gebhart/patrepeval huggingface dataset:
GeneAlign: a coding exon prediction tool based on phylogenetical comparisons (2006)

GeneAlign is a coding exon prediction tool for predicting protein coding genes by measuring the homologies between a sequence of a genome and related sequences, which have been annotated, of other genomes. Identifying protein coding genes is one of most important tasks in newly sequenced genomes. With increasing numbers of gene annotations verified by experiments, it is feasible to identify genes in the newly sequenced genomes by comparing to annotated genes of phylogenetically close organisms. GeneAlign applies CORAL, a heuristic linear time alignment tool, to determine if regions flanked by the candidate signals (initiation codon-GT, AG-GT and AG-STOP codon) are similar to annotated coding exons. Employing the conservation of gene structures and sequence homologies between protein coding regions increases the prediction accuracy. GeneAlign was tested on Projector dataset of 491 human-mouse homologous sequence pairs. At the gene level, both the average sensitivity and the average specificity of GeneAlign are 81%, and they are larger than 96% at the exon level. The rates of missing exons and wrong exons are smaller than 1%. GeneAlign is a free tool available at http://genealign.hccvs.hc.edu.tw.
Pasieka Illness Questionnaire: its value in primary hyperparathyroidism (2004)

The present study supports the use of the Pasieka Illness Questionnaire as a useful method to measure disease-specific symptoms in patients with 1 degrees HPT and is applicable to Australian patients. It also shows, once again, that parathyroid surgery produces a significant improvement in the preoperative symptoms of 1 degrees HPT.
S116015 Development of damage diagnosis of a gear using laser beam : A proposal of a method of estimating the state on a gear tooth surface before damaged (2012)

We developed a new diagnostic method by using laser beam. A tooth surface is irradiated by zonal laser beam from an oblique direction, and then the irradiated laser beam line is shifted along the height of the tooth according to gear rotation. The variation of the voltage proportional to laser reflection between initial and present conditions are compared, and it can be grasped condition on the tooth surface such as initial or abnormal abrasion, pitting, etc. We furthermore developed a method of automatic and remote damage diagnosis on a gear tooth surface according to various gear spec by using the angle-distance relation map which made from pre-measured data of a same material and heat-treating, and taking into account the influence of adjacent teeth. The measured data was agreed well with the predicted data made with this method, therefore we can diagnosis the condition of various products automatically.
Aqueous Processing of Na0.44MnO2 Cathode Material for the Development of Greener Na-Ion Batteries (2017)

The implementation of aqueous electrode processing of cathode materials is a key for the development of greener Na-ion batteries. Herein, the development and optimization of the aqueous electrode processing for the ecofriendly Na<sub>0.44</sub>MnO<sub>2</sub> (NMO) cathode material, employing carboxymethyl cellulose (CMC) as binder, are reported for the first time. The characterization of such an electrode reveals that the performances are strongly affected by the employed electrolyte solution, especially, the sodium salt and the use of electrolyte's additives. In particular, the best results are obtained using the 1 M solution of NaPF<sub>6</sub> in EC/DEC (ethylene carbonate/diethyl carbonate) 3:7 (v/v) + 2 wt % FEC (fluoroethylene carbonate). With this electrolyte, the outstanding capacity of 99.7 mA h g<sup>-1</sup> is delivered by the CMC-NMO cathode after 800 cycles at a 1C charge/discharge rate. On the basis of this excellent long-term performance, a full sodium cell, composed of a CMC-based NMO cathode and hard carbon from biowaste (corn cob), has been assembled and tested. The cell delivers excellent performances in terms of specific capacity, capacity retention, and long-term cycling stability. After 75 cycles at a C/5 rate, the capacity of the NMO in the full-cell approaches 109 mA h g<sup>-1</sup> with a Coulombic efficiency of 99.9%.
Spatial and Temporal Coexistence of Stimulated Scattering Processes under Crossed-Laser-Beam Irradiation (1999)

Spatial and temporal coexistence of ion-acoustic waves (IAW) and electron-plasma waves (EPW), driven, respectively, by stimulated Brillouin and Raman scattering, at significant levels of amplitude, has been observed under the modified conditions of a laser-plasma interaction. The results were obtained using a secondary interaction beam to modify the growth of the instabilities and the multiplexing technique of a streak camera to simultaneously record the temporal and spatial evolution of Thomson-scattered light from both the IAW and the EPW.
Potential of Pseudarthrobacter chlorophenolicus BF2P4-5 as a Biofertilizer for the Growth Promotion of Tomato Plants (2022)

BF2P4-5 was isolated from the rhizosphere soil of tomato plants, and its potential to promote plant growth was investigated in tomato plants. An in vitro test revealed that the strain could fix nitrogen, solubilize phosphate and potassium, and synthesize indole acetic acid. The bacterial strain was identified and characterized as a kind of Pseudarthrobacter chlorophenolicus based on the analysis of culture characteristics, physiological and biochemical characteristics, and 16S rRNA gene sequence (GenBank accession number OP135548.1). pH 7.0, 15% NaCl, and 35 °C temperature were ideal for optimal strain growth under culture conditions. Tomato plants grown on a cocopeat substrate were inoculated with BF2P4-5 suspension (OD600 2.0). Positive control plants were inoculated with Nitrogen Phosphorus Potassium (NPK) fertilizer. This BF2P4-5 strain and NPK treatments were complemented with a negative control, in which only tap water was applied to tomato roots, thus, establishing three distinct treatment modalities with five replications each. Two months of greenhouse trials of inoculated tomato plants improved growth parameters. Interestingly, in most of the growth metrics evaluated, tomato plants treated with strain BF2P4-5 showed little to no variation with NPK fertilizer treatment, including plant height, stem length, girth, leaf number per plant, and chlorophyll content, when compared to uninoculated plants. Furthermore, the conditions for the cocopeat plants, including pH, EC, and moisture, were within acceptable limits. Furthermore, inoculation with BF2P4-5 increased the nitrogen, phosphorus, and potassium content available in the cocopeat medium. The results showed that the strain exhibited traits for the promotion of plant growth and could be deployed as an eco-friendly microbial biofertilizer for tomatoes and probably other essential crops.
Circulating Tumor Cells (CTCs) and Epithelial Mesenchymal Transition (EMT) in Breast Cancer: Describing the Heterogeneity of Microscopic Disease. (2009)

Abstract Background: Circulating tumor cells (CTCs) are an independent predictor of survival in metastatic breast cancer (BC) patients. CTC are readily detected by CellSearch System based on their expression of EpCAM. Epithelial-mesenchymal transition (EMT) gives rise to cells with stem cell-like properties with increased chemotherapy resistance. Human mammary epithelial cells (HMEC) transformed by the EMT transcription factor TWIST1 and spiked into normal peripheral blood (PB) are not detected by EpCAM enrichment based conventional detection methods compared to non-transformed HMECs. We hypothesize that CTCs undergoing EMT and resultant loss of epithelial markers may escape detection by conventional detection methods. The aim of this study was to detect CTCs based on expression of EMT genes in breast cancer patient's peripheral blood.Methods: This prospective ongoing study of breast cancer patients consisted of 16 (57.1%) patients with metastatic disease, 19 (67.9%) patients with inflammatory breast cancer (IBC) and 12 (42.9%) patients with primary, non-IBC breast cancer, respectively. Isolated peripheral blood mononuclear cells (PBMC) were depleted of cells of hematopoietic origin (CD45+) using anti-CD45 coated magnetic beads. RNA extracted from CD45-depleted (CD45-) PBMC were interrogated for expression of TWIST1, SNAIL1, SLUG, ZEB1, FOXC2 and EpCAM gene transcripts by quantitative reverse transcription-PCR. Expressions of gene transcripts in CD45- PBMC from patients were compared to those of CD45- PBMC of healthy donors (HD). Expression of one or more gene transcripts was considered a positive result. Concurrently, a 7.5 mL PB sample was collected for determination of CTC by CellSearch.Results: Median age was 54 year (range: 34-72 years). Overall, the median CTC count by CellSearch was 2 (range; 0-750) per 7.5 mL of PB. TWIST1, SNAIL1, SLUG, ZEB1 and FOXC2 were overexpressed in CD45- PBMC in 7%, 4 %, 4%, 0% and 14 % of patients, respectively. At least one of the EMT genes was overexpressed in 6 (21%) of patients. TWIST1 and SLUG were overexpressed only in IBC patients (10.5% and 5.3% of patients, respectively). Patients with triple negative breast cancer more commonly overexpressed EMT genes compared to non-triple negative patients (30.8% vs. 13.3%). There was no correlation between expression of EMT genes, EpCAM expression or CTC count measured by CellSearch, respectively.Conclusions: These data suggest that EMT genes may be involved in the dissemination of CTCs. Loss of epithelial antigen on CTC due to EMT, triggered by high expression of these genes, may be responsible for their undetection by conventional methods in a fraction of patients with early or advanced breast cancer. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 3011.
Platform for Model-Based Design and Testing for Deep Brain Stimulation (2018)

Deep Brain Stimulation (DBS) is effective at alleviating symptoms of neurological disorders such as Parkinson's disease. Yet, despite its safety-critical nature, there does not exist a platform for integrated design and testing of new algorithms or devices. Consequently, we introduce a model-based design framework for DBS controllers based on a physiologically relevant basal-ganglia model (BGM) that we capture as a network of nonlinear hybrid automata, synchronized via neural activation events. The BGM is parametrized by the number of neurons used to model each of the BG regions, which supports tradeoffs between fidelity and complexity of the model. Our hybrid-automata representation is exploited for design of software (Simulink) and hardware (FPGA) BGM platforms, with the latter enabling real-time model simulation and device testing. We demonstrate that the BGM platform is capable of generating physiologically relevant responses to DBS, and validate the BGM using a set of requirements obtained from existing work. We present the use of our framework for design and test of DBS controllers with varying levels of adaptation/feedback. Our evaluations are based on Quality-of-Control metrics that we introduce for runtime monitoring of DBS effectiveness.
Permittivity measurement for biological application using micromachined probe (2005)

We implemented a micromachined probe for the measurement of biological properties using MEMS technology. We experimentally showed the suitability of the micromachined probe in biological applications through liquids and solid experiments. The micromachined probe consists of a CPW and strip line between benzo cyclo butene (BCB) layers because it has excellent properties such as high resistivity, low loss tangent and low permittivity at higher frequencies. The aperture size of the micromachined probe is only 650 /spl mu/m /spl times/ 70 /spl mu/m. We measured the permittivity of a number of well- known liquids - 0.5, 0.9 and 1.3 % saline, acetone, and muscle and fat of pork - as biological samples using the micromachined probe after liquid calibration. In this paper, we first demonstrate that the micromachined probe can provide broadband measurement of measurable solid materials, such as biological samples, and also of well-known liquids at microwave frequencies.
Hand Motion Tracking using MDPF Method (2006)

Hand motion tracking is a challenging problem due to the complexity of searching in a high dimensional configuration space for an optimal estimate. This paper represents the hand feasible configurations as a discrete space, which avoids learning to find parameters as general configuration space representations do, meanwhile, it arrange the discrete data on the KD-tree which supports fast nearest neighbor retrieval and it is easy to be modified when new samples are embedded. To track hand motion efficiently, this paper presents a MDPF (Multi-Directional search with Particle Filter) algorithm, in which a 'global' optimization and a 'local' optimization are combined to obtain the best matching configuration. The 'local' method, which is designed to run in multiple processors, could choose more representative samples for global efficiently, and the global method guards the tracking process towards a global minimum. The Experiment results show that this approach is robust and efficient for tracking 3D hand motion.
A Soft Sensorized Microfluidic Tubular Actuating Gripper (2020)

Abstract One of the key challenges in soft robotics today is in providing sensory feedback of an object to a gripper. In this work, a soft microtubular actuator which can not only interact but also sense its environment is reported. As the sensor is enclosed within the same structure as the actuator, the sensor is able to conform well to the whole range of actuating motion and is able to provide accurate sensor readings. As a proof of concept, the sensorized microtubular actuator is deployed as a microgripper. The microgripper demonstrates the ability to grip a variety of objects, including an ant, without damaging it. While similar grippers with integrated sensing elements do exist, the grippers produced in this work have a maximum diameter of 2 mm, which translate to a tenfold reduction in size over the state of the art. This allows the microgripper to conduct in situ monitoring of strain levels or establish if contact with an object has been made. The sensor experiences minimal electrical drift and hysteresis despite repeated loading cycles (1000 cycles). Taken together, these advantages demonstrate the potential of the microgripper for a variety of applications, especially in soft medical robotics.
Response of normal human keratinocytes to sulfur mustard: cytokine release†‡ (2001)

Cytokines play a major role in both acute and chronic inflammatory processes, including those produced by sulfur mustard (2,2'-dichlorodiethyl sulfide, HD). This study describes responses of normal human epidermal keratinocytes (NHEK) to HD, defined by interleukin-1beta (IL-1beta), IL-6, IL-8 and tumor necrosis factor alpha (TNF-alpha) release. Commercially available enzyme-linked immunosorbent assay (ELISA) kits were used to measure the cytokine release in NHEK during exposure to 100 and 300 microM of HD. Exposure to 100 microM HD increased the release of cytokines. The amounts of IL-8 and TNF-alpha present in cell suspensions increased up to 59-fold and 4-fold, respectively, above control levels when NHEK were exposed to 300 microM HD. Exposure of NHEK to 300 microM HD had a highly variable effect on the release of IL-1beta, where sometimes the secretion of IL-1beta increased above baseline level and at other times it decreased in cell suspensions. Supernatants were collected from cell culture flasks 24 h after exposure of 100 and 300 microM HD and significantly increased levels of IL-6 were observed. Interleukin-6 was released in a concentration-dependent manner, 3.6-fold up to 8.4-fold, respectively, in supernatant. These pro-inflammatory mediators IL-1beta, IL-8, TNF-alpha and IL-6 may play an important role in HD injury. The present findings suggest that the cytokine changes detected could be used as potential biomarkers of cutaneous vesicant injury.
Utility of DNA Repair Protein Foci for the Detection of Putative BRCA1 Pathway Defects in Breast Cancer Biopsies (2009)

The DNA damage response pathway controlled by the breast cancer and Fanconi anemia (FA) genes can be disrupted by genetic or epigenetic mechanisms in breast cancer. Defects in this pathway may render the affected tumors hypersensitive to DNA-damaging agents. The identification of these defects poses a challenge because of the large number of genes involved in the FA/BRCA pathway. Many pathway components form subnuclear repair protein foci upon exposure to ionizing radiation in vitro, but it was unknown whether foci can be detected in live cancer tissues. Thus, the goal of this pilot study was to identify pathway defects by using a novel ex vivo foci biomarker assay on tumor biopsies. Fresh pretreatment biopsy specimens from patients with locally advanced sporadic breast cancer were irradiated or mock-treated in the laboratory (ex vivo). Foci formation of DNA repair proteins BRCA1, FANCD2, and RAD51 was detected by immunofluorescence microscopy. Three out of seven tumors showed intact radiation-induced foci formation, whereas the other four tumors exhibited a defective foci response. Notably, three of the foci-defective tumors were estrogen receptor/progesterone receptor/HER2-negative (triple-negative), a phenotype that has been associated with BRCA1 deficiency. In conclusion, in this pilot study, we report the successful detection of BRCA1, FANCD2, and RAD51 foci in breast cancer biopsies irradiated ex vivo. Our approach represents a potentially powerful biomarker assay for the detection of pre-existing and functionally important defects within the complex FA/BRCA pathway, which may ultimately allow us to tailor cancer treatment to the DNA repair profile of individual tumors.
RHCE*ceTI encodes partial c and partial e and is often in cis to RHD*DIVa (2012)

RHD*DIVa and RHCE*ceTI almost always, but not invariably, travel together. This haplotype is found in people of African ancestry and the RBCs can demonstrate aberrant reactivity with anti-C. RHCE*ceTI encodes partial c and e antigens. We confirm that RHD zygosity assays are unreliable in samples with RHD*DIVa.
Mechanism of Action of Acamprosate. Part I. Characterization of Spermidine‐Sensitive Acamprosate Binding Site in Rat Brain (1998)

It has been suggested that the anticraving drug, acamprosate, acts via the glutamatergic system, but the exact mechanism of action is still unknown. The aim of this study was to characterize [3H]acamprosate binding and establish whether this showed any relation to sites on the NMDA receptor complex. We found saturable specific binding of [3H]acamprosate to rat brain membranes with a KD of 120 microM and a Bmax of 450 pmol/mg of protein. This acamprosate binding site was sensitive to inhibition by spermidine (IC50: 13.32 +/- 1.1 microM; Hill coefficient = 1.04), and arcaine and glutamate both potentiated the inhibitory effect of spermidine. Acamprosate binding to the acamprosate binding site was also sensitive to inhibition by divalent cations (Ca2+, Mg2+, and Sr2+). Conversely, acamprosate displaced [14C]spermidine binding from rat brain membranes with an IC50 of 645 microM and a Hill coefficient = 1.74. This inhibitory effect of acamprosate was not affected by arcaine, and was associated with a significant reduction in Bmax and binding affinity for spermidine, suggesting an allosteric interaction between acamprosate and a spermidine binding site. These data are consistent with an effect of acamprosate on the NMDA receptor protein complex, and acamprosate was also found to alter binding of [3H]dizocilpine to rat brain membranes. When no agonists were present in vitro (minimal NMDA receptor activation), acamprosate markedly potentiated [3H]dizocilpine binding at concentrations in the 5 to 200 microM range. However, under conditions of maximal receptor activation (100 microM glutamate, 30 microM glycine), acamprosate only inhibited [3H]dizocilpine binding (at concentrations concentrations >100 microM). When these binding studies were performed in the presence of 1 microM spermidine, the enhancing effects of acamprosate on [3H]dizocilpine binding were inhibited. The results show that acamprosate binds to a specific spermidine-sensitive site that modulates the NMDA receptor in a complex way. Together, with data from al Quatari et al. (see next paper), this work suggests that acamprosate acts as "partial co-agonist" at the NMDA receptor, so that low concentrations enhance activation when receptor activity is low, whereas higher concentrations are inhibitory to high levels of receptor activation. This may be relevant to the clinical effects of acamprosate in alcohol-dependent patients during abstinence.
High-Voltage Biomolecular Sensing Using a Bacteriophage Portal Protein Covalently Immobilized Within a Solid-State Nanopore (2022)

Abstract The application of nanopores as label-free, single-molecule biosensors for electrical or optical probing of structural features in biomolecules has been widely explored. While biological nanopores (membrane proteins and bacteriophage portal proteins) and solid-state nanopores (thin films and two-dimensional materials) have been extensively employed, the third class of nanopores known as hybrid nanopores, where an artificial membrane substitutes the organic support membrane of proteins, has been only sparsely studied, due to challenges in implementation. G20c portal protein contains a natural DNA pore that is used by viruses for filling their capsid with viral genomic DNA. We have previously developed a lipid-free hybrid nanopore by “corking” the G20c portal protein into a SiN x nanopore. Herein, we demonstrate that through chemical functionalization of the synthetic nanopore, covalent linkage between the solid-state pore and the G20c portal protein considerably improves the hybrid pore stability, lifetime, and voltage resilience. Moreover, we demonstrate electric-field-driven and motor protein-mediated transport of DNA molecules through this hybrid pore. Our integrated protein/solid-state hybrid nanopore can serve as a robust and durable framework for sensing and sequencing at high voltages, potentially providing higher resolution, higher signal-to-noise ratio, and higher throughput compared to the more conventional membrane-embedded protein platforms.
Iodine-131-labeled diphosphonates for the palliative treatment of bone metastases: I. Organ distribution and kinetics of I-131 BDP3 in rats. (1984)

I-131-labeled alpha-amino-(4-hydroxybenzylidene)-diphosphonate (BDP3) was examined in Sprague-Dawley rats for its bone affinity and other biokinetical characteristics. Iodine-131 BDP3 exhibited high bone affinity, with rapid blood clearance and renal excretion. Total-body retention measurements revealed an effective half-life of the activity of t1/2 = 169 hr. Similar kinetics were found in rat femurs, with t1/2 = 158 hr. Rats bearing osteosarcomas showed an enhanced uptake with a slower clearance (t1/2 = 177 hr). The amount of I-131 BDP3 excreted in urine agreed with the total body retention values. Fifty percent was excreted in the urine, as unchanged I-131 BDP3, by 24 hr after application. Almost no activity was found in the feces of the rats. LD50 measurements in rats amounted to 64 mg/kg. Because of these biokinetical characteristics and the simple labeling procedure, I-131 BDP3 is suggested as a radiopharmaceutical for the palliative treatment of pain that often accompanies disseminated bone metastases.