gebhart/patrepeval huggingface dataset:
Plant-fed versus chemicals-fed rhizobacteria of Lucerne: Plant-only teabags culture media not only increase culturability of rhizobacteria but also recover a previously uncultured Lysobacter sp., Novosphingobium sp. and Pedobacter sp. (2017)

In an effort to axenically culture the previously uncultivable populations of the rhizobacteria of Lucerne (Medicago sativa L.), we propose plant-only teabags culture media to mimic the nutritional matrix available in the rhizosphere. Here, we show that culture media prepared from Lucerne powder teabags substantially increased the cultivability of Lucerne rhizobacteria compared with a standard nutrient agar, where we found that the cultivable populations significantly increased by up to 60% of the total bacterial numbers as estimated by Quantitative Real-time Polymerase Chain Reaction (qRT-PCR). Cluster analysis of 16S rDNA Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) of cultivable Colony-Forming Units (CFUs) revealed a more distinct composition and separation of bacterial populations recovered on the plant-only teabags culture media than those developed on a standard nutrient agar. Further, the new plant medium gave preference to the micro-symbiont Sinorhizobium meliloti, and succeeded in isolating a number of not-yet-cultured bacteria, most closely matched to Novosphingobium sp., Lysobacter sp. and Pedobacter sp. The present study may encourage other researchers to consider moving from the well-established standard culture media to the challenging new plant-only culture media. Such a move may reveal previously hidden members of rhizobacteria, and help to further explore their potential environmental impacts.
Proposal of Pseudo Source and Drain MOSFETs for Evaluating 10-nm Gate MOSFETs (1997)

We propose a Pseudo source and drain metal oxide semiconductor field effect transistors (Ps-MOSFET) for investigating the electrical characteristics and physical phenomena in 10-nm gate MOSFETs. The Ps-MOSFET consists of a lower gate and an upper gate which electrically induce pseudo source and drain regions at the silicon surface. In this structure, the pseudo source/drain regions act as doped source/drain regions in a MOSFET. Since the pseudo source/drain regions are extremely shallow, short-channel effects are expected to be suppressed in this structure. To minimize the channel length and the leakage current, we optimized the substrate doping concentration to be approximately 10 18 cm -3 by using a two-dimensional numerical simulation. In this case, we obtained a channel length of approximately 16 nm for 10-nm gate Ps-MOSFETs. Under this optimal doping condition, numerical calculations showed satisfactory transistor operations for the 10-nm gate Ps-MOSFETs: ON/OFF current ratio ∼10 6 and subthreshold slope ∼100 mV/decade. We also showed by calculation that the direct source-drain tunneling current was not negligible in the sub-10-nm regime.
Progressive Texture Video Streaming for Lossy Packet Networks (2001)

In this work we present an efficient video compression scheme which supports a fast bit rate adaptation independent of the encoder. The proposed scheme generates an embedded bitstream for each frame or, by appropriate multiplexing, for each group of picture. This rate-scalability is supported by an embedded bitstream which allows decoding at multiple rates, or to be more specific at virtually any rate. This video codec is successfully combined with an unequal erasure protection scheme to reduce the effects of packet losses. An optimized rate allocation scheme to trade-off source rate and redundancy is presented. Experimental results show the potential of the presented combination. I.
The Ozone Solubility and its Decay in Aqueous Solutions: Crucial Issues in Ozonated Chemistries for Semiconductor Cleaning (2001)

The use of ozone is becoming more and more popular for the cleaning of semiconductor structures, e.g. for pregate cleaning (e.g. thin oxide growth 1 and organic monolayer removal ) and photoresist stripping . Fundamental knowledge about the physicochemical behaviour of ozone in aqueous solutions is a necessity for optimizing these processes. Two crucial parameters are the solubility and the decomposition of ozone in DI-water. The ozone decomposition is driven by a variety of radicals which are formed as reaction products between water, ozone and “impurities”. Moreover these radicals may be more reactive than ozone itself. It is thus of importance to optimize both parameters to achieve the best conditions for each application.
OVERSEER: a prototype expert system for monitoring drug treatment in the psychiatric clinic (1989)

This paper describes the development of OVERSEER: a prototype knowledge-based system that monitors the drug treatment of psychiatric patients in real time. Using treatment protocols developed by the expert clinician, OVERSEER monitors the drug treatment process and issues alerts when standard clinical practices are not followed or when laboratory results are abnormal. Written in Prolog, OVERSEER is designed to interface directly with the hospital's database, and, thereby, utilizes all available pharmacy and laboratory data. Moreover, unlike the interactive expert systems developed for the psychiatric clinic, OVERSEER does not require extensive data entry by the clinician. Consequently, the chief benefit of OVERSEER's monitoring approach is the unobtrusive manner in which it evaluates psychopharmacological treatment and provides information regarding patient management to the hospital.
Calcium Signal Transmission between Ryanodine Receptors and Mitochondria (2000)

Control of energy metabolism by increases of mitochondrial matrix [Ca(2+)] ([Ca(2+)](m)) may represent a fundamental mechanism to meet the ATP demand imposed by heart contractions, but the machinery underlying propagation of [Ca(2+)] signals from ryanodine receptor Ca(2+) release channels (RyR) to the mitochondria remains elusive. Using permeabilized cardiac (H9c2) cells we investigated the cytosolic [Ca(2+)] ([Ca(2+)](c)) and [Ca(2+)](m) signals elicited by activation of RyR. Caffeine, Ca(2+), and ryanodine evoked [Ca(2+)](c) spikes that often appeared as frequency-modulated [Ca(2+)](c) oscillations in these permeabilized cells. Rapid increases in [Ca(2+)](m) and activation of the Ca(2+)-sensitive mitochondrial dehydrogenases were synchronized to the rising phase of the [Ca(2+)](c) spikes. The RyR-mediated elevations of global [Ca(2+)](c) were in the submicromolar range, but the rate of [Ca(2+)](m) increases was as large as it was in the presence of 30 microm global [Ca(2+)](c). Furthermore, RyR-dependent increases of [Ca(2+)](m) were relatively insensitive to buffering of [Ca(2+)](c) by EGTA. Therefore, RyR-driven rises of [Ca(2+)](m) appear to result from large and rapid increases of perimitochondrial [Ca(2+)]. The falling phase of [Ca(2+)](c) spikes was followed by a rapid decay of [Ca(2+)](m). CGP37157 slowed down relaxation of [Ca(2+)](m) spikes, whereas cyclosporin A had no effect, suggesting that activation of the mitochondrial Ca(2+) exchangers accounts for rapid reversal of the [Ca(2+)](m) response with little contribution from the permeability transition pore. Thus, rapid activation of Ca(2+) uptake sites and Ca(2+) exchangers evoked by RyR-mediated local [Ca(2+)](c) signals allow mitochondria to respond rapidly to single [Ca(2+)](c) spikes in cardiac cells.
Photothermal erosion of surfaces analyzed with the help of the mirage effect (1999)

Photothermal erosion of organic surfaces by the absorption of intensive heat pulses has been measured with the help of the mirage effect. Erosion effects and heat sources at the solid surface and heat sources due to chemical reactions of gaseous erosion products in front of the heated surface have been identified.
Fabricated Micro‐Nano Devices for In vivo and In vitro Biomedical Applications (2013)

In recent years, the innovative use of microelectromechanical systems ( MEMSs ) and nanoelectromechanical systems ( NEMSs ) in biomedical applications has opened wide opportunities for precise and accurate human diagnostics and therapeutics. The introduction of nanotechnology in biomedical applications has facilitated the exact control and regulation of biological environments. This ability is derived from the small size of the devices and their multifunctional capabilities to operate at specific sites for selected durations of time. Researchers have developed wide varieties of unique and multifunctional MEMS / NEMS devices with micro and nano features for biomedical applications ( BioMEMS / NEMS ) using the state of the art microfabrication techniques and biocompatible materials. However, the integration of devices with the biological milieu is still a fundamental issue to be addressed. Devices often fail to operate due to loss of functionality, or generate adverse toxic effects inside the body. The in vitro and in vivo performance of implantable BioMEMS such as biosensors, smart stents, drug delivery systems, and actuation systems are researched extensively to understand the interaction of the BioMEMS devices with physiological environments. BioMEMS developed for drug delivery applications include microneedles, microreservoirs, and micropumps to achieve targeted drug delivery. The biocompatibility of BioMEMS is further enhanced through the application of tissue and smart surface engineering. This involves the application of nanotechnology, which includes the modification of surfaces with polymers or the self‐assembly of monolayers of molecules. Thereby, the adverse effects of biofouling can be reduced and the performance of devices can be improved in in vivo and in vitro conditions. WIREs Nanomed Nanobiotechnol 2013, 5:544–568. doi: 10.1002/wnan.1227 This article is categorized under: Diagnostic Tools &gt; Biosensing Diagnostic Tools &gt; Diagnostic Nanodevices Nanotechnology Approaches to Biology &gt; Nanoscale Systems in Biology
Optimization approaches to volumetric modulated arc therapy planning (2015)

Volumetric modulated arc therapy (VMAT) has found widespread clinical application in recent years. A large number of treatment planning studies have evaluated the potential for VMAT for different disease sites based on the currently available commercial implementations of VMAT planning. In contrast, literature on the underlying mathematical optimization methods used in treatment planning is scarce. VMAT planning represents a challenging large scale optimization problem. In contrast to fluence map optimization in intensity-modulated radiotherapy planning for static beams, VMAT planning represents a nonconvex optimization problem. In this paper, the authors review the state-of-the-art in VMAT planning from an algorithmic perspective. Different approaches to VMAT optimization, including arc sequencing methods, extensions of direct aperture optimization, and direct optimization of leaf trajectories are reviewed. Their advantages and limitations are outlined and recommendations for improvements are discussed.
Experimental evaluation of digital beamforming for 5G multi-site massive MIMO (2017)

In order to tackle rapidly increasing traffic, Massive MIMO using beamforming (BF) is promising technique for fifth-generation (5G) mobile communication systems. Authors have recently proposed the joint processing of digital fixed BF and channel state information (CSI)-based precoding (Digital FBCP) that is suitable for low-SHF-band Massive MIMO. It has been also clarified that Digital FBCP is efficient in not-only single-site but also multi-site environment by introducing extended precoding technique. Although the previous works evaluate only in computer simulations, this paper aims to evaluate real-field performances by using 5G low-SHF-band massive MIMO prototype. First we measure low-SHF-band (5.2 GHz-band) CSI data in outdoor experiment, and then, this paper optimizes beam parameter in computer simulations exploiting the measured data. Finally, we show the throughput performance of Digital FBCP in multi-site environments.
Allodepleted T‐cell immunotherapy after haploidentical haematopoietic stem cell transplantation without severe acute graft‐versus‐host disease (GVHD) in the absence of GVHD prophylaxis (2019)

Graft-versus-host disease (GVHD) is a major cause of transplant-related mortality (TRM) after allogeneic haematopoietic stem cell transplantation (HSCT) and presents a challenge in haploidentical HSCT. GVHD may be prevented by ex vivo graft T-cell depletion or in vivo depletion of proliferating lymphocytes. However, both approaches pose significant risks, particularly infections and relapse, compromising survival. A photodepletion strategy to eliminate alloreactive T cells from mismatched donor lymphocyte infusions (enabling administration without immunosuppression), was used to develop ATIR101, an adjunctive therapy for use after haploidentical HSCT. In this phase I dose-finding study, 19 adults (median age: 54 years) with high-risk haematological malignancies were treated with T-cell-depleted human leucocyte antigen-haploidentical myeloablative HSCT followed by ATIR101 at doses of 1 × 10<sup>4</sup> -5 × 10<sup>6</sup> CD3<sup>+</sup> cells/kg (median 31 days post-transplant). No patient received post-transplant immunosuppression or developed grade III/IV acute GVHD, demonstrating the feasibility of ATIR101 infusion for evaluation in two subsequent phase 2 studies. Additionally, we report long-term follow -up of patients treated with ATIR101 in this study. At 1 year, all 9 patients receiving doses of 0·3-2 × 10<sup>6</sup> CD3<sup>+</sup> cells/kg ATIR101 remained free of serious infections and after more than 8 years, TRM was 0%, relapse-related mortality was 33% and overall survival was 67% in these patients.
Injectable and Glucose-Responsive Hydrogels Based on Boronic Acid–Glucose Complexation (2016)

Injectable hydrogels have been widely used for a number of biomedical applications. Here, we report a new strategy to form an injectable and glucose-responsive hydrogel using the boronic acid–glucose complexation. The ratio of boronic acid and glucose functional groups is critical for hydrogel formation. In our system, polymers with 10–60% boronic acid, with the balance being glucose-modified, are favorable to form hydrogels. These hydrogels are shear-thinning and self-healing, recovering from shear-induced flow to a gel state within seconds. More importantly, these polymers displayed glucose-responsive release of an encapsulated model drug. The hydrogel reported here is an injectable and glucose-responsive hydrogel constructed from the complexation of boronic acid and glucose within a single component polymeric material.
Studies on a Family with HB J Calabria (α2β264 (E8 GLY → ASP) (1979)

Hb J Calabria is a fast moving hemoglobin variant which was found in an Italian family by Vecchio et al (1), and in a French family by Blouquit et al. who studied its functional properties (2). The original family described by Vecchio et al. in which both Hb J Calabria and beta-thalassemia were present has been reexamined and is the subject of the present study. Hematological and clinical features of the carriers are described. The heterozygous carriers of Hb J Calabria showed only mild variable subclinical anemia and levels of the abnormal hemoglobin ranging from about 33 to 42%. The Hb J Calabria/beta-thalassemia double heterozygote showed a moderate chronic hemolytic anemia with alterations of the RBC indices and morphology in addition to splenomegaly. The relationship between structural abnormality, functional properties and clinical expression of Hb J Calabria is discussed.
Fabrication and verification for the micro holographic optical pickup (2010)

In this paper, we describe an optical configuration with a holographic optical element (HOE) for the small-form-factor (SFF) pickup head. This system adopts a finite-conjugate objective lens for both red and blue wavelength. A holographic optical element is used for simplifying the optical configuration which provides a better approach for alignment. In addition to demonstrating this OPH by using existing discrete components, flip chip bonder with high accuracy alignment was to integrate it. Fabrication process of the micro holographic optical pickup has been successfully verified. The experimental results verify the optical performance and the system have been demonstrated.
β-Defensin 1 Plays a Role in Acute Mucosal Defense against Candida albicans (2015)

Candida is an opportunistic fungal pathogen that colonizes the mucosal tract of humans. Pathogenic infection occurs in the presence of conditions causing perturbations to the commensal microbiota or host immunity. Early innate immune responses by the epithelium, including antimicrobial peptides (AMPs) and cytokines, are critical for protection against overgrowth. Reduced salivary AMP levels are associated with oral Candida infection, and certain AMPs, including human β-defensins 1-3, have direct fungicidal activity. In this study, we demonstrate that murine β-defensin 1 (mBD1) is important for control of early mucosal Candida infection and plays a critical role in the induction of innate inflammatory mediators. Mice deficient in mBD1, as compared with wild-type mice, exhibit elevated oral and systemic fungal burdens. Neutrophil infiltration to the sites of mucosal Candida invasion, an important step in limiting fungal infection, is significantly reduced in mBD1-deficient mice. These mice also exhibit defects in the expression of other AMPs, including mBD2 and mBD4, which may have direct anti-Candida activity. We also show that mBD1 deficiency impacts the production of important antifungal inflammatory mediators, including IL-1β, IL-6, KC, and IL-17. Collectively, these studies demonstrate a role for the mBD1 peptide in early control of Candida infection in a murine model of mucosal candidiasis, as well as in the modulation of host immunity through augmentation of leukocyte infiltration and inflammatory gene regulation.
Study of Iron-Based Superconductor by Means of X-ray, Neutron, Muon Beams (2015)

An advanced hydride-ion substitution method on LaFeAsO uncovered the second superconducting (SC) phase with a higher Tc of 36 K (x～0.35) in addition to the first SC phase with the maximum Tc of 26 K (x～0.1). To investigate the origin of the two SC domes and whether a certain hidden phase exists beyond the second SC phase, we have performed a multi-probe study in the range 0.40 ≤ x ≤ 0.51 using X-ray, neutron and muon beams. We discover an antiferromagnetic phase and a unique structural transition in heavily electron-doped LaFeAsO1−xHx (x～0.5), which is regarded as a second parent phase.
Physical localization and genetic mapping of the fertility restoration geneRfoin canola (Brassica napusL.) (2009)

The Ogu cytoplasm for male sterility and its fertility restorer gene Rfo in canola (Brassica napus L.) were originally introgressed from radish (Raphanus sativus L.) and have been widely used for canola hybrid production and breeding. The objective of this study was to determine the physical location of the Rfo locus in the canola genome using fluorescence in situ hybridization and genetic mapping. For physical localization of the Rfo gene, two bacterial artificial chromosome (BAC) clones, G62 and B420, which were closely linked to the Rfo gene, were used as probes to hybridize with the somatic metaphase chromosomes of a canola hybrid variety, PHI-46 (46H02), containing the Rfo fragment. The results showed that both clones were physically located at the end of one large metacentric chromosome. By simultaneous use of two BAC clones and 45S rDNA repeated sequences as the probes, we demonstrated that the large metacentric chromosome probed with the two BAC clones did not carry 45S rDNA repeated sequences. The chromosome was 3.65 +/- 0.74 microm in average length (20 cells) and ranked second in size among the chromosomes without 45S rDNAs. The centromere index of the chromosome (20 cells) was calculated as 43.74 +/- 4.19. A comparison with previously reported putative karyotypes of B. napus (AACC) and its diploid ancestors Brassica rapa L. (AA) and Brassica oleracea L. (CC) suggests that the chromosome carrying the Rfo fragment might belong to one of three large metacentric chromosomes of the C genome. Genetic mapping has confirmed the localization of the Rfo fragment to the distal region of linkage group N19, which corresponds to the C genome in B. napus. This study has provided the evidence of the location of the Rfo gene on canola chromosomes and established a basic framework for further physical mapping and manipulation of the gene.
Applying slope constrained Q-type aspheres to develop higher performance lenses (2011)

It has recently been shown that the coefficients that specify the aspheric departure from a spherical surface in high NA lithographic lenses routinely require more significant digits than are available in even double precision computers when they are described as part of a power series in aperture-squared. The Q-type aspheric description has been introduced to solve this problem. An important by-product of this new surface description is that it allows the slope of a surface to be directly constrained during optimization. Results show that Q-type aspheric surfaces that are optimized with slope constraints are not only more testable, an original motivation, but, they can also lead to solutions that are less sensitive to assembly induced misalignments for lithographic quality lenses. Specifically, for a representative NA 0.75 lens, the sensitivity to tilt and decenter is reduced by more than 3X, resulting in significantly higher lens performance in-use.
Aquaporin locus (12q13.12) might contribute to susceptibility of temporomandibular joint disorder associated with periodontitis (2020)

Aquaporins (AQPs) are membrane channels that provide for transport of water and other small molecules across the lipid bilayer of cells. Their function is essential for physiologic processes such as cell volume regulation, chondrocyte hypertrophy during appendicular skeletal growth, water reabsorption in the kidney tubules, and water excretion by the salivary glands. The ten AQP isoforms show tissue specificity and are involved in different pathologies and inflammatory diseases. This study addresses the hypothesis that arthritis, periodontitis, and temporomandibular joint disorders (TMDs) can be influenced by variation in the AQP genes at 12q13.12 locus. Salivary samples of 688 individuals were obtained from the Dental Registry and DNA Repository project at the University of Pittsburgh. Ten polymorphisms in four AQP genes (AQP1, 2, 5, and 6) were genotyped and correlated to disease status as reported by patients. Associations were found between the single nucleotide polymorphism (SNP) rs467323 in AQP2 and TMD in both genotypic (p = 0.03) and recessive (p = 0.02) models, and between rs1996315 in AQP6 and periodontitis (p = 0.05). Combined analysis of TMD and periodontitis showed an association with rs3741559 in AQP2 (p = 0.02). When conducting haplotype analysis of rs467323 and rs10875989 in AQP2, the haplotype CT showed an association with the TMD phenotype (p = 0.007). Our results suggest that the aquaporin locus at 12q13.12 may contribute to the pathogenesis of inflammatory conditions such as periodontitis and TMD. Thus, oral and skeletal health are correlated and potential susceptibility screening strategies may be developed.
Di-macrocyclic terephthalamide ligands as chelators for the PET radionuclide zirconium-89 (2014)

The development of bifunctional chelators (BFCs) which can stably chelate zirconium-89 ((89)Zr) while being conjugated to targeting molecules is an area of active research. Herein we report the first octadentate terephthalamide ligands, which are easily radiolabeled with (89)Zr and are highly stable in vitro. They represent a novel class of chelators, which are worthy of further development as BFCs for (89)Zr.