Miracle-dz/UniFAR-FTUs huggingface dataset:
Digestible lysine requirements of male broilers from 1 to 42 days of age reassessed

Three experiments were conducted separately to estimate the digestible Lys (dig. Lys) requirements of Cobb × Cobb 500 male broilers using different statistical models. For each experiment, 1,200 chicks were housed in 48 floor pens in a completely randomized design with 6 treatments and 8 replicates. Broilers were fed diets with increasing dig. Lys levels from 1 to 12 d (Exp. 1), from 12 to 28 d (Exp. 2), and 28 to 42 d (Exp. 3). Increasing dig. Lys levels were equally spaced from 0.97 to 1.37% in Exp. 1, 0.77 to 1.17% in Exp. 2, and 0.68 to 1.07% in Exp. 3. The lowest dig. Lys diets were not supplemented with L-Lysine and all other essential AA met or exceeded recommendations. In Exp. 3, six birds per pen were randomly selected from each replication to evaluate carcass and breast yields. Digestible Lys requirements were estimated by quadratic polynomial (QP), linear broken-line (LBL), quadratic broken-line (QBL), and exponential asymptotic (EA) models. Overall, dig. Lys requirements varied among response variables and statistical models. Increasing dietary dig. Lys had a positive effect on BW, carcass and breast yields. Levels of dig. Lys that optimized performance using QP, LBL, QBL, and EA models were 1.207, 1.036, 1.113, and 1.204% for BWG and 1.190, 1.027, 1.100, and 1.172% for FCR in Exp. 1; 1.019, 0.853, 0.944; 1.025% for BWG and 1.050, 0.879, 1.032, and 1.167% for FCR in Exp. 2; and 0.960, 0.835, 0.933, and 1.077% for BWG, 0.981, 0.857, 0.963, and 1.146% for FCR in Exp. 3. The QP, LBL, QBL, and EA also estimated dig. Lys requirements as 0.941, 0.846, 0.925, and 1.070% for breast meat yield in Exp. 3. In conclusion, Lys requirements vary greatly according to the statistical analysis utilized; therefore, the origin of requirement estimation must be taken into account in order to allow adequate comparisons between references.
The influence of platelets, plasma and red blood cells on functional haemostatic assays

Functional whole blood haemostatic assays are used increasingly to guide transfusion therapy and monitor medical treatment and are also applied for in-vitro evaluations of the haemostatic potential of stored platelets. We investigated how the cellular and plasmatic elements, both isolated and combined, influenced the two methodologically different assays, thrombelastography (TEG) and impedance aggregometry (Multiplate). Platelet-rich plasma (200 × 109/l) or pure plasma (0 platelets), with and without added red blood cells (RBCs), hematocrit 0, 0.15 or 0.29, were produced in vitro from platelet concentrates, fresh frozen plasma and stored RBC. Pure platelets were investigated by removing plasma components from platelet concentrates by diafiltration against the platelet storage solution Intersol. Plasma was readded by diafiltration against plasma in Intersol. Haemostatic function was evaluated by TEG and Multiplate. In the TEG, increasing amounts of RBC reduced clot strength and clot kinetics (α-angle), most markedly in plasma/RBC without platelets. In contrast, RBC in a platelet concentrate matrix enhanced Multiplate aggregation in response to weak agonists (ADP and arachidonic acid). Furthermore, removing plasma from platelet concentrates eliminated the TEG response and diminished the Multiplate aggregation response, but readding plasma to the pure platelet concentrates restored the response. Each of the elements in whole blood, plasma, platelets and RBC, affected the Multiplate and TEG results differently. The results emphasize that the concentrations of all cellular and plasmatic components in whole blood should be taken into account when interpreting results obtained by TEG and multiplate.
A slow sustained increase in cytosolic Ca2+ levels mediates stalk gene induction by differentiation inducing factor in Dictyostelium.

During Dictyostelium stalk cell differentiation, cells vacuolate, synthesize a cellulose cell wall and die. This process of programmed cell death is accompanied by expression of the prestalk gene ecmB and induced by the differentiation inducing factor DIF. Using cell lines expressing the recombinant Ca2+‐sensitive photoprotein apoaequorin, we found that 100 nM DIF increases cytosolic Ca2+ ([Ca2+]i) levels from approximately 50 to 150 nM over a period of 8 h. The Ca2+‐ATPase inhibitor 2,5‐di(tert‐butyl)‐1,4‐hydroquinone (BHQ) induced a similar increase in [Ca2+]i levels and induced expression of the prestalk gene ecmB to the same level as DIF. The [Ca2+]i increases induced by DIF and BHQ showed similar kinetics and preceded ecmB gene expression by approximately 1–2 h. The Ca2+ chelator 1,2‐bis(o‐aminophenoxy)‐ethane‐N,N,N′N′‐tetra‐acetic acid (BAPTA) efficiently inhibited the BHQ‐induced [Ca2+]i increase and blocked DIF‐induced expression of the ecmB gene. These data indicate that the effects of DIF on stalk gene expression are mediated by a sustained increase in [Ca2‐]i. Sustained [Ca2+]i elevation mediates many forms of programmed cell death in vertebrates. The Dictyostelium system may be the earliest example of how this mechanism developed during early eukaryote evolution.
Segmentally arranged somatotopy within the face representation of human primary somatosensory cortex

Though somatotypic representation within the face in human primary somatosensory cortex (S1) to innocuous stimuli is controversial; previous work suggests that painful heat is represented based on an “onion‐skin” or segmental pattern on the face. The aim of this study was to determine if face somatotopy for brush stimuli in S1 also follows this segmental representation model. Twelve healthy subjects (nine men: three women) underwent functional magnetic resonance imaging to measure blood oxygen level dependent signals during brush (1 Hz, 15 s) applied to their faces. Separate functional scans were collected for brush stimuli repetitively applied to each of five separate stimulation sites on the right side of the face. These sites were arranged in a vertical, horizontal, and circular manner encompassing the three divisions of the trigeminal nerve. To minimize inter‐individual morphological differences in the post‐central gyrus across subjects, cortical surface‐based registration was implemented before group statistical image analysis. Based on activation foci, somatotopic activation in the post‐central gyrus was detected for brush, consistent with the segmental face representation model. Hum Brain Mapp, 2009. © 2008 Wiley‐Liss, Inc.
Modeling Alzheimer's disease immune therapy mechanisms: Interactions of human postmortem microglia with antibody‐opsonized amyloid beta peptide

The induction of an antibody response to amyloid beta (Aβ) peptide has become a strategy for the treatment of Alzheimer's disease (AD). This has proven effective in reducing the plaque burden in transgenic mice that develop Aβ plaques similar to human AD patients. The mechanism for enhanced clearance of Aβ is partly due to the interaction of immunoglobulin Fcγ receptor‐expressing microglia and specific antibody‐opsonized Aβ deposits. This interaction can stimulate Fcγ receptor‐mediated phagocytosis, but also results in inflammatory activation of these cells. Consequently, interaction of microglia with antibody‐antigen complexes could exacerbate the existing inflammation in the brains of AD patients. In this study, we used substrate‐bound Aβ and cultured human microglia from AD and non‐demented cases to model interaction of microglia and antibody‐opsonized plaques in AD brains. Enhanced production of tumor necrosis factor‐α, macrophage colony stimulating factor, interleukin‐10, and superoxide ions was detected. We also demonstrated enhanced uptake of opsonized Aβ by microglia, which was reduced significantly in the presence of excess IgG, indicative of the involvement of Fcγ receptor‐mediated mechanisms. Human microglia were shown in this study to express mRNA for Fcγ receptors I, IIa, IIb, and III. The expression of Fcγ receptor II was augmented by proinflammatory stimulation. These results suggest that initial interactions of human microglia with antibody‐opsonized amyloid could result in increased inflammation. The consequence of this on inflammatory pathology in AD brains needs to be considered before immunization is used as a strategy for treating AD. © 2002 Wiley‐Liss, Inc.
Sample selection of multi-trial data for data-driven haptic texture modeling

In data-driven haptic texture rendering, the rendering quality is highly dependent on the quality of the inputoutput model training. The data in input model should be sufficient both in terms of quantity and coverage of the input space. Furthermore, the ever increasing input dimensions, to attain more realistic rendering makes the task of model building even more difficult. In order to address these problems, this paper proposes a novel sample selection algorithm. Our algorithm provides an efficient method of combining modeling data across multiple independent trials, whereby the significant model points are selected from each independent trial while the outliers are being eliminated. This study also provides a generic haptic model which equips other haptic modeling algorithms to benefit from the sample selection algorithm. The algorithm was evaluated using two isotropic and two non isotropic haptic texture datasets. The results showed that the algorithm provides upward of a two fold compression rate for model points, while at the same time the rendering quality remains unaffected.
Q fever in the United States; epidemiologic studies of an outbreak among stock handlers and slaughterhouse workers.

During the month of March 1946 there occurred in Amarillo, Texas, an explosive outbreak of an acute febrile illness which has since been identified as Q fever. The other papers in this series will give the details of the clinical features observed in the cases and the evidence on which the diagnosis of Q fever depends. It is the purpose of this report to give the background of the outbreak with descriptions of the industries involved as well as the sequence of events pertinent to the epidemiologic investigations. Amarillo is a city of about 70,000 inhabitants located near the center of the Texas panhandle. It is surrounded by country well suited to the raising of livestock and thereby has become a center for this industry. Since the city is situated at the junction of several large railroads by which cattle are shipped to the east, a feeder station has been
Optical Coherence Tomography Imaging for Glaucoma – Today and Tomorrow

AbstractDigital imaging technologies for glaucoma diagnostics have evolved rapidly over the recent years. From time-domain optical coherence tomography (OCT) to spectral-domain and swept-source OCTs, the application of OCT for analysis of the anterior chamber angle and the optic nerve head (ONH) is expanding. The second-generation anterior segment swept-source OCT is able to image the configuration of the anterior chamber angle in 3 dimensions in less than 1 second and perform 360-degree analysis of the anterior chamber angle width for detection of angle closure. The morphology, density, and dimensions of the crystalline lens in relation to the anterior chamber can now be examined from the anterior corneal surface to the posterior lens surface, facilitating the investigation of the involvement of the crystalline lens in primary angle closure. Spectral-domain and swept-source OCTs have improved the measurement reliability of the lamina cribrosa and the neuroretinal rim configurations. Studying the deformation of the lamina cribrosa and ONH surfaces is relevant to decipher the mechanisms of ONH damage in the development and progression of glaucoma. Software and algorithms for automatic analysis of the anterior chamber angle dimensions and deformation of the ONH and lamina cribrosa surfaces are required to process large volumetric data sets, and they are under active development. It is expected that new imaging technologies will improve the detection and risk assessment of angle-closure and open-angle glaucomas.
Distribution of NMDA receptor subunit proteins NR2A, 2B, 2C and 2D in rat brain

The regional distribution of the NMDA receptor subunits NR2A, 2B, 2C and 2D was visualized in adult rat brain using the histo-blot technique with newly developed subunit-specific antisera. NR2A immunoreactivity was found in almost all regions of the brain, whereas NR2B staining was restricted to forebrain, and NR2D immunoreactivity to diencephalic, mesencephalic and brain stem structures. NR2C staining was confined to cerebellum, thalamus and olfactory bulb. Thus, NMDA receptors containing the NR2A subunit are likely to represent a receptor subtype predominant throughout the brain, while those containing the NR2B, NR2C or NR2D subunit represent more region-specific receptor subtypes. The regionally overlapping distribution of certain NR2 subunits points to the existence of NMDA receptors containing more than one NR2 subunit variant.
Chlamydia pneumoniae infection in patients with diffuse panbronchiolitis and COPD.

STUDY OBJECTIVES To determine the possible association of Chlamydia pneumoniae infection with diffuse panbronchiolitis (DPB) and with COPD. DESIGN Prospective case-control study. SETTING Division of Respiratory Diseases, Kawasaki Medical School Hospital. PARTICIPANTS Fifteen DPB and 77 COPD patients who had acute exacerbations of respiratory conditions and 35 and 120 control subjects, respectively, matched for age, sex, and smoking status. MEASUREMENTS AND RESULTS Nasopharyngeal swabs and paired serum samples were obtained from all patients and control subjects for isolation and antibody testing of C pneumoniae. C pneumoniae was isolated from one DPB patient and from no COPD patients or control subjects. Serologic evidence of acute C pneumoniae infection was observed in one DPB patient (6.7%) and six COPD patients (7.8%). The prevalence and mean titer of C pneumoniae IgG and IgA antibodies were significantly higher in COPD patients than in control subjects (p<0.001). However, no such differences were observed between DPB patients and control subjects. CONCLUSIONS This study showed that C pneumoniae infection may be associated with acute exacerbations of COPD and that chronic C pneumoniae infection is common in COPD but not in DPB.
Treatment of latent tuberculosis infection in HIV infected persons.

BACKGROUND Individuals with HIV infection are at an increased risk of developing active tuberculosis. It is known that treatment of latent tuberculosis infection (LTBI), also referred to as preventive therapy or chemoprophylaxis, helps to prevent progression to active disease in human immunodeficiency virus (HIV) negative populations. However, the extent and magnitude of protection (if any) associated with preventive therapy in those infected with HIV should be quantified. OBJECTIVES To determine the effectiveness of tuberculosis preventive therapy in reducing the risk of active tuberculosis and death in persons infected with HIV. SEARCH STRATEGY We searched the Cochrane Controlled Trials Register (CCTR), MEDLINE, EMBASE, AIDSLINE, AIDSTRIALS and AIDSDRUGS. We also scanned reference lists of articles and contacted authors and other researchers in the field. SELECTION CRITERIA We included studies in which HIV positive individuals were randomly allocated to preventive therapy for TB and placebo, or to alternative TB preventive therapy regimens. Participants could be tuberculin skin test positive or negative, but without active tuberculosis. DATA COLLECTION AND ANALYSIS Two reviewers independently applied study selection criteria, assessed study quality and extracted data. Effects were assessed using relative risk for dichotomous data and weighted mean difference for continuous data. MAIN RESULTS 11 trials were included with a total of 8,130 randomized participants. Preventive therapy (any anti-TB drug) versus placebo was associated with a lower incidence of active tuberculosis (RR 0.64, 95% CI 0.51 to 0.81). This benefit was more pronounced in individuals with a positive tuberculin skin test (RR 0.38, 95% CI 0.25 to 0.57) than in those who had a negative test (RR 0.83, 95% CI 0.58 to 1.18.). Limited data suggest that the initial protective effect against tuberculosis may decline over the short to medium term. Efficacy was similar for all regimens (regardless of drug type, frequency or duration of treatment). However, compared to INH monotherapy, short -course multi-drug regimens were much more likely to require discontinuation of treatment due to adverse effects. Overall, there was no evidence that preventive therapy versus placebo reduced all-cause mortality (RR 0.95, 95% CI 0.85 to 1.06), although a favourable trend was found in people with a positive tuberculin test (RR 0.80, 95% CI 0.63 to 1.02). REVIEWER'S CONCLUSIONS Treatment of latent tuberculosis infection (LTBI) reduces the risk of active tuberculosis in HIV positive individuals with a positive tuberculin skin test. The choice of regimen will depend on factors such as cost, adverse effects, adherence and drug resistance. Future studies should assess these aspects. In addition, trials evaluating the long-term effects of anti-tuberculosis chemoprophylaxis and the influence of level of immunocompromise on effectiveness are needed.
Reproducibility of Renal Function Measurements in Adult Men with Diabetic Nephropathy: Research and Clinical Implications

Background/Aim: Measurement of the renal function is critical to follow progression of kidney disease. Short-term and long-term variabilities in these measurements have significant impacts on clinical decision making and clinical trials. The goal of this study was to describe the variability in these measurements and to calculate minimum sample size estimates over varying time frames for clinical trials. Methods: We studied 44 elderly men with diabetic nephropathy who participated in a clinical trial. Glomerular filtration rate and renal plasma flow were measured by continuous infusion technique with five urine collection periods on two occasions 4 months apart. Protein and creatinine excretion rates were measured in the same specimens. In addition, two consecutive 24-hour specimens every month for 4 months were collected to analyze urine protein, creatinine, urea nitrogen, and electrolytes. A hierarchical random effects model was used to analyze the reproducibility from hour to hour, from day to day, and from month to month. Results: A total of 824 urine specimens were analyzed, of which 412 constituted specimens collected in the short term and 412 were 24-hour urine collections. Hour-to-hour variation accounted for 45% for urinary clearance of iothalamate, but for only 0.5% of the variability in plasma clearance of iothalamate. Day-to-day variability in 24-hour urinary excretion rates for creatinine was 46% and for protein 10%. Month-to-month variability in 24-hour excretion rates for creatinine was 11% and for protein 19%. The urine protein/creatinine ratio had a day-to-day variability of 2% and a month-to-month variability of 19%. Sample size requirements can be reduced by correcting for urine creatinine for some but not all urinary analytes. Conclusions: In nephrotic men with diabetic nephropathy, the coefficient of variation in the month-to-month protein excretion rate is 36%. Approximately 28 patients in each arm of two groups are needed to detect a difference in protein excretion rate of 28% (1 g/day in this study). The coefficient of variation in plasma iothalamate clearance over 4 months is 16%. To detect a 10% change in glomerular filtration rate between two groups, 44 patients per group are needed. To be deemed statistically significant, a change in daily protein excretion rate of at least 72% over month(s) is needed in individual patients.
Analysis of nerve fibers and their distribution in histologic sections of the human brain

The field of quantitative analysis and subsequent mapping of the cerebral cortex has developed rapidly. New powerful tools have been applied to investigate large regions of complex folded gyrencephalic cortices in order to detect structural transition regions that might partition different cortical fields of disjunct neuronal functions. We have developed a new mapping approach based on axoarchitectonics, a method of cortical visualization that previously has been used only indirectly with regard to myeloarchitectonics. Myeloarchitectonic visualization has the disadvantage of producing strong agglomerative effects of closely neighbored nerve fibers. Therefore, single and neurofunctional‐relevant parameters such as axonal branchings, axon areas, and axon numbers have not been determinable with satisfying precision. As a result, different staining techniques had to be explored in order to achieve a suitable histologic staining for axon visualization. The best results were obtained after modifying the Naoumenko‐Feigin staining for axons. From these contrast‐rich stained histologic sections, videomicroscopic digital image tiles were generated and analyzed using a new fiber analysis framework. Finally, the analysis of histologic images provided topologic ordered parameters of axons that were transferred into parameter maps. The axon parameter maps were analyzed further via a recently developed traverse generating algorithm that calculated test lines oriented perpendicular to the cortical surface and white matter border. The gray value coded parameters of the parameter maps were then transferred into profile arrays. These profile arrays were statistically analyzed by a reliable excess mass approach we recently developed. We found that specific axonal parameters are preferentially distributed throughout granular and agranular types of cortex. Furthermore, our new procedure detected transition regions originally defined by changes of cytoarchitectonic layering. Statistically significant inhomogeneities of the distribution of certain axon quantities were shown to indicate a subparcellation of areas 4 and 6. The quantification techniques established here for the analysis of spatial axon distributions within larger regions of the cerebral cortex are suitable to detect inhomogeneities of laminar axon patterns. Hence, these techniques can be recommended for systematic and observer‐supported cortical area mapping and parcellation studies. Microsc. Res. Tech. 63:220–243, 2004. © 2004 Wiley‐Liss, Inc.
Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.).

Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP-based wheat markers have been made available via the use of next-generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial-scale breeding programmes. To identify exome-based co-dominant SNP-based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re-sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co-dominant. Validation of a subset of these putative co-dominant markers confirmed that 96% were true polymorphisms and 65% were co-dominant SNP assays. The new co-dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web-based database to facilitate their use on genotyping programmes worldwide.