusion as an instrument for institutional ownership. Results indicate that institutions fail to decrease compensation levels, but do increase equity performance sensitivities. The results are robust to various model specifications. CRRA simulations suggest that the level premium paid to CEOs is consistent with a utility-neutral shift in compensation structure. At first glance, this seems to support the hypothesis that CEO labor markets are efficient. However, results using an additional measure of the CEO’s ability to extract rents are inconsistent with this conclusion. The level premium is negatively related to institutional ownership concentration. This suggests that the IR constraint is slack, but less so the more powerful the institutional owners. * The author thanks James Claus, Bob Kimmel, Abbie Smith, Steven Kaplan, Gilbert Fellingham, Per Strömberg, Mark Garmaise, Rob Vishny, Randy Cohen, Brian Hall, Alon Brav, Eugene Fama, Craig Clawson, Karl Deither, and Lars Lefgren and seminar participants at Chicago for helpful discussions. Special thanks are due to Luigi Zingales. I am, of course, responsible for any errors.
Fast demand forecast of Electric Vehicle Charging Stations for cell phone application

This paper describes the core cellphone application algorithm which has been implemented for the prediction of energy consumption at Electric Vehicle (EV) Charging Stations at UCLA. For this interactive user application, the total time of accessing database, processing the data and making the prediction, needs to be within a few seconds. We analyze four relatively fast Machine Learning based time series prediction algorithms for our prediction engine: Historical Average, k-Nearest Neighbor, Weighted k-Nearest Neighbor, and Lazy Learning. The Nearest Neighbor algorithm (k Nearest Neighbor with k=1) shows better performance and is selected to be the prediction algorithm implemented for the cellphone application. Two applications have been designed on top of the prediction algorithm: one predicts the expected available energy at the station and the other one predicts the expected charging finishing time. The total time, including accessing the database, data processing, and prediction is about one second for both applications.
Central Pressure: Variability and Impact of Cardiovascular Risk Factors: The Anglo-Cardiff Collaborative Trial II

Pulse pressure varies throughout the arterial tree, resulting in a gradient between central and peripheral pressure. Factors such as age, heart rate, and height influence this gradient. However, the relative impact of cardiovascular risk factors and atheromatous disease on central pressure and the normal variation in central pressure in healthy individuals are unclear. Seated peripheral (brachial) and central (aortic) blood pressures were assessed, and the ratio between aortic and brachial pulse pressure (pulse pressure ratio, ie, 1/amplification) was calculated in healthy individuals, diabetic subjects, patients with cardiovascular disease, and in individuals with only 1 of the following: hypertension, hypercholesterolemia, or smoking. The age range was 18 to 101 years, and data from 10 613 individuals were analyzed. Compared with healthy individuals, pulse pressure ratio was significantly increased (ie, central systolic pressure was relatively higher) in individuals with risk factors or disease (P<0.01 for all of the comparisons). Although aging was associated with an increased pulse pressure ratio, there was still an average±SD difference between brachial and aortic systolic pressure of 11±4 and 8±3 mm Hg for men and women aged >80 years, respectively. Finally, stratifying individuals by brachial pressure revealed considerable overlap in aortic pressure, such that >70% of individuals with high-normal brachial pressure had similar aortic pressures as those with stage 1 hypertension. These data demonstrate that cardiovascular risk factors affect the pulse pressure ratio, and that central pressure cannot be reliably inferred from peripheral pressure. However, assessment of central pressure may improve the identification and management of patients with elevated cardiovascular risk.
Inferring phylogenetic relationships avoiding forbidden rooted triplets

To construct a phylogenetic tree or phylogenetic network for describing the evolutionary history of a set of species is a well-studied problem in computational biology. One previously proposed method to infer a phylogenetic tree/network for a large set of species is by merging a collection of known smaller phylogenetic trees on overlapping sets of species so that no (or as little as possible) branching information is lost. However, little work has been done so far on inferring a phylogenetic tree/network from a specified set of trees when in addition, certain evolutionary relationships among the species are known to be highly unlikely. In this paper, we consider the problem of constructing a phylogenetic tree/network which is consistent with all of the rooted triplets in a given set C and none of the rooted triplets in another given set F. Although NP-hard in the general case, we provide some efficient exact and approximation algorithms for a number of biologically meaningful variants of the problem.
Gambierol Acts as a Functional Antagonist of Neurotoxin Site 5 on Voltage-Gated Sodium Channels in Cerebellar Granule Neurons

The marine toxin gambierol, a polyether ladder toxin derived from the marine dinoflagellate Gambierdiscus toxicus, was evaluated for interaction with voltage-gated sodium channels (VGSCs) in cerebellar granule neuron (CGN) cultures. At concentrations ranging from 10 nM to 10 μM, gambierol alone had no effect on the intracellular Ca2+ concentration [Ca2+]i of exposed CGN cultures. Furthermore, there was no evidence of neurotoxicity in CGN cultures exposed for 2 h to gambierol (1 nM–10 μM). However, gambierol was a potent inhibitor (IC50 = 189 nM) of the elevation of [Ca2+]i that accompanies exposure of CGN cultures to the VGSC activator brevetoxin-2 (PbTx-2). To further explore the potential interaction of gambierol with VGSCs, the influence of gambierol on PbTx-2-induced neurotoxicity was assessed. Gambierol reduced the PbTx-2-induced efflux of lactate dehydrogenase in exposed CGN cultures in a concentration-dependent manner (IC50 = 471 nM). It is noteworthy that the potencies of gambierol as an inhibitor of both PbTx-2-induced Ca2+ influx and cytotoxicity were coincident. Finally, the inhibitory effects of gambierol on PbTx-2-induced elevation of [Ca2+]i were compared with those of brevenal, a natural inhibitor of the toxic effects of brevetoxin isolated from cultures of Karina brevis. Like gambierol, brevenal inhibited PbTx-2-induced elevation of [Ca2+]i in a concentration-dependent manner (IC50 = 108.6 nM). These results provide evidence for gambierol acting as a functional antagonist of neurotoxin site 5 on neuronal VGSCs.
A reformulation of the hoop conjecture

A reformulation of the hoop conjecture based on the concept of trapped circle is presented. The problems of severe compactness in every spatial direction, and of how to superpose the hoops with the surface of the black hole, are resolved. A new conjecture concerning “peeling” properties of dynamical/trapping horizons is propounded. A novel geometric Hoop inequality is put forward. The possibility of carrying over the results to arbitrary dimension is discussed.
Asymmetries of the balanced SSFP profile. Part II: White matter

The signal profile measured in balanced steady‐state free precession has been shown to exhibit tissue‐dependent asymmetries that were hypothesized to relate to properties of the tissue microenvironment. It was proposed that balanced steady‐state free precession asymmetry may reflect subtle features of the frequency distribution in tissue. The present work investigates the large balanced steady‐state free precession asymmetries observed in white matter. First, maps quantifying the asymmetry are presented, which demonstrate considerable heterogeneity within white matter, with some tracts exhibiting significant asymmetry and others having a nearly symmetric profile. These maps are compared with a diffusion‐tensor atlas and indicate that the highest asymmetry is found in tracts oriented perpendicular to the main magnetic field. Measurements conducted at multiple repetition times suggest that the asymmetries are characterized by relatively small frequency shifts. These results are discussed in the context of previous work studying gradient‐recalled echo (GRE) signal behavior in white matter, and it is suggested that these two techniques are detecting closely related phenomena. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.