Miracle-dz/UniFAR-FTUs huggingface dataset:
Performance of the Karius Plasma Next Generation Sequencing Test in Determining the Etiologic Diagnosis of Febrile Neutropenia: Results from a Pilot Study

Abstract Background Blood cultures (BC) fail to detect a pathogen in most patients with neutropenic fever (NF). We examined the performance of the Karius next generation sequencing plasma test (plasma NGS) compared with that of BC in chemotherapy-induced NF. Methods Patients 18 years or older with absolute neutrophil count <500 cells/mm3 anticipated for > 7 days were enrolled at the time of BC collection (T0) due to fever. Plasma samples were collected at T0 and twice weekly until neutrophil recovery or discharge. Samples were shipped to the Karius CLIA/CAP laboratory (Redwood City, CA) where cell-free plasma was prepared, DNA extracted, and NGS performed. After removing human reads, remaining sequences were aligned to a curated pathogen database. Organisms present at a significance- level above a predefined threshold were reported. T0 BC and plasma NGS results were compared, excluding organisms (eg, viruses) not recoverable by BC. Positive agreement was defined as plasma NGS identification of at least one isolate seen on BC. Plasma NGS+/BC- results underwent adjudication by 3 infectious diseases specialists. Diagnosis was Definite if microbiology confirmed NGS result within 7 days of enrollment; Probable if clinical, radiologic, and laboratory data were compatible with plasma NGS test result; and otherwise Indeterminate. Results The first 18 patients were evaluated. At the time of enrollment, 6 patients were on antibiotics and 3 were on antifungals. There were 4 positive BC (each monomicrobial) at T0 and all were concordant with plasma NGS. The plasma NGS test identified additional organisms in 2 of the BC+ patients with surgical abdomen. Compared with BC, plasma NGS positive agreement was 100% (4/4) with lack of agreement in 43% (6/14). All 8 NGS+/BC- cases were deemed Probable by adjudication. These included patients with single or mixed organisms in patients with enterocolitis or severe mucositis. In one sample, Aspergillus fumigatus was detected in a patient with new lung nodules. Conclusion The etiologic diagnosis of NF is frequently unknown, leading to broad antibiotics and sometimes delay of targeted treatment. Plasma NGS may provide useful data for managing NF given its ability to detect a breadth of pathogens even when patients are pretreated with antibiotics. Disclosures H. Seng, Karius, Inc: Employee, Salary; D. Hollemon, Karius, Inc: Employee, Salary; D. Hong, Karius, Inc.: Collaborator, Research support and Salary T. A. Blawkamp, Karius Inc.: Board Member and Employee, Salary; M. Kertesz, Karius Inc.: Board Member and Employee, Salary
Nutrigenomics: The Impact of Biomics Technology on Nutrition Research

The interaction between the human body and nutrition is an extremely complex process involving multi-organ physiology with molecular mechanisms on all levels of regulation (genes, gene expression, proteins, metabolites). Only with the recent technology push have nutritional scientists been able to address this complexity. Both the challenges and promises that are offered by the merge of ‘biomics’ technologies and mechanistic nutrition research are huge, but will eventually evolve in a new nutrition research concept: nutritional systems biology. This review describes the principles and technologies involved in this merge. Using nutrition research examples, including gene expression modulation by carbohydrates and fatty acids, this review discusses applications as well as limitations of genomics, transcriptomics, proteomics, metabolomics, and systems biology. Furthermore, reference is made to gene polymorphisms that underlie individual differences in nutrient utilization, resulting in, e.g., different susceptibility to develop obesity.
Model characterization and performance evaluation of GaN FET in DC-DC POL regulators

An accurate circuit and device model is a valuable tool for developing new topologies, building successful designs, and shortening time to market. The input, output, and reverse transfer capacitance of power MOSFET are of vital importance to the MOSFET as they determine the dynamic behavior of the device during switching transients. In this study, the static characteristics of a specific GaN device have firstly been modeled using Synopsys Saber Power MOSFET Tool to get basic device performance including dc characteristics and ac characteristics. By comparison of simulated static and dynamic characteristics to manufacture's datasheet, good agreements were obtained between the device model and experimental result. Approaches to improve the model have been investigated and limitations of the model have been discussed. Then the model is applied and validated in a 24 W 8-24 V/1.2 V dc-dc point-of-load (POL) power converter. For comparison, simulation and experimental results are also presented for the power converter based on GaN FETs. A good agreement between the measured and simulated data can be seen.
Optimization Study of Coumarin 7-Hydroxylase Enzyme Activity in Mouse Brain and Liver

In this study, the optimum conditions (pH, amount of protein, substrate concentration, incubation time) of a cytochrome P450 dependent enzyme, coumarin 7-hydroxylase (COH), activity were determined in microsomal fractions of mouse liver and brain. It’s indicated that different reaction conditions are required for this enzyme activity in mouse liver and brain microsomes. The results obtained, reveal the requirement of optimization studies on COH activity for different tissues of mouse.
Caffeine activates mouse TRPA1 channels but suppresses human TRPA1 channels

Caffeine has various well-characterized pharmacological effects, but in mammals there are no known plasma membrane receptors or ion channels activated by caffeine. We observed that caffeine activates mouse transient receptor potential A1 (TRPA1) in heterologous expression systems by Cai2+ imaging and electrophysiological analyses. These responses to caffeine were confirmed in acutely dissociated dorsal root ganglion sensory neurons from WT mice, which are known to express TRPA1, but were not seen in neurons from TRPA1 KO mice. Expression of TRPA1 was detected immunohistochemically in nerve fibers and bundles in the mouse tongue. Moreover, WT mice, but not KO mice, showed a remarkable aversion to caffeine-containing water. These results demonstrate that mouse TRPA1 channels expressed in sensory neurons cause an aversion to drinking caffeine-containing water, suggesting they mediate the perception of caffeine. Finally, we observed that caffeine does not activate human TRPA1; instead, it suppresses its activity.
Evaluación del estado de salud bucodental y su relación con estilos de vida saludables en la provincia de Salamanca

La caries es un importante problema de salud publica. El objetivo del estudio fue evaluar el estado de salud oral, objetiva y percibida, de la poblacion atendida en el Centro de Salud Sisinio de Castro de la provincia de Salamanca, asi como su relacion con los estilos de vida saludables y su influencia en la calidad de vida de los pacientes.Se realizo un estudio descriptivo transversal en una muestra de 518 pacientes (261 ninos y 257 adultos). Las fuentes de informacion fueron: 1) Cuestionario en el que se recogia informacion sobre los estilos de vida y la influencia de la salud oral sobre la calidad de vida; 2) La exploracion fisica objetiva para conocer la presencia de patologia.En adultos observamos un indice CAOD de 11,98 y un indice de restauracion del 17%. La caries fue mayor en varones que han fumado alguna vez y en consumidores de alcohol; en las mujeres fue mayor en las sedentarias, no consumen pescado o consumen diariamente cereales y bebidas refrescantes. En general, los pacientes con patologia oral consideran buena su salud general, ven alterada el poder sonreir, y estan insatisfechos con su estetica.En la poblacion infantil el indice CAOD global fue de 1,55. y el indice co de 0,52, a los 5-6 anos, y de 2,32, a los 12 anos. La patologia oral guarda relacion con el nivel de estudios, el consumo de leche, pescado y verduras, el consumo de pasteleria y la realizacion de programas de fluor.Conclusion: La caries sigue siendo un problema importante relacionado con factores de riesgo determinantes de la salud general que repercute sobre la calidad de vida de los pacientes. Es necesario establecer sistemas de vigilancia de estos factores que permitan planificar programas de prevencion y control.
The dimensions of the Sense Machine do not work with feature norms. Sense Machine leads to a unitary system that identifies human behavior as special complexes of instinctual

A major field of application of linguistic texts is to reflect the ordinary activities of life as well as the interpersonal relationships of people. Previous approaches of cognitive science have still not achieved a successful breakthrough. Until now the human factor has been neglected in the process. For the semantic grasp of such natural language texts a new system called Sense Machine is presented here. This system uses a psychologically based method to dismantle terms in a fashion similar to nuclear physics that dismantles an atom. The components of dismantling consist of psychological Basic Activity Elements. They build a unitary Code of Behaviors through a variety of combinations. A special Code variety corresponds to a special behavior. This Code gives the computer, the topic and the motivation of human behavior without text corpora in real time during a dialog. Longer texts can be psychologically evaluated.
Preferential attachment with power law growth in the number of new edges

The Barabasi-Albert model is used to explain the formation of power laws in the degree distributions of networks. The model assumes that the principle of preferential attachment underlies the growth of networks, that is, new nodes connects to a fixed number of nodes with a probability that is proportional to their degrees. Yet, for empirical networks the number of new edges is often not constant, but varies as more nodes become part of the network. This paper considers an extension to the original Barabasi-Albert model, in which the number of edges established by a new node follows a power law distribution with support in the total number of nodes. While most new nodes connect to a few nodes, some new nodes connect to a larger number. We first characterize the dynamics of growth of the degree of the nodes. Second, we identify sufficient conditions under which the expected value of the average degree of the network is asymptotically stable. Finally, we show how the dynamics of the model resemble the evolution of protein interaction networks, Twitter, and Facebook.
Polymeric micelles for oral drug administration enabling locoregional and systemic treatments

Introduction: Amphiphilic block copolymers are recognized components of parenteral drug nanocarriers. However, their performance in oral administration has barely been evaluated to any great extent. Areas covered: This review provides an overview of the methods used to prepare drug-loaded polymeric micelles and to evaluate their stability in gastrointestinal (GI) fluids, and then analyzes in detail recent in vitro and in vivo results about their performance in oral drug delivery. Oral administration of polymeric micelles has been tested for a variety of therapeutic purposes, namely, to increase apparent drug solubility in the GI fluids and facilitate absorption, to penetrate in pathological regions of the GI tract for locoregional treatment, to carry the drug directly toward the blood stream minimizing presystemic loses, and to target the drug after oral absorption to specific tissue or cells in the body. Expert opinion: Each therapeutic purpose demands micelles with different performance regarding stability in the GI tract, ability to overcome physiological barriers and drug release patterns. Depending on the block copolymer composition and structure, a wealth of self-assembled micelles with different morphologies and stability can be prepared. Moreover, copolymer unimers can play a role in improving drug absorption through the GI mucosa, either by increasing membrane permeability to the drug and/or the carrier or by inhibiting drug efflux transporters or first-pass metabolism. Therefore, polymeric micelles can be pointed out as versatile vehicles to increase oral bioavailability of drugs that exhibit poor solubility or permeability and may even be an alternative to parenteral carriers when targeting is pursued.
Application of multiplanar ligamentotaxis to external fixation of distal radius fractures.

Distal Radius Fractures Of all fractures that can occur in the hand and wrist, those of the distal radius have the greatest potential to impair function. Fractures of the distal radius are most frequently generated by the high-energy impact to the outstretched hand as a result of a fall. Numerous classification systems for distal radius fractures have been devised14,18,19'26'30'31'33'37-39'41. As first described by Colles13, these extra-articular fractures of the distal radial metaphysis are associated with dorsal displacement of the distal fragment. In many of these fractures, the dorsal cortex and distal fragment are comminuted. Frequently, serious disruption of the distal radial articulations occurs and malalignment of the distal radioulnar joint may result from fracture displacement34. Anatomic reduction of comminuted fractures of the distal radius is often a challenge, as these inherently unstable fractures are prone to collapse and displacement14,22,24,55
Only a Small Subset of the Horizontally Transferred Chromosomal Genes in Escherichia coli Are Translated into Proteins*S

Horizontally transferred genes are believed to play a critical role in the divergence of bacterial strains from a common ancestor, but whether all of these genes express functional proteins in the cell remains unknown. Here, we used an integrated LC-based protein identification technology to analyze the proteome of Escherichia coli strain K12 (JM109) and identified 1,480 expressed proteins, which are equivalent to ∼35% of the total open reading frames predicted in the genome. This subset contained proteins with cellular abundance of several dozens to hundreds of thousands of copies, and included nearly all types of proteins in terms of chemical characteristics, subcellular distribution, and function. Interestingly, the subset also contained 138 of 164 gene products that are currently known to be essential for bacterial viability (84% coverage). However, the subset contained only a very small population (10%) of protein products from genes mapped within K-loops, which are “hot spots” for the integration of foreign DNAs within the K12 genome. On the other hand, these genes in K-loops appeared to be transcribed to RNAs almost as efficiently as the native genes in the bacterial cell as monitored by DNA microarray analysis, raising the possibility that most of the recently acquired foreign genes are inadequate for the translational machinery for the native genes and do not generate functional proteins within the cell.
Dynamical Analysis of bantam-Regulated Drosophila Circadian Rhythm Model

MicroRNAs (miRNAs) interact with 3′untranslated region (UTR) elements of target genes to regulate mRNA stability or translation, and play a crucial role in regulating many different biological processes. bantam, a conserved miRNA, is involved in several functions, such as regulating Drosophila growth and circadian rhythm. Recently, it has been discovered that bantam plays a crucial role in the core circadian pacemaker. In this paper, based on experimental observations, a detailed dynamical model of bantam-regulated circadian clock system is developed to show the post-transcriptional behaviors in the modulation of Drosophila circadian rhythm, in which the regulation of bantam is incorporated into a classical model. The dynamical behaviors of the model are consistent with the experimental observations, which shows that bantam is an important regulator of Drosophila circadian rhythm. The sensitivity analysis of parameters demonstrates that with the regulation of bantam the system is more sensitive to perturbations, indicating that bantam regulation makes it easier for the organism to modulate its period against the environmental perturbations. The effectiveness in rescuing locomotor activity rhythms of mutated flies shows that bantam is necessary for strong and sustained rhythms. In addition, the biological mechanisms of bantam regulation are analyzed, which may help us more clearly understand Drosophila circadian rhythm regulated by other miRNAs.
Estimation of Inequality Indices Based on Ranked Set Sampling

Measuring the income inequality is a major concern of the economists. Therefore, numerous indices have been devised to show different features of the income inequality. In general, the simple random sampling procedure is commonly utilized to estimate the inequality measures, while the ranked set sampling is a more cost saving method which increases the precision and the efficiency of the inequality estimators. In this paper the advantages of the ranked set sampling when measuring the amount of the income inequality are examined. Through using Monte Carlo simulation technique, this paper proves that the ranked set sampling, increases the precision of inequality indices estimations. In the end, a real income data set is analyzed to illustrate the obtained results.
Induction of a Striking Systemic Cytokine Cascade prior to Peak Viremia in Acute Human Immunodeficiency Virus Type 1 Infection, in Contrast to More Modest and Delayed Responses in Acute Hepatitis B and C Virus Infections

ABSTRACT Characterization of the immune responses induced in the initial stages of human immunodeficiency virus type 1 (HIV-1) infection is of critical importance for an understanding of early viral pathogenesis and prophylactic vaccine design. Here, we used sequential plasma samples collected during the eclipse and exponential viral expansion phases from subjects acquiring HIV-1 (or, for comparison, hepatitis B virus [HBV]or hepatitis C virus [HCV]) to determine the nature and kinetics of the earliest systemic elevations in cytokine and chemokine levels in each infection. Plasma viremia was quantitated over time, and levels of 30 cytokines and chemokines were measured using Luminex-based multiplex assays and enzyme-linked immunosorbent assays. The increase in plasma viremia in acute HIV-1 infection was found to be associated with elevations in plasma levels of multiple cytokines and chemokines, including rapid and transient elevations in alpha interferon (IFN-α) and interleukin-15 (IL-15) levels; a large increase in inducible protein 10 (IP-10) levels; rapid and more-sustained increases in tumor necrosis factor alpha and monocyte chemotactic protein 1 levels; more slowly initiated elevations in levels of additional proinflammatory factors including IL-6, IL-8, IL-18, and IFN-γ; and a late-peaking increase in levels of the immunoregulatory cytokine IL-10. Notably, there was comparatively little perturbation in plasma cytokine levels during the same phase of HBV infection and a delayed response of more intermediate magnitude in acute HCV infection, indicating that the rapid activation of a striking systemic cytokine cascade is not a prerequisite for viral clearance (which occurs in a majority of HBV-infected individuals). The intense early cytokine storm in acute HIV-1 infection may have immunopathological consequences, promoting immune activation, viral replication, and CD4+ T-cell loss.
Use of vibrational angioplasty for the treatment of chronic total coronary occlusions: Preliminary results

The aim of the study was to investigate the feasibility and clinical safety of vibrational angioplasty in the treatment of chronic total coronary occlusions and evaluate the clinical and angiographic factors that are predictive of the procedural success and complications of the procedure. Seventy‐eight patients with chronic total occlusions (>3 months) resistant to conventional techniques were treated by vibrational angioplasty using a variety of conventional guidewires. Lesions were successfully crossed in 67 (85.9%) cases and antegrade flow was achieved in 59 (75.5%). Major complications (myocardial infarction and tamponade) occurred in two (2.5%) patients, but no fatalities ensued. Angiographically detectable dissections were seen in 23 (29.5%) patients but only resulted in vessel compromise and reclosure in 5 cases. Multiple stepwise logistic regression analysis identified the duration (<6 months, P = 0.008) and the length of the occlusion (<15 mm, P = 0.03) as independent predictors of final success and the age of the patient (<55 years, P = 0.006) as the only independent predictor of procedural complications. Vibrational angioplasty is a safe technique useful in the treatment of chronic coronary occlusive disease. Patients in whom the procedure is likely to prove most successful may be easily identified by clinical and angiographic features (duration and length of occlusion). Cathet. Cardiovasc. Intervent. 46:98–104, 1999. © 1999 Wiley‐Liss, Inc.
Nutritional and antinutritional levels of some local vegetables from Delta State, Nigeria

Levels of nutritional and antinutritional factors of five leafy edible green vegetables from Delta State, Nigeria were studied. These vegetables are consumed generally in this area and recently, Jatropha Curcus was added to the list of common vegetables. Analyses were done using standard analytical methods. Crude protein, crude lipid, carbohydrate, moisture, ash, crude fiber and colorific values, had values of 6.16±0.22-6.72±0.15, 4.20±0.15-4.80±0.18, 2.96±0.16-3.96±0.22, 78.78±1.42-81.77±1.45, 1.52±0.04-2.00±0.03, 1.60±0.02-4.50±0.14% and 78.92±1.55 to 83.84±1.87Kcal/100 g, respectively. The mineral contents were; sodium 4.44±0.22-5.24±0.21 ug/g, calcium 1.07±0.22-4.82±0.14, potassium 0.97±0.06-0.98±0.05, magnesium 1.45±0.15, -1.95±0.16 ug/g, iron 0.09±0.01-0.61±0.02 ug/g, zinc ND-0.09±0.002 ug/g, phosphorus 0.89±0.05-2.82±0.07 ug/g and copper ND-0.24±0.01 ug/g. The antinutrient compositions were oxalate 0.88±0.12-2.20±0.25 ug/g, phytate 6.89±0.25-13.00±0.45 ug/g and hydrocyanide 0.13±0.04-0.23±0.01 ug/g. These results showed that these vegetables contained an appreciable amount of nutrients, mineral elements and low levels of anti-nutrients and could be included in diets to supplement our daily allowance needed by the body. Key words: Local vegetables, minerals, nutrients, antinutritional.