Miracle-dz/UniFAR-FTUs huggingface dataset:
Soluble Epoxide Hydrolase: Sex Differences and Role in Endothelial Cell Survival

Objective—Sex differences in cerebral ischemic injury are, in part, arrtibutable to the differences in cerebrovascular perfusion. We determined whether the brain microvascular endothelial cells (ECs) isolated from the female brain are more resistant to ischemic injury compared with male ECs, and whether the difference is attributable to lower expression of soluble epoxide hydrolase and higher levels of vasoprotective epoxyeicosatrienoic acids (EETs). We also determined whether protection by EETs is linked to the inhibition of rho-kinase (ROCK). Methods and Results—EC ischemic damage was measured after oxygen–glucose deprivation (OGD) using propidium iodide (PI) and cleaved caspase-3 labeling. Expression of soluble epoxide hydrolase was determined by quantitative polymerase chain reaction and immunocytochemistry, EETs levels by liquid chromatography-tandem mass spectrometry, and ROCK activity by ELISA. EC damage was higher in males compared with females, which correlated with higher soluble epoxide hydrolase mRNA, stronger immunoreactivity, and lower EETs compared with female ECs. Inhibition of soluble epoxide hydrolase abolished the sex difference in EC damage. ROCK activity was higher in male versus female ECs after OGD, and sex differences in EC damage and ROCK activity were abolished by 14,15-EET and ROCK inhibition. Conclusion—Sex differences in ischemic brain injury are, in part, attributable to differences in EET-mediated inhibition of EC ROCK activation after ischemia.
Comparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1

Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10−6) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.
Contact Pressures at Osteochondral Donor Sites in the Knee

The purposes of this study were to determine whether any of the commonly recommended osteochondral donor sites are nonarticulating throughout a functional range of knee motion, and to determine the differential contact pressures for these sites. Ten commonly recommended sites for osteochondral harvest were evaluated with pressure-sensitive film through a functional range of motion with a model that simulated nonweightbearing resistive extension of the knee. All 10 donor sites demonstrated a significant contact pressure through 0° to 110° of knee motion. The different color density measurements between donor sites were also significant. Although donor sites 1, 2, 9, and 10 demonstrated significantly less contact pressure than the sites with the greatest contact pressure, the difference in mean pressures was small. No osteochondral donor site tested was free from contact pressure. It is currently unknown whether articular contact at these osteochondral donor sites will lead to degenerative changes or any other problems.
Evaluation of an Online Platform for Multiple Sclerosis Research: Patient Description, Validation of Severity Scale, and Exploration of BMI Effects on Disease Course

Objectives To assess the potential of an online platform, PatientsLikeMe.com (PLM), for research in multiple sclerosis (MS). An investigation of the role of body mass index (BMI) on MS disease course was conducted to illustrate the utility of the platform. Methods First, we compared the demographic characteristics of subjects from PLM and from a regional MS center. Second, we validated PLM’s patient-reported outcome measure (MS Rating Scale, MSRS) against standard physician-rated tools. Finally, we analyzed the relation of BMI to the MSRS measure. Results Compared with 4,039 MS Center patients, the 10,255 PLM members were younger, more educated, and less often male and white. Disease course was more often relapsing remitting, with younger symptom onset and shorter disease duration. Differences were significant because of large sample sizes but small in absolute terms. MSRS scores for 121 MS Center patients revealed acceptable agreement between patient-derived and physician-derived composite scores (weighted kappa = 0.46). The Walking domain showed the highest weighted kappa (0.73) and correlation (rs = 0.86) between patient and physician scores. Additionally, there were good correlations between the patient-reported MSRS composite and walking scores and physician-derived measures: Expanded Disability Status Scale (composite rs = 0.61, walking rs = 0.74), Timed 25 Foot Walk (composite rs = 0.70, walking rs = 0.69), and Ambulation Index (composite rs = 0.81, walking rs = 0.84). Finally, using PLM data, we found a modest correlation between BMI and cross-sectional MSRS (rho = 0.17) and no association between BMI and disease course. Conclusions The PLM population is comparable to a clinic population, and its patient-reported MSRS is correlated with existing clinical instruments. Thus, this online platform may provide a venue for MS investigations with unique strengths (frequent data collection, large sample sizes). To illustrate its applicability, we assessed the role of BMI in MS disease course but did not find a clinically meaningful role for BMI in this setting.
Socket/stump interface dynamic pressure distributions recorded during the prosthetic stance phase of gait of a trans-tibial amputee wearing a hydrocast socket

Force sensing resistors (FSR) have been used to measure dynamic stump/socket interface pressures during the gait of a trans-tibial amputee. A total of 350 pressure sensors were attached to the inner wall of a hydrocast socket. Data were sampled at 150Hz during approximately 0.8 seconds of prosthetic stance of gait. The dynamic pressure distributions within a hand cast socket reported by Convery and Buis (1998) are compared with those monitored within a hydrocast socket for the same amputee. The pressure gradients within the hydrocast socket are less than that of the hand cast Patellar-Tendon-Bearing (PTB) socket. The proximal “ring” of high pressure in the hand cast PTB socket is replaced with a more distal pressure in the hydrocast socket.
Vitamin D Levels, Microvascular Complications, and Mortality in Type 1 Diabetes

OBJECTIVE To evaluate vitamin D as a predictor of all-cause mortality, progression from normoalbuminuria to micro- or macroalbuminuria, and the development of background or proliferative retinopathy in patients with type 1 diabetes. RESEARCH DESIGN AND METHODS A prospective observational follow-up study in which an inception cohort of type 1 diabetic patients was followed from onset of diabetes diagnosed between 1979 and 1984. Plasma vitamin D [25(OH)D3] levels were determined by high performance liquid chromatography/tandem mass spectrometry in 227 patients before the patients developed microalbuminuria. Values equal to or below the 10% percentile (15.5 nmol/L) were considered severe vitamin D deficiency. RESULTS Median (range) vitamin D was 44.6 (1.7–161.7) nmol/L. Vitamin D level was not associated with age, sex, urinary albumin excretion rate (UAER), or blood pressure. During follow-up, 44 (18%) patients died. In a Cox proportional hazards model, the hazard ratio for mortality in subjects with severe vitamin D deficiency was 2.7 (1.1–6.7), P = 0.03, after adjustment for UAER, HbA1c, and conventional cardiovascular risk factors (age, sex, blood pressure, cholesterol, smoking). Of the 220 patients, 81 (37%) developed microalbuminuria and 27 (12%) of these progressed to macroalbuminuria. Furthermore, 192 (87%) patients developed background retinopathy, whereas 34 (15%) progressed to proliferative retinopathy. Severe vitamin D deficiency at baseline did not predict the development of these microvascular complications. CONCLUSIONS In patients with type 1 diabetes, severe vitamin D deficiency independently predicts all-cause mortality but not development of microvascular complications in the eye and kidney. Whether vitamin D substitution in type 1 diabetic patients can improve the prognosis remains to be investigated.
Wireless MEMS-Based Accelerometer Sensor Boards for Structural Vibration Monitoring: A Review

Monitoring and analysing the integrity of structures and machinery is important for economic, operational, and mission critical reasons. In recent years, there has been growing interest in performing structural health monitoring (SHM) by monitoring structural dynamic response via micro electro-mechanical system accelerometers. In addition, the possibility of embedding these devices within a wireless sensor network and allowing measured data to be wirelessly transmitted has contributed to the development of many new applications not possible just a few years ago. These sensors, for use in SHM applications, need to detect low-amplitude and low frequency vibrations, operations which are not always feasible with the conventional low-cost sensor boards. Since the late 1990s, several accelerometer board prototypes have been proposed for achieving accurate vibration monitoring. This paper presents a summary review of the systems developed in the ten years following 2006 with particular emphasis on the sensing characteristics, performances, and applications of the designed sensor boards for microvibration detection and analysis.
Inhibitors of poly(adenosine diphosphoribose) synthetase, examination of metabolic perturbations, and enhancement of radiation response in Chinese hamster cells.

3-Aminobenzamide, a specific inhibitor of poly(adenosine diphosphoribose) synthesis, has been shown to enhance the response of mammalian cells to ionizing radiation and alkylating agents. Observations such as these usually have been taken to be an indication of the involvement of poly(adenosine diphosphoribose) in the repair of DNA damage. It has been reported that some inhibitors of adenosine diphosphoribosyl transferase (ADPRT) affect cell viability, glucose metabolism, and DNA synthesis when present at low concentrations in the growth medium for extended periods (e.g., lymphoid cells exposed to a few millimolar for 24 h [Milam, K. M., and Cleaver, J. E. Science (Wash. DC), 223: 589, 1984]). The latter report questioned previous interpretations of radiation results based on the use of ADPRT inhibitors which enhance cell killing. We have studied the enhanced radiation lethality of Chinese hamster cells using higher concentrations of these inhibitors, but for shorter periods, in an effort to determine if metabolic perturbations are produced and if they are relatable to enhanced cell killing. The compounds used were 2-aminobenzamide, 3-aminobenzamide, 4-aminobenzamide, benzamide, and nicotinamide, compounds which show a large variation in their potency as inhibitors of ADPRT. It was found that none of the compounds was toxic at the highest doses used (20 mM for 2 h) and that, during a 2-h period, the potent inhibitor 3-aminobenzamide had little or no effect on DNA synthesis. Two h is long enough to yield a near-maximum radiosensitization with 3-aminobenzamide. Although glucose metabolism was affected to varying degrees (up to a 50% inhibition by 4-aminobenzamide in 2 h), there was no correlation between effectiveness in inhibiting ADPRT and effectiveness in inhibiting glucose metabolism. A correlation was observed, however, between the inhibitory potential of ADPRT and the enhancement of radiation response. When used for sufficiently short times, we conclude that the effects at even high concentrations of a potent inhibitor of ADPRT (e.g., 3-aminobenzamide) are consistent with an involvement of poly(adenosine diphosphoribose) synthesis in the expression of a radiation-induced end point like cell killing.
Description of Hot Compressive Stress-Strain Curves Using Transfer Functions

Mathematical descriptions of true stress/true strain curves, experimentally obtained on cylindrical specimens under hot compressive conditions, are of great importance and are widely investigated. An additional black-box modelling approach using transfer functions (TF) is tested. For tested 51CrV4 steel, a TF of third order is employed for description of true stress (output) depending on the strain rate (input). Sets of TF coefficients are determined using numerical optimization techniques for each testing temperature and strain rate. To avoid scattering of TF parameters, time in Laplacian transformation is replaced with strain, while TF input is the strain rate. Obtained models cover deformations starting practically from zero to 0.7. Average absolute relative error for models based on TF of the third order and of the second order are 0.93% and 3.64%.
Plasma Concentration of Uroguanylin in Patients on Maintenance Dialysis Therapy

Background: Uroguanylin, originally isolated from urine, is a new natriuretic peptide. Its plasma level is increased in association with renal impairment and fluid retention in patients with renal diseases. Methods: Uroguanylin concentrations were measured in patients on hemodialysis (HD, n = 76) and those on continuous ambulatory peritoneal dialysis (CAPD, n = 10) using a sensitive ra- dioimmunoassay for human uroguanylin. Results: Plasma concentrations of immunoreactive (ir)-uroguanylin in the patients on HD and CAPD (212.0 ± 17.4 and 245.3 ± 39.5 fmol/ml) were significantly higher than the value for the normal controls (5.0 ± 0.3 fmol/ml). Plasma ir-uroguanylin levels before the start of regular HD were correlated with predialysis excess weight based on their dry weights (r = 0.33, p < 0.01) and with dialysis duration (r = 0.26, p < 0.05). The plasma levels in patients with HD, for whom high-flux membranes were used, were decreased at the end of regular HD as compared with the prior levels (p < 0.05), but not in those who underwent HD with conventional membranes. Conclusion: These findings suggest that the plasma ir-uroguanylin level is related to the patient’s volume status as well as renal impairment. Whether the accumulation of uroguanylin has a pathological effect has yet to be determined.
A Porcine Epidemic Diarrhea Virus Outbreak in One Geographic Region of the United States: Descriptive Epidemiology and Investigation of the Possibility of Airborne Virus Spread

This study describes a spring 2013 outbreak of porcine epidemic diarrhea virus (PEDv), using data from 222 swine sites in 14 counties area in 4 contiguous states in the United States. During the outbreak, the premises-level incidence of PEDv was 40.5 percent (90/222 sites). One of the three companies from which data were collected had a lower incidence (19.5 percent) than the other two companies (41.1 and 47.2 percent). Sow sites had the highest incidence of PEDv during the outbreak (80.0 percent). Spatial analysis showed that PEDv was clustered rather than randomly distributed, which suggested that sites near a positive site had increased risk of acquiring PEDv infection. Meteorological data were used to investigate the hypothesis that PEDv was spread by air. If airborne dissemination played a role in this outbreak, we would expect the direction of disease spread to correlate with the predominant wind direction. Two methods were used to determine the direction of disease spread—linear direction mean analysis in ArcGIS and the direction test in ClusterSeer. The former method indicated PEDv spread was south to slightly southwest, and the latter indicated spread was to the southeast. The predominant wind direction during the month of the outbreak was toward the south, with some southeast and southwest winds; the strongest wind gusts were toward the southwest. These findings support the hypothesis that PEDv was spread by air. The results, however, should be interpreted cautiously because we did not have information on direct and indirect contacts between sites, such as movement of trucks, feed, pigs or people. These types of contacts should be evaluated before pathogen spread is attributed to airborne mechanisms. Although this study did not provide a definitive assessment of airborne spread of PEDv, we believe the findings justify additional research to investigate this potential mechanism of transmission.
Combining Neural Networks and Log-linear Models to Improve Relation Extraction

The last decade has witnessed the success of the traditional feature-based method on exploiting the discrete structures such as words or lexical patterns to extract relations from text. Recently, convolutional and recurrent neural networks has provided very effective mechanisms to capture the hidden structures within sentences via continuous representations, thereby significantly advancing the performance of relation extraction. The advantage of convolutional neural networks is their capacity to generalize the consecutive k-grams in the sentences while recurrent neural networks are effective to encode long ranges of sentence context. This paper proposes to combine the traditional feature-based method, the convolutional and recurrent neural networks to simultaneously benefit from their advantages. Our systematic evaluation of different network architectures and combination methods demonstrates the effectiveness of this approach and results in the state-of-the-art performance on the ACE 2005 and SemEval dataset.
Influence of Curing Pressure on Unconfined Compressive Strength of Cemented Clay

The soil-cement columns are generally installed and cured in the soft clay layers under confining pressure. The strength of the soil-cement columns may be influenced by confining pressure during curing period. In this study, the main objective was to study the influence of curing pressure on unconfined compressive strength of cemented clay. A series of unconfined compression tests was performed on a cement admixed clay sample cured under pressure values of 0 kPa (atmospheric pressure), 25kPa, 50kPa and 100 kPa using a typical unconfined compression equipment. The test samples with values of cement content of 0.5, 1.0 and 2.0 percent were cured for 28 days.The stress-strain curves obtained from all tests show a peak value of stress. The unconfined compressive strength or peak stress obviously increased with increasing cement content for all curing pressure conditions. It can be observed that the strength of samples gradually increased with curing pressure for cement content of 0.5 percent. For cement contents of 1.0 and 2.0 percent, the strengths of samples cured under pressures of 25 kPa dramatically increased from the strength of samples cured without pressure (0 kPa), however, the strengths of samples for curing pressures of 25, 50 and 100 kPa were not clearly different.
Adaptation of lodgepole pine and interior spruce to climate: implications for reforestation in a warming world

We investigated adaptation to climate in populations of two widespread tree species across a range of contrasting environments in western Canada. In a series of common garden experiments, bud phenology, cold hardiness, and seedling growth traits were assessed for 254 populations in the interior spruce complex (Picea glauca, P. engelmannii, and their hybrids) and for 281 populations of lodgepole pine (Pinus contorta). Complex multitrait adaptations to different ecological regions such as boreal, montane, coastal, and arid environments accounted for 15–20% of the total variance. This population differentiation could be directly linked to climate variables through multivariate regression tree analysis. Our results suggest that adaptation to climate does not always correspond linearly to temperature gradients. For example, opposite trait values (e.g., early versus late budbreak) may be found in response to apparently similar cold environments (e.g., boreal and montane). Climate change adaptation strategies may therefore not always be possible through a simple shift of seed sources along environmental gradients. For the two species in this study, we identified a relatively small number of uniquely adapted populations (11 for interior spruce and nine for lodgepole pine) that may be used to manage adaptive variation under current and expected future climates.
Global landscape of recent inferred Darwinian selection for Homo sapiens

By using the 1.6 million single-nucleotide polymorphism (SNP) genotype data set from Perlegen Sciences [Hinds, D. A. , Stuve, L. L. , Nilsen, G. B. , Halperin, E. , Eskin, E. , Ballinger, D. G. , Frazer, K. A. & Cox, D. R. (2005) Science 307, 1072-1079], a probabilistic search for the landscape exhibited by positive Darwinian selection was conducted. By sorting each high-frequency allele by homozygosity, we search for the expected decay of adjacent SNP linkage disequilibrium (LD) at recently selected alleles, eliminating the need for inferring haplotype. We designate this approach the LD decay (LDD) test. By these criteria, 1.6% of Perlegen SNPs were found to exhibit the genetic architecture of selection. These results were confirmed on an independently generated data set of 1.0 million SNP genotypes (International Human Haplotype Map Phase I freeze). Simulation studies indicate that the LDD test, at the megabase scale used, effectively distinguishes selection from other causes of extensive LD, such as inversions, population bottlenecks, and admixture. The approximately 1,800 genes identified by the LDD test were clustered according to Gene Ontology (GO) categories. Based on overrepresentation analysis, several predominant biological themes are common in these selected alleles, including host-pathogen interactions, reproduction, DNA metabolism/cell cycle, protein metabolism, and neuronal function.
Using an achiasmic human visual system to quantify the relationship between the fMRI BOLD signal and neural response

Achiasma in humans causes gross mis-wiring of the retinal-fugal projection, resulting in overlapped cortical representations of left and right visual hemifields. We show that in areas V1-V3 this overlap is due to two co-located but non-interacting populations of neurons, each with a receptive field serving only one hemifield. Importantly, the two populations share the same local vascular control, resulting in a unique organization useful for quantifying the relationship between neural and fMRI BOLD responses without direct measurement of neural activity. Specifically, we can non-invasively double local neural responses by stimulating both neuronal populations with identical stimuli presented symmetrically across the vertical meridian to both visual hemifields, versus one population by stimulating in one hemifield. Measurements from a series of such doubling experiments show that the amplitude of BOLD response is proportional to approximately 0.5 power of the underlying neural response. Reanalyzing published data shows that this inferred relationship is general. DOI: http://dx.doi. org/10.7554/eLife.09600. 001