gebhart/patrepeval huggingface dataset:
Regulation of intracellular pH (2004)

The approach that most animal cells employ to regulate intracellular pH (pH(i)) is not too different conceptually from the way a sophisticated system might regulate the temperature of a house. Just as the heat capacity (C) of a house minimizes sudden temperature (T) shifts caused by acute cold and heat loads, the buffering power (beta) of a cell minimizes sudden pH(i) shifts caused by acute acid and alkali loads. However, increasing C (or beta) only minimizes T (or pH(i)) changes; it does not eliminate the changes, return T (or pH(i)) to normal, or shift steady-state T (or pH(i)). Whereas a house may have a furnace to raise T, a cell generally has more than one acid-extruding transporter (which exports acid and/or imports alkali) to raise pH(i). Whereas an air conditioner lowers T, a cell generally has more than one acid-loading transporter to lower pH(i). Just as a house might respond to graded decreases (or increases) in T by producing graded increases in heat (or cold) output, cells respond to graded decreases (or increases) in pH(i) with graded increases (or decreases) in acid-extrusion (or acid-loading) rate. Steady-state T (or pH(i)) can change only in response to a change in chronic cold (or acid) loading or chronic heat (or alkali) loading as produced, for example, by a change in environmental T (or pH) or a change in the kinetics of the furnace (or acid extrudes) or air conditioner (or acid loaders). Finally, just as a temperature-control system might benefit from environmental sensors that provide clues about cold and heat loading, at least some cells seem to have extracellular CO(2) or extracellular HCO(3)(-) sensors that modulate acid-base transport.
Burkholderia thailandensis outer membrane vesicles exert antimicrobial activity against drug-resistant and competitor microbial species (2020)

Gram-negative bacteria secrete outer membrane vesicles (OMVs) that play critical roles in intraspecies, interspecies, and bacteria-environment interactions. Some OMVs, such as those produced by Pseudomonas aeruginosa, have previously been shown to possess antimicrobial activity against competitor species. In the current study, we demonstrate that OMVs from Burkholderia thailandensis inhibit the growth of drug-sensitive and drug-resistant bacteria and fungi. We show that a number of antimicrobial compounds, including peptidoglycan hydrolases, 4-hydroxy-3-methyl-2-(2-non-enyl)-quinoline (HMNQ) and long-chain rhamnolipid are present in or tightly associate with B. thailandensis OMVs. Furthermore, we demonstrate that HMNQ and rhamnolipid possess antimicrobial and antibiofilm properties against methicillin-resistant Staphylococcus aureus (MRSA). These findings indicate that B. thailandensis secretes antimicrobial OMVs that may impart a survival advantage by eliminating competition. In addition, bacterial OMVs may represent an untapped resource of novel therapeutics effective against bio-film-forming and multidrug-resistant organisms.
Energetics of Nanoparticle Exsolution from Perovskite Oxides (2018)

The presence of active metal nanoparticles on the surface significantly increases the electrochemical performance of ABO<sub>3</sub> perovskite oxide materials. While conventional deposition methods can improve the activity, in situ exsolution produces nanoparticles with far greater stability. The migration of transition metal atoms toward the surface is expected to affect the exsolution process. To study the energetics, we use ab initio computations combined with experiments in a SrTiO<sub>3</sub>-based model system. Our calculations show that Ni preferentially segregates toward the (100)-oriented and SrTiO-terminated surfaces, note that this orientation is identical to one reported by the Irvine and Gorte groups. Vacancies in the Sr-site and O-site promote the segregation of Ni, while placing La on the Sr-site has an opposite effect. The corresponding experiments are in agreement with the computational predictions. Fast nanoparticle growth and activity enhancement are found in STO system with Sr vacancies and without La. The approach developed in this Letter could be used to study the mechanism of exsolution in other material systems, and possibly lead to the development of new compositions capable of nanoparticle exsolution with higher activity and stability.
Regression-based formulas for predicting change in RBANS subtests with older adults (2004)

Repeated neuropsychological assessments are common with older adults, and the determination of clinically significant change across time is an important issue. Regression-based prediction formulas have been utilized with other patient and healthy control samples to predict follow-up test performance based on initial performance and demographic variables. Comparisons between predicted and observed follow-up performances can assist clinicians in making the determination of change in the individual patient. The current study developed regression-based prediction equations for the twelve subtests of the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS) in a sample of 223 community dwelling older adults. All algorithms included both initial test performances and demographic variables. These algorithms were then validated on a separate elderly sample (n = 222). Minimal differences were present between Observed and Predicted follow-up scores in the Validation sample, suggesting that the prediction formulas would be useful for practitioners who assess older adults. A case example is presented that utilizes the formulas.
Role of root microbiota in plant productivity (2015)

The growing human population requires increasing amounts of food, but modern agriculture has limited possibilities for increasing yields. New crop varieties may be bred to have increased yields and be more resistant to environmental stress and pests. However, they still require fertilization to supplement essential nutrients that are normally limited in the soil. Soil microorganisms present an opportunity to reduce the requirement for inorganic fertilization in agriculture. Microorganisms, due to their enormous genetic pool, are also a potential source of biochemical reactions that recycle essential nutrients for plant growth. Microbes that associate with plants can be considered to be part of the plant's pan-genome. Therefore, it is essential for us to understand microbial community structure and their 'metagenome' and how it is influenced by different soil types and crop varieties. In the future we may be able to modify and better utilize the soil microbiota potential for promoting plant growth.
rBC2LCN, a new probe for live cell imaging of human pluripotent stem cells (2013)

Cell surface biomarkers have been applied to discriminate pluripotent human embryonic stem cells and induced pluripotent stem cells from differentiated cells. Here, we demonstrate that a recombinant lectin probe, rBC2LCN, a new tool for fluorescence-based imaging and flow cytometry analysis of pluripotent stem cells, is an alternative to conventional pluripotent maker antibodies. Live or fixed colonies of both human embryonic stem cells and induced pluripotent stem cells were visualized in culture medium containing fluorescent dye-labeled rBC2LCN. Fluorescent dye-labeled rBC2LCN was also successfully used to separate live pluripotent stem cells from a mixed cell population by flow cytometry.
Improved Consistent Weighted Sampling Revisited (2017)

Min-Hash is a popular technique for efficiently estimating the Jaccard similarity of binary sets. Consistent Weighted Sampling (CWS) generalizes the Min-Hash scheme to sketch weighted sets and has drawn increasing interest from the community. Due to its constant-time complexity independent of the values of the weights, Improved CWS (ICWS) is considered as the state-of-the-art CWS algorithm. In this paper, we revisit ICWS and analyze its underlying mechanism to show that there actually exists dependence between the two components of the hash-code produced by ICWS, which violates the condition of independence. To remedy the problem, we propose an Improved ICWS (I$^2$CWS) algorithm which not only shares the same theoretical computational complexity as ICWS but also abides by the required conditions of the CWS scheme. The experimental results on a number of synthetic data sets and real-world text data sets demonstrate that our I$^2$CWS algorithm can estimate the Jaccard similarity more accurately, and also compete with or outperform the compared methods, including ICWS, in classification and top-$K$ retrieval, after relieving the underlying dependence.
Synthesis and Characterization of Biphenyl-Based Lithium Solvated Electron Solutions (2012)

We report on the electric conductivity measurements and FTIR studies carried out on lithium solvated electron solutions (Li-SES) using biphenyl as the electron receptor and tetrahydrofuran (THF) as the solvent. Conductivity measurements carried out on samples with varying compositions of lithium, biphenyl (β), and THF reveal the highest conductivity of 12.0 mS/cm is achieved with the solution composition Li(1.0)β(THF)(8.2) and a metallic behavior. Characteristic fingerprint peaks attributed to the solvated electron solution appear in the FTIR spectra. Also, from the FTIR spectra, we propose a reaction mechanism of lithium reaction with biphenyl in THF in that Li(1)β(THF)(n1) (1 Li atom pairing with 1 biphenyl molecule) is formed first followed by Li(2)β(THF)(n1) (2 Li atoms pairing with 1 biphenyl molecule). A better understanding of the physical properties of the Li-SES is a prerequisite in view of their optimal applications as liquid anodes in lithium batteries.
Association of p16 Homozygous Deletions with Clinicopathologic Characteristics and EGFR/KRAS/p53 Mutations in Lung Adenocarcinoma (2008)

p16 HDs occur early in the development of lung adenocarcinomas and with similar frequencies among EGFR type, KRAS type, and non-EGFR/KRAS type lung adenocarcinomas. Tobacco carcinogens would not be a major factor inducing p16 HDs in lung adenocarcinoma progression.
Rule-base structure identification in an adaptive-network-based fuzzy inference system (1994)

We summarize Jang's architecture of employing an adaptive network and the Kalman filtering algorithm to identify the system parameters. Given a surface structure, the adaptively adjusted inference system performs well on a number of interpolation problems. We generalize Jang's basic model so that it can be used to solve classification problems by employing parameterized t-norms. We also enhance the model to include weights of importance so that feature selection becomes a component of the modeling scheme. Next, we discuss two ways of identifying system structures based on Jang's architecture: the top-down approach, and the bottom-up approach. We introduce a data structure, called a fuzzy binary boxtree, to organize rules so that the rule base can be matched against input signals with logarithmic efficiency. To preserve the advantage of parallel processing assumed in fuzzy rule-based inference systems, we give a parallel algorithm for pattern matching with a linear speedup. Moreover, as we consider the communication and storage cost of an interpolation model. We propose a rule combination mechanism to build a simplified version of the original rule base according to a given focus set. This scheme can be used in various situations of pattern representation or data compression, such as in image coding or in hierarchical pattern recognition.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Developments in label‐free microfluidic methods for single‐cell analysis and sorting (2018)

Advancements in microfluidic technologies have led to the development of many new tools for both the characterization and sorting of single cells without the need for exogenous labels. Label-free microfluidics reduce the preparation time, reagents needed, and cost of conventional methods based on fluorescent or magnetic labels. Furthermore, these devices enable analysis of cell properties such as mechanical phenotype and dielectric parameters that cannot be characterized with traditional labels. Some of the most promising technologies for current and future development toward label-free, single-cell analysis and sorting include electronic sensors such as Coulter counters and electrical impedance cytometry; deformation analysis using optical traps and deformation cytometry; hydrodynamic sorting such as deterministic lateral displacement, inertial focusing, and microvortex trapping; and acoustic sorting using traveling or standing surface acoustic waves. These label-free microfluidic methods have been used to screen, sort, and analyze cells for a wide range of biomedical and clinical applications, including cell cycle monitoring, rapid complete blood counts, cancer diagnosis, metastatic progression monitoring, HIV and parasite detection, circulating tumor cell isolation, and point-of-care diagnostics. Because of the versatility of label-free methods for characterization and sorting, the low-cost nature of microfluidics, and the rapid prototyping capabilities of modern microfabrication, we expect this class of technology to continue to be an area of high research interest going forward. New developments in this field will contribute to the ongoing paradigm shift in cell analysis and sorting technologies toward label-free microfluidic devices, enabling new capabilities in biomedical research tools as well as clinical diagnostics. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices.
The role of skeletal muscle insulin resistance in the pathogenesis of the metabolic syndrome (2007)

We examined the hypothesis that insulin resistance in skeletal muscle promotes the development of atherogenic dyslipidemia, associated with the metabolic syndrome, by altering the distribution pattern of postprandial energy storage. Following ingestion of two high carbohydrate mixed meals, net muscle glycogen synthesis was reduced by approximately 60% in young, lean, insulin-resistant subjects compared with a similar cohort of age-weight-body mass index-activity-matched, insulin-sensitive, control subjects. In contrast, hepatic de novo lipogenesis and hepatic triglyceride synthesis were both increased by >2-fold in the insulin-resistant subjects. These changes were associated with a 60% increase in plasma triglyceride concentrations and an approximately 20% reduction in plasma high-density lipoprotein concentrations but no differences in plasma concentrations of TNF-alpha, IL-6, adiponectin, resistin, retinol binding protein-4, or intraabdominal fat volume. These data demonstrate that insulin resistance in skeletal muscle, due to decreased muscle glycogen synthesis, can promote atherogenic dyslipidemia by changing the pattern of ingested carbohydrate away from skeletal muscle glycogen synthesis into hepatic de novo lipogenesis, resulting in an increase in plasma triglyceride concentrations and a reduction in plasma high-density lipoprotein concentrations. Furthermore, insulin resistance in these subjects was independent of changes in the plasma concentrations of TNF-alpha, IL-6, high-molecular-weight adiponectin, resistin, retinol binding protein-4, or intraabdominal obesity, suggesting that these factors do not play a primary role in causing insulin resistance in the early stages of the metabolic syndrome.
In vivo imaging of a diabetogenic CD8+ T cell response during type 1 diabetes progression (2008)

Type 1 diabetes is preceded by a long, protracted period of pancreatic islet inflammation by autoreactive lymphocytes. Noninvasive imaging of islet inflammation prior to the onset of hyperglycemia might have diagnostic and therapeutic implications, but this is not currently possible. Here, MRI is used to track, noninvasively, the accumulation diabetogenic CD8+ T-cells during type 1 diabetes progression in nonobese diabetic (NOD) mice. The contrast agent is an MRI probe (MN-NRP-V7) that specifically labels CD8+ T-cells recognizing residues 206-214 of islet-specific glucose-6-phosphatase catalytic subunit related protein (IGRP(206-214)) in the context of the major histocompatibility complex (MHC) class I molecule H-2K(d). This probe consists of superparamagnetic iron oxide nanoparticles (MN) coated with K(d) molecules presenting NRP-V7, a high-avidity mimotope of IGRP(206-214). NOD mice of different ages (5, 8, 15, and 24 weeks) were imaged by MRI before and after a single intravenous injection of MN-NRP-V7 or unmodified MN nanoparticles. MN-NRP-V7 accumulation, as determined by semiquantitative MRI analysis of pancreas-associated T(2) relaxation time, was antigen-specific, age-dependent, and well correlated with the numbers of MN-NRP-V7-labeled CD8+ T-cells recovered from the pancreata of the treated mice. Antigen/MHC-coupled nanoparticles represent a promising new avenue for noninvasive imaging of lymphocyte inflammation in organ-specific autoimmunity and transplantation.
Advances in gene therapies for limb-girdle muscular dystrophies (2014)

Limb-girdle muscular dystrophies (LGMDs) comprise a heterogeneous group of genetically determined disorders in which degeneration of the skeletal muscle is prominent. As no efficient pharmacological therapies exist that are able to reverse the course of these diseases, alternative regenerative therapies based on cell transfer or gene transfer approaches have been developed. These latter therapies will be the topic of this mini-review. To date, recombinant adeno-associated viral vectors have been reported as the best available gene transfer vectors for gene therapies targeting skeletal muscle tissue, due to their high tropism for this tissue, long-term stability, and low immunogenicity, among other features. However, the fact that these vectors cannot package large gene sizes represents a hurdle for the treatment of LGMDs caused by defects in large genes. Preclinical studies based on the transfer of disease-causing genes or muscle regulator genes that could ameliorate the course of the disease have led to a few clinical trials in which safety and efficacy studies are currently being performed. However, important barriers such as difficulties in delivering the viral vectors through all the affected skeletal muscles, the degenerative stage of the muscle at the time of treatment, and the potential immune response against the protein encoded by the transferred gene need to be overcome in order to maximize the efficacy of the therapies and prevent the development of the diseases.
Decoding the dynamic representation of musical pitch from human brain activity (2018)

In music, the perception of pitch is governed largely by its tonal function given the preceding harmonic structure of the music. While behavioral research has advanced our understanding of the perceptual representation of musical pitch, relatively little is known about its representational structure in the brain. Using Magnetoencephalography (MEG), we recorded evoked neural responses to different tones presented within a tonal context. Multivariate Pattern Analysis (MVPA) was applied to "decode" the stimulus that listeners heard based on the underlying neural activity. We then characterized the structure of the brain's representation using decoding accuracy as a proxy for representational distance, and compared this structure to several well established perceptual and acoustic models. The observed neural representation was best accounted for by a model based on the Standard Tonal Hierarchy, whereby differences in the neural encoding of musical pitches correspond to their differences in perceived stability. By confirming that perceptual differences honor those in the underlying neuronal population coding, our results provide a crucial link in understanding the cognitive foundations of musical pitch across psychological and neural domains.
A modeling study of borehole radar for oilfield applications (2002)

Abstract This paper examines the suitability of borehole radar for near-wellbore imaging. The maximum imaging range is primarily determined by the conductivity of the formation in which the borehole lies and the reflectivity of the targets. Under similar medium contrast, formation interfaces result in much stronger reflections than fractures. Complex horizontal borehole geometries are modeled with a 3-D finite-difference time-domain (FDTD) code. Borehole effects, which are often almost insurmountable for acoustic methods, are very small for radar. As a result, the reflections in general are visually identifiable on the synthetic radar waveforms even before any signal processing. Therefore, borehole radar is a promising approach to map structures in the immediate vicinity of the borehole for a penetration depth of at least a few meters in relatively less-conductive reservoirs (e.g., &lt; 0.03 S/m). As such, it complements borehole acoustic methods and has potential for geosteering applications.
Ethical principles in practice. Evidence from participatory action research. (2008)

A significant challenge for all participants in the autism spectrum disorder participatory action research (AD PAR) project, including the Ministry of Education, the local project teams (LPT) and mentors, was the lack of availability of a single ethics approval process for the project in its entirety and, in particular, one that could accommodate the iterative, dynamic and participant-led action research process. To address this gap, participants in the AD PAR project adoptedanswer that could be routinely applied to ethical dilemmas. A guiding framework of ethical principles proved useful for participants. Central to the success of the AD PAR project was participants' ability to self-reflect, question and share resolutions. In essence, reflections on ethical dilemmas as they arose were an interwoven strand through the life cyclesof the ASD PAR project.
Use of hormones in doping and cancer risk. (2020)

Hormones with anabolic properties such as growth hormone (GH) and insulin-like growth factor-1 (IGF-1) are commonly abused among professional and recreational athletes to enhance physical ability. Despite their adverse effects are well-documented, the use of GH and IGF-1 has recently grown. This article highlights the anabolic activity related to mechanisms of cancer development and progression. GH/IGF-1 axis is able to activate cellular mechanisms that modulate every key stage of cancer formation and progression, such as inhibition of apoptosis, resistance to treatments, and induction of angiogenesis, metastatic process and cell proliferation. Results from pre-clinical studies and epidemiological observations in patients with an excess of GH and IGF-1 production or treated with these hormones showed a positive association with the risk to develop several types of cancer. In conclusion, athletes should be made aware that long-term treatment with doping agents might increase the risk of developing cancer, especially if associated with other licit or illicit drugs and/or high-protein diet.