Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation of BacT/ALERT plastic culture bottles for use in testing of whole‐blood‐derived leukoreduced platelet‐rich‐plasma‐derived platelets

BACKGROUND: Bacterial detection of platelet (PLT)‐rich‐plasma (PRP)‐derived PLTs presents unique challenges for countries that do not allow pooling before storage. This study validated the BacT/ALERT for use in testing pooled PRP‐derived PLTs with nine contaminating organisms.
Localization and expression of cartilage oligomeric matrix protein by human rheumatoid and osteoarthritic synovium and cartilage

Synovium and cartilage from patients with osteoarthritis or rheumatoid arthritis were analyzed for expression of cartilage oligomeric matrix protein. Immunostaining of synovium with antiserum to cartilage oligomeric matrix protein demonstrated positive staining in both diseases. In osteoarthritis, there was positive staining within the synovial cells and immediately subjacent connective tissue, with less intense staining in the deeper connective tissue. In rheumatoid arthritis, there was less intense staining within the synovial cells and marked intense staining in the deeper connective tissue. In situ hybridization performed with an antisense digoxigenin‐labeled riboprobe to human cartilage oligomeric matrix protein confirmed the presence of cartilage oligomeric matrix protein mRNA in the cells of the synovial lining in both types of synovium. Quantitative polymerase chain reaction with a cartilage oligomeric matrix protein MIMIC demonstrated increased cartilage oligomeric matrix protein mRNA in rheumatoid cartilage and synovium as compared with osteoarthritic cartilage and synovium, respectively; mRNA levels in rheumatoid synovium were similar to those from osteoarthritic chondrocytes. As a result of the high expression of cartilage oligomeric matrix protein from rheumatoid synovium, inflammatory synovium should be considered as a potential tissue source of cartilage oligomeric matrix protein in any investigation of biological markers of cartilage metabolism. The upregulated expression of cartilage oligomeric matrix protein in inflammatory tissues suggests its in vivo regulation by cytokines.
An in vitro method for studying digestion in the pig

1. An in vitro method, using duodenal and ileal digesta and faeces from pigs as inocula for the preparation of three incubation media for simulating the digestive processes in the pig, was proposed. The kinetics of degradation in these three media of three feed samples (pig-grower diet, sugar-beet pulp and wheat bran) with crude protein (nitrogen × 6.25) contents varying from 111 to 196 g/kg, starch contents from 10 to 446 g/kg and dietary fibre contents from 168 to 686 g/kg, were studied. 2. The method was investigated by incubating the feeds in the three media for up to 96 h, and determining the rate and extent of disappearance of feed components. 3. For each feed the 96 h dry matter disappearance was almost equal for all media, although the rate of disappearance varied considerably, with ileal digesta the most potent, particularly for the high-fibre feeds, and duodenal digesta the least. The patterns of disappearance of individual components were similar in all media, with the exception of crude protein which was apparently less degraded in ileal and especially faecal media. 4. Results suggest that a combination of a short (6–12 h) and a long (48–72 h) in vitro incubation could be employed to simulate digestion in the small and large intestine respectively of the pig.
Hepatitis C Virus Infection in Pregnant Women and its Vertical Transmission in Jeddah, Saudi Arabia

The aim of this study was to evaluate the prevalence of Hepatitis C virus (HCV) infection among pregnant women and the possibility of its transmission through the vertical route and through breast-feeding. Blood samples were collected from 300 pregnant women at the perinatal period and at delivery from the cord blood of their newborns, and from other 300 randomly selected breast-fed infants. Serum transaminases, anti-HCV Ab and HCV-RNA by PCR for only those with positive anti- HCV Ab were investigated. Results revealed that 9 (3%) mothers were positive for anti-HCV Ab and 8 (2.7%) were positive for HCV-RNA (viral load was below 5,000 copies / ml). However, only 5 newborns of HCV-RNA positive mothers showed positive results in (1.6%) for anti- HCV Ab, while all of them were negative by HCV-RNA. Meanwhile, all of the breast-fed infants were negative for anti- HCV Ab. Thus, this study could not reveal HCV transmission from mother to infant during the period of observation, yet a vertical transmission of HCV Ab was noticed. It is felt that it is not necessary to advise against breast-feeding prevention by mothers with HCV infection as long as there is no nipple cracking
Variola Virus-Specific Diagnostic Assays: Characterization, Sensitivity, and Specificity

ABSTRACT A public health response relies upon rapid and reliable confirmation of disease by diagnostic assays. Here, we detail the design and validation of two variola virus-specific real-time PCR assays, since previous assays cross-reacted with newly identified cowpox viruses. The assay specificity must continually be reassessed as other closely related viruses are identified.
Factors Determining the Composition of Inositol Trisphosphate Receptor Hetero-oligomers Expressed in COS Cells*

COS-7 cells were transiently transfected with type I and type III myo-inositol 1,4,5-trisphosphate receptor (IP3R) isoforms to study the processes underlying assembly and oligomerization of these tetrameric proteins. A FLAG epitope was engineered on to the N terminus of the type III IP3R to distinguish the transfected from the endogenous isoform. This was not necessary for the type I IP3R, since the endogenous levels of this isoform were extremely low. Based on sucrose gradient analysis, the transfected type I or FLAG-type III IP3Rs assembled into tetramers. Confocal immunofluorescence experiments confirmed that the constructs were primarily targeted to the endoplasmic reticulum. Recombinant type I IP3R expressed in COS cells over a 48-h period showed a negligible capacity to form hetero-oligomers with endogenous type III IP3Rs, based upon co-immunoprecipitation assays. However, substantial formation of hetero-oligomers was observed between recombinant receptors when the cells were simultaneously transfected with type I and FLAG-type III IP3Rs. Co-immunoprecipitation experiments using lysates from metabolically labeled cells allowed the quantitation of homo- and hetero-oligomers in cells transfected with different ratios of type I and FLAG-type III IP3R DNA. These studies show that the relative expression level of the two isoforms influences the fraction of hetero-oligomers formed. However, the proportion of hetero-oligomers formed were less than predicted by a binomial model in which the association of subunits is assumed to be random. In doubly transfected cells, the early kinetics of 35S label incorporation into homotetramers showed a lag period corresponding to the time taken to synthesize a full-length receptor. However, hetero-oligomers were synthesized with a longer lag period, suggesting that there may be kinetic constraints that favor homo-oligomers over hetero-oligomers.
MRBAYES: Bayesian inference of phylogenetic trees

SUMMARY The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. AVAILABILITY MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology. rochester.edu/software.html.
A New Approach to the Synthesis of Trinucleotide Phosphoramidites - Synthons for the Generation of Oligonucleotide/Peptide Libraries

Abstract Trinucleotide phosphoramidites that correspond to the codons of all 20 amino acids were synthesized in high yield in 5g scale. Precursors of those amidites - trinucleotide phosphotriesters - have been prepared using the phosphotriester approach without protection of the 3′-hydroxyl function. More than 10 oligonucleotides up to 90 bases long have been synthesized by a phosphite-triester approach using new synthons. The 67-mer (12 random codons) has been used to generate a display library of 2 × 108 complexity.
Ultra wideband indoor channel measurements using a wideband plate monopole antenna

A Vector Network Analyzer (VNA) was used to determine the ultra wideband (UWB) indoor propagation channel capacity and mean and standard deviation of the RMS delay spread. A wideband plate monopole antenna was designed and tested to work as a receiver over the frequency band 2.4–3.9 GHz. The standard 1–12 GHz horn was used as the transmitter antenna. The channel capacity was calculated and plotted against signal to noise ratio (S/N). The UWB channel transfer function was also measured. The output of the measurements was in the form of power delay profile (PDP) of the channel and the output of the data processing was the mean and standard deviation of root-mean-square (RMS) delay spread. Both mean and standard deviation values are increased with the increase of transmitter-receiver separation for the non line of site (NLOS) scenarios.
Kinetic Alpha Complexes and Their Implementation ∗

Motivated by an application in cell biology, we describe an extension of the kinetic data structures framework from Delaunay triangulations to fixed-radius alpha complexes. Our algorithm is implemented using CGAL, following the exact geometric computation paradigm. We report on several techniques to accelerate the computation that turn our implementation applicable to the underlying biological problem.
Treatment Costs, Cost Offset, and Cost-Effectiveness of Collaborative Management of Depression

Objective This report estimates the treatment costs, cost-offset effects, and cost-effectiveness of Collaborative Care of depressive illness in primary care. Study Design Treatment costs, cost-offset effects, and cost-effectiveness were assessed in two randomized, controlled trials. In the first randomized trial (N = 217), consulting psychiatrists provided enhanced management of pharmacotherapy and brief psychoeducational interventions to enhance adherence. In the second randomized trial (N = 153), Collaborative Care was implemented through brief cognitive-behavioral therapy and enhanced patient education. Consulting psychologists provided brief psychotherapy supplemented by educational materials and enhanced pharmacotherapy management. Results Collaborative Care increased the costs of treating depression largely because of the extra visits required to provide the interventions. There was a modest cost offset due to reduced use of specialty mental health services among Collaborative Care patients, but costs of ambulatory medical care services did not differ significantly between the intervention and control groups. Among patients with major depression there was a modest increase in cost-effectiveness. The cost per patient successfully treated was lower for Collaborative Care than for Usual Care patients. For patients with minor depression, Collaborative Care was more costly and not more cost-effective than Usual Care. Conclusions Collaborative Care increased depression treatment costs and improved the cost-effectiveness of treatment for patients with major depression. A cost offset in specialty mental health costs, but not medical care costs, was observed. Collaborative Care may provide a means of increasing the value of treatment services for major depression.
Learning English through actions: a study of mobile-assisted language learning

This study investigated the impact of taking photos using mobile phones on the English phrase-learning performance of English as a second-language learners. A total of 116 students enrolled in a college in Central Taiwan participated in this study. The participants were divided randomly into two groups: a control group and an experimental group (EG). The control group was assigned an online phrase-reading activity for the purpose of phrase learning, whereas the EG was instructed to engage in phrase learning by taking photos using their mobile phones. The study primarily investigated the participants' daily encounters with newly acquired phrases through the use of photos taken using mobile phones, which were associated with the sentences they constructed. The results of the study indicated that the students in the EG significantly outperformed the control students on the delayed posttest, and the EG exhibited a significantly higher level of perception toward the phrase-learning activities compared with that of the control group.
Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP–metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, including p-coumaric acid and caffeic acid, we found strong associations (P values to ) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype–phenotype gap of complex agronomic traits.
Growth rate-dependent control, feedback regulation and steady-state mRNA levels of the threonyl-tRNA synthetase gene of Escherichia coli.

The expression of the gene thrS encoding threonyl-tRNA synthetase is under the control of two apparently different regulatory loops: translational feedback regulation and growth rate-dependent control. The translational feedback regulation is due to the binding of threonyl-tRNA synthetase to a site located in the leader RNA of thrS, upstream of the initiation codon, which mimics the anticodon stem and loop of tRNA(Thr). This binding competes with that of the ribosome and thus inhibits translation initiation. Here, we investigate the mechanism of growth rate-dependent control, i.e. the mechanism by which the synthetase accumulates at high growth rates. We show that growth rate-dependent control acts at the level of translation and requires feedback regulation since mutations that abolish feedback regulation also abolish growth rate-dependent control. We also show that tRNA(Thr), which accumulates at high growth rates, is one of the effectors of growth rate-dependent control since its accumulation can cause derepression independently of growth rate. We show that this tRNA(Thr)-dependent derepression is also dependent on feedback regulation since mutations which abolish feedback also prevent derepression. Based on these results and previous data concerning the mechanism of translational feedback regulation, we propose that threonyl-tRNA synthetase growth rate-dependent control is the consequence of the accumulation at high growth rates of two effectors, the ribosome and tRNA(Thr). We also study the growth rate-dependence of the steady state level of thrS mRNA and show that the steady state level of thrS mRNA increases at high growth rates. This increase is dependent on the translational feedback regulation and can also be detected, independently of growth rate, when thrS mRNA translation is derepressed. Consistently with the model of growth rate-dependent control above, we propose that at high growth rates, the mRNA is well translated and thus stabilised and that, at low growth rates, because of its low translation, thrS mRNA is rapidly degraded.
Contested evidence: a Dutch reimbursement decision taken to court

Abstract This paper examines a remarkable lawsuit in health care rationing. The Patients Association for Interstitial Cystitis sued the Dutch National Health Care Institute for alleged misconduct against Interstitial Cystitis patients, as the Institute decided that bladder instillations with chondroitin sulphate or hyaluronic acid are no longer covered by the basic health insurance. The patients’ organisation challenged the Institute for basing its standpoint on scientific evidence; overruling clinical expertise and patients’ experiences. While scientific advice is often solicited in public health issues, simultaneously, the authority of scientific advice is increasingly being questioned in the public domain. Also, the judiciary is frequently called upon to adjudicate in rationing decisions. Based on an ethnographic study of the National Health Care Institute, drawing on insights from the field of Science and Technology Studies, we analyse this lawsuit as a negotiation of what knowledge counts in reimbursement decisions.
Identification of a novel missense mutation (563G>a) in the ABO gene associated with a Bel phenotype

A BO serologic typing sometimes shows discrepant results that are often due to ABO gene variants, which influence ABO transferase activity. The human ABO genes consist of seven exons; Exons 6 and 7 encode for the catalytic domain of the protein. ABO serologic typing was performed in a 36-year-old woman who was hospitalized in the Aichi Medical University Hospital for resection of a gynecologic cancer; the results showed ABO discrepancies (forward, O; reverse, B). This prompted us to characterize the ABO phenotypes and to perform gene analysis. Here, we describe a novel missense mutation in the ABO gene that can perturb the binding to uridine diphosphate galactose in a pedigree with the Bel phenotype.
Statistical Approaches to Inferring Object Shape from Single Images

Depth inference is a fundamental problem of computer vision with a broad range of potential applications. Monocular depth inference techniques, particularly shape from shading dates back to as early as the 40's when it was rst used to study the shape of the lunar surface. Since then there has been ample research to develop depth inference algorithms using monocular cues. Most of these are based on physical models of image formation and rely on a number of simplifying assumptions that do not hold for real world and natural imagery. Very few make use of the rich statistical information contained in real world images and their 3D information. There have been a few notable exceptions though. The study of statistics of natural scenes has been concentrated on outdoor scenes which are cluttered. Statistics of scenes of single objects has been less studied, but is an essential part of daily human interaction with the environment. Inferring shape of single objects is a very important computer vision problem which has captured the interest of many researchers over the past few decades and has applications in object recognition, robotic grasping, fault detection and Content Based Image Retrieval (CBIR). This thesis focuses on studying the statistical properties of single objects and their range images which can bene t shape inference techniques. I acquired two databases: Single Object Range and HDR (SORH) and the Eton Myers Database of single objects, including laser-acquired depth, binocular stereo, photometric stereo and High Dynamic Range (HDR) photography. I took a data driven approach and studied the statistics of color and range images of real scenes of single objects along with whole 3D objects and uncovered
Characterization of dFMR1, a Drosophila melanogaster Homolog of the Fragile X Mental Retardation Protein

ABSTRACT Fragile X syndrome is the most common inherited form of mental retardation. It is caused by loss of FMR1 gene activity due to either lack of expression or expression of a mutant form of the protein. In mammals, FMR1 is a member of a small protein family that consists of FMR1, FXR1, and FXR2. All three members bind RNA and contain sequence motifs that are commonly found in RNA-binding proteins, including two KH domains and an RGG box. The FMR1/FXR proteins also contain a 60S ribosomal subunit interaction domain and a protein-protein interaction domain which mediates homomer and heteromer formation with each family member. Nevertheless, the specific molecular functions of FMR1/FXR proteins are unknown. Here we report the cloning and characterization of a Drosophila melanogaster homolog of the mammalian FMR1/FXR gene family. This first invertebrate homolog, termed dfmr1, has a high degree of amino acid sequence identity/similarity with the defined functional domains of the FMR1/FXR proteins. The dfmr1 product binds RNA and is similar in subcellular localization and embryonic expression pattern to the mammalian FMR1/FXR proteins. Overexpression of dfmr1 driven by the UAS-GAL4 system leads to apoptotic cell loss in all adult Drosophila tissues examined. This phenotype is dependent on the activity of the KH domains. The ability to induce a dominant phenotype by overexpressing dfmr1 opens the possibility of using genetic approaches in Drosophila to identify the pathways in which the FMR1/FXR proteins function.
Study of the Effect of the Operating Frequency of a GaN Lamb Wave Device to Viscosity and Protein Sensing

Shear-operating frequency is known to affect the sensitivity of acoustic wave sensor devices to both chemical and biological sensing, e.g., the detection of solutions' viscosity and protein adsorption. Lamb wave devices have been considered to be limited to low operating frequencies (5-40 MHz) due to their configuration. Here, acoustic devices based on single crystalline GaN membrane were used for liquid-based applications by monitoring the lowest symmetrical mode S0 of a Lamb wave in the range of 142-458 MHz. We evaluated the response of the acoustic devices by monitoring the amplitude and phase of the wave during the application of various concentrations of glycerol on the device surface. In addition, we demonstrated a strong correlation between mass sensitivity and device operating frequency, as measured during the specific binding of biotinylated IgG on the neutravidin modified membrane. Importantly, our results indicate that a decisive parameter in choosing the optimum frequency is the nature of the final application. Lower operating frequencies (<;200 MHz) appear to be more suitable for viscosity measurements, while higher ones (~300 MHz) should be selected for biosensing applications.
Active gels as a description of the actin‐myosin cytoskeleton

This short review presents a qualitative introduction to the hydrodynamic theory of active polar gels and its applications to the mechanics of the cytoskeleton. Active polar gels are viscoelastic materials formed by polar filaments maintained in a nonequilibrium state by constant consumption of energy. In the cytoskeleton of eukaryotic cells, actin filaments are treadmilling and form a viscoelastic gel interacting with myosin molecular motors driven by the hydrolysis of adenosine triphosphate; one can thus consider the actomyosin cytoskeleton as an active polar gel. The hydrodynamic description is generic as it only relies on symmetry arguments. We first use the hydrodynamic approach to discuss the spontaneous generation of flow in an active polar film. Then we give two examples of applications to lamellipodium motility and to instabilities of cortical actin.