gebhart/patrepeval huggingface dataset:
The Role of Hot13p and Redox Chemistry in the Mitochondrial TIM22 Import Pathway (2004)

The small Tim proteins in the mitochondrial intermembrane space participate in the TIM22 import pathway for assembly of the inner membrane. Assembly of the small TIM complexes requires the conserved "twin CX3C" motif that forms juxtapositional intramolecular disulfide bonds. Here we identify a new intermembrane space protein, Hot13p, as the first component of a pathway that mediates assembly of the small TIM complexes. The small Tim proteins require Hot13p for assembly into a 70-kDa complex in the intermembrane space. Once assembled the small TIM complexes escort hydrophobic inner membrane proteins en route to the TIM22 complex. The mechanism by which the small Tim proteins bind and release substrate is not understood, and we investigated the affect of oxidant/reductant treatment on the TIM22 import pathway. With in organello import studies, oxidizing agents arrest the ADP/ATP carrier (AAC) bound to the Tim9p-Tim10p complex in the intermembrane space; this productive intermediate can be chased into the inner membrane upon subsequent treatment with reductant. Moreover, AAC import is markedly decreased by oxidant treatment in Deltahot13 mitochondria and improved when Hot13p is overexpressed, suggesting Hot13p may function to remodel the small TIM complexes during import. Together these results suggest that the small TIM complexes have a specialized assembly pathway in the intermembrane space and that the local redox state of the TIM complexes may mediate translocation of inner membrane proteins.
Antagonists of growth hormone-releasing hormone inhibit the proliferation of experimental non-small cell lung carcinoma. (2003)

Recent studies show that antagonists of growth hormone-releasing hormone (GH-RH) inhibit proliferation of various cancers indirectly through blockage of the endocrine GH-insulin-like growth factor (IGF) I axis and directly by an action on tumor cells involving the suppression of autocrine/paracrine IGF-I, IGF-II, or GH-RH. The effectiveness of therapy with GH-RH antagonist JV-1-38 and its mechanisms of action were investigated in NCI-H838 non-small cell lung carcinoma (NSCLC) xenografted s.c. into nude mice and in vitro. Treatment with GH-RH antagonist JV-1-38 significantly (P < 0.05-0.001) inhibited tumor growth as demonstrated by a 58% decrease in final tumor volume, 54% reduction in tumor weight, and the extension of tumor-doubling time from 8.5 +/- 1.38 to 12 +/- 1.07 days as compared with controls. Using ligand competition assays with (125)I-labeled GH-RH antagonist JV-1-42, specific high-affinity binding sites for GH-RH were found on tumor membranes. Reverse transcription-PCR revealed the expression of mRNA for GH-RH and splice variant 1 (SV(1)) of GH-RH receptor in H838 tumors. Reverse transcription-PCR analysis also demonstrated that H838 tumors express IGF-I and IGF-I receptors. Tumoral concentration of IGF-I and its mRNA expression were significantly decreased by 25% (P = 0.05) and 65% (P < 0.001), respectively, in animals receiving JV-1-38, whereas serum IGF-I levels remained unchanged. In vitro studies showed that H838 cells secreted GH-RH and IGF-I into the medium. The growth of tumor cells in vitro was stimulated by IGF-I and inhibited by GH-RH antagonist JV-1-38 and a GH-RH antiserum. Our results extend the findings on the involvement of IGF-I in NSCLC and suggest that GH-RH may be an autocrine growth factor for H838 NSCLC. The antitumorigenic action of GH-RH antagonists could be partly direct and mediated by SV(1) of tumoral GH-RH receptors. The finding of GH-RH and SV(1) of GH-RH receptors in NSCLC provides a new approach to the treatment of this malignancy based on the use of antagonistic analogues of GH-RH.
A fast pitch searching algorithm using correlation characteristics in CELP vocoder (2002)

The major drawback in the code excited linear prediction (CELP) type vocoders is their large computational requirements. In the present paper a simple method is proposed to reduce the pitch searching time in the pitch filter almost without degradation of quality. Based upon the observational regularity of the correlation function of speech, the searching range can be restricted to the positive side in pitch search. This is done by skipping the negative side with the width which is estimated from the previous positive envelope. In addition to that, the maximum number of available lags can be limited by the threshold, LT, which is set on 58 empirically. So, only the limited numbers of lags are considered in pitch search, which is less than a half of that of the full search method. By using the proposed method in pitch search, its required computations are greatly reduced. Experimental results show 51% time reduction almost without lowering the speech quality in segmental SNR measures.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A Combined Therapeutic Approach to Manage Oral Halitosis: A 3‐Month Prospective Case Series (2005)

The evaluated therapeutic approach demonstrated its efficacy in the management of oral halitosis, demonstrating statistically significant improvements in both organoleptic and VSC values at 1 and 3 months. The proposed clinical protocol significantly affected the microbial composition in tongue coating, saliva, and subgingival microflora.
INFANT AVOIDANCE DURING A TACTILE TASK PREDICTS AUTISM SPECTRUM BEHAVIORS IN TODDLERHOOD (2015)

The experience of touch is critical for early communication and social interaction; infants who show aversion to touch may be at risk for atypical development and behavior problems. The current study aimed to clarify predictive associations between infant responses to tactile stimuli and toddler autism spectrum, internalizing, and externalizing behaviors. This study measured 9-month-old infants' (N = 561; 58% male) avoidance and negative affect during a novel tactile task in which parents painted infants' hands and feet and pressed them to paper to make a picture. Parent reports on the Pervasive Developmental Problems (PDP), Internalizing, and Externalizing scales of the Child Behavior Checklist were used to measure toddler behaviors at 18 months. Infant observed avoidance and negative affect were significantly correlated; however, avoidance predicted subsequent PDP scores only, independent of negative affect, which did not predict any toddler behaviors. Findings suggest that incorporating measures of responses to touch in the study of early social interaction may provide an important and discriminating construct for identifying children at greater risk for social impairments related to autism spectrum behaviors.
Architectures and algorithms for user customization of CNNs (2018)

In this paper we present a convolutional neural network architecture that supports user customization through incremental transfer learning. The architecture consists of a large basic inference engine and a small augmenting engine. After training the basic inference engine and augmenting engine on a large general dataset, the basic inference engine is fixed. For user customization, only the augmenting engine is re-trained on-device using a small user specific dataset provided by the user. To accelerate the training of the augmenting engine we map this to a coarsegrained reconfigurable array processor. The complete network architecture is evaluated using the Caffe framework, and a C-code equivalent network is implemented and tested on a CGRA processor. Experiments with NIST '19 and our user-specific datasets show an increase in accuracy of the system from 76.3% to 93.2% after user customization. Mapping this code to a CGRA gives us a speed up of 45x and a 49- and 3-fold reduced energy consumption over an ARMv7 processor and a 3-way VLIW processor, respectively, showing the potential of CGRAs as DNN processors.
Technology and integration of poly-crystalline diamond piezoresistive position sensor for cochlear implant probe (2005)

The possible use of polycrystalline diamond (poly-C) as a piezoresistive position sensor in a cochlear prosthesis is being investigated for the first time. The fabrication process of the poly-C thin film was optimized for compatibility and integration with the Si-based bulk micromachining technology of the cochlear probe. In-situ doped poly-C, films, with a thickness of 1 /spl mu/m, were grown on insulating substrates using MPCVD and patterned by ECR-assisted plasma etching. The piezoresistors can be used as position sensors to detect the curvature and position of the probe during implant surgery. The film quality, electrical properties, contact resistance and piezoresistivity of the poly-C sensors were characterized, which demonstrated a successful integration of diamond technology with the microsystem technology. A gauge factor of 28 was achieved for the poly-C sensors on the probe.
The Pbx Interaction Motif of Hoxa1 Is Essential for Its Oncogenic Activity (2011)

Hoxa1 belongs to the Hox family of homeodomain transcription factors involved in patterning embryonic territories and governing organogenetic processes. In addition to its developmental functions, Hoxa1 has been shown to be an oncogene and to be overexpressed in the mammary gland in response to a deregulation of the autocrine growth hormone. It has therefore been suggested that Hoxa1 plays a pivotal role in the process linking autocrine growth hormone misregulation and mammary carcinogenesis. Like most Hox proteins, Hoxa1 can interact with Pbx proteins. This interaction relies on a Hox hexapeptidic sequence centred on conserved Tryptophan and Methionine residues. To address the importance of the Hox-Pbx interaction for the oncogenic activity of Hoxa1, we characterized here the properties of a Hoxa1 variant with substituted residues in the hexapeptide and demonstrate that the Hoxa1 mutant lost its ability to stimulate cell proliferation, anchorage-independent cell growth, and loss of contact inhibition. Therefore, the hexapeptide motif of Hoxa1 is required to confer its oncogenic activity, supporting the view that this activity relies on the ability of Hoxa1 to interact with Pbx.
Effects of rose hip intake on risk markers of type 2 diabetes and cardiovascular disease: a randomized, double-blind, cross-over investigation in obese persons (2011)

Daily consumption of 40 g of rose hip powder for 6 weeks can significantly reduce cardiovascular risk in obese people through lowering of systolic blood pressure and plasma cholesterol levels.
Relationship between development and disease in the urinary system (1995)

腎臓は, 中間中胚葉に由来するが, とくにウォルフ管の末端部から伸び出した尿管芽と骨盤部の中間中胚葉である造後腎胚芽組織から, 後腎として生じる. 分岐を繰り返す尿管芽の末端部に誘導された造後腎胚芽組織内の小胞から, 糸球体とネフロンの尿細管部が生じる. 糸球体ははじめコンマ状, さらにS字状の形をとり未熟な毛細血管ループとして成立する. 人間における胎生後期, ラットにおける生後初期の腎機能の発達は, 糸球体数の増加によってではなく, おもに未熟な糸球体の成長によるサイズの増加によって行われる. この糸球体サイズの成長にあたっては, 糸球体毛細血管の総延長の増加, ならびに分岐数の増加が認められるが, それとともに糸球体基底膜の表面積もいちじるしく増大する. この糸球体基底膜の表面積を増加させる装置ではないかと注目されているのが, 膨出部outpocketsという構造であるが, 渡辺らの最近の研究では, この膨出部は成長期にわたって糸球体の周縁部にのみ認められる. 周縁部で作られた基底膜物質が, 糸球体全体にどのように再配分されるかという機構については, まだ分かっていない. またこのような成長期の糸球体では, 片腎摘出などの処置により糸球体が異常に大型化し, 糸球体障害が起こることが知られている.
Rewiring of the corticospinal tract in the adult rat after unilateral stroke and anti-Nogo-A therapy (2013)

Adult Long Evans rats received a photothrombotic stroke that destroyed >90% of the sensorimotor cortex unilaterally; they were subsequently treated intrathecally for 2 weeks with a function blocking antibody against the neurite growth inhibitory central nervous system protein Nogo-A. Fine motor control of skilled forelimb grasping improved to 65% of intact baseline performance in the anti-Nogo-A treated rats, whereas control antibody treated animals recovered to only 20% of baseline scores. Bilateral retrograde tract tracing with two different tracers from the intact and the denervated side of the cervical spinal cord, at different time points post-lesion, indicated that the intact corticospinal tract had extensively sprouted across the midline into the denervated spinal hemicord. The original axonal arbours of corticospinal tract fibres that had recrossed the midline were subsequently withdrawn, leading to a complete side-switch in the projection of a subpopulation of contralesional corticospinal tract axons. Anterograde tracing from the contralesional cortex showed a 2-3-fold increase of midline crossing fibres and additionally a massive sprouting of the pre-existing ipsilateral ventral corticospinal tract fibres throughout the entire cervical enlargement of the anti-Nogo-A antibody-treated rats compared to the control group. The laminar distribution pattern of the ipsilaterally projecting corticospinal tract fibres was similar to that in the intact spinal cord. These plastic changes were paralleled by a somatotopic reorganization of the contralesional motor cortex where the formation of an ipsilaterally projecting forelimb area was observed. Intracortical microstimulation of the contralesional motor cortex revealed that low threshold currents evoked ipsilateral movements and electromyography responses at frequent cortical sites in the anti-Nogo-A, but not in the control antibody-treated animals. Subsequent transection of the spared corticospinal tract in chronically recovered animals, treated with anti-Nogo-A, led to a reappearance of the initial lesion deficit observed after the stroke lesion. These results demonstrate a somatotopic side switch anatomically and functionally in the projection of adult corticospinal neurons, induced by the destruction of one sensorimotor cortex and the neutralization of the CNS growth inhibitory protein Nogo-A.
Synthesis of analogs of the radiation mitigator JP4-039 and visualization of BODIPY derivatives in mitochondria (2013)

JP4-039 is a lead structure in a series of nitroxide conjugates that are capable of accumulating in mitochondria and scavenging reactive oxygen species (ROS). To explore structure-activity relationships (SAR), new analogs with variable nitroxide moieties were prepared. Furthermore, fluorophore-tagged analogs were synthesized and provided the opportunity for visualization in mitochondria. All analogs were tested for radioprotective and radiomitigative effects in 32Dcl3 cells.
Integrated process for high conversion and high yield protein PEGylation (2016)

Over the past decades, PEGylation has become a powerful technique to increase the in vivo circulation half-life of therapeutic proteins while maintaining their activity. The development of new therapeutic proteins is likely to require further improvement of the PEGylation methods to reach even better selectivity and yield for reduced costs. The intensification of the PEGylation process was investigated through the integration of a chromatographic step in order to increase yield and conversion for the production of mono-PEGylated protein. Lysozyme was used as a model protein to demonstrate the feasibility of such approach. In the integrated reaction/separation process, chromatography was used as fractionation technique in order to isolate and recycle the unreacted protein from the PEGylated products. This allows operating the reactor with short reaction times so as to minimize the production of multi-PEGylated proteins (i.e., conjugated to more than one polymer). That is, the reaction is stopped before the desired product (i.e., the mono-PEGylated protein) can further react, thus leading to limited conversion but high yield. The recycling of the unreacted protein was then considered to drive the protein overall conversion to completion. This approach has great potential to improve processes whose yield is limited by the further reaction of the product leading to undesirable by-products. Biotechnol. Bioeng. 2016;113: 1711-1718. © 2016 Wiley Periodicals, Inc.
Switchable Materials for Smart Windows (2016)

This article reviews the basic principles of and recent developments in electrochromic, photochromic, and thermochromic materials for applications in smart windows. Compared with current static windows, smart windows can dynamically modulate the transmittance of solar irradiation based on weather conditions and personal preferences, thus simultaneously improving building energy efficiency and indoor human comfort. Although some smart windows are commercially available, their widespread implementation has not yet been realized. Recent advances in nanostructured materials provide new opportunities for next-generation smart window technology owing to their unique structure-property relations. Nanomaterials can provide enhanced coloration efficiency, faster switching kinetics, and longer lifetime. In addition, their compatibility with solution processing enables low-cost and high-throughput fabrication. This review also discusses the importance of dual-band modulation of visible and near-infrared (NIR) light, as nearly 50% of solar energy lies in the NIR region. Some latest results show that solution-processable nanostructured systems can selectively modulate the NIR light without affecting the visible transmittance, thus reducing energy consumption by air conditioning, heating, and artificial lighting.
E-Beam Evaporated Glass and MgO Layers for Gas Panel Fabrication (1978)

An electron-beam evaporation process has been developed that is capable of depositing stable, thick, borosilicate glass films (0.5–50 µm) on various substrates at a rate exceeding 0.5 µm/min. A very low stress of 4–10 ×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> N/m <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> in compression was obtained in freshly deposited glass films, and a further reduction below measurable levels of stress was observed after a thermal annealing at 500°C. The effects of evaporation parameter variation and thermal annealing on the film properties of the borosilicate glass layers, as well as the MgO secondary emission layers employed in the fabrication of gas discharge display panels, are presented.
Photosensitive polynorbornene based dielectric. I. Structure–property relationships (2004)

Abstract In the microelectronics industry, the drive for increasing device speed, level of functionality and shrinking size has placed significant demands on the performance characteristics of polymer dielectrics. In this study, a negative acting, photodefinable dielectric formulation based on a copolymer of decylnorborne (decylNB) and epoxynorbornene (AGENB) was investigated for use in electronics packaging. The structure–property relations of this copolymer were investigated. Copolymer composition and processing conditions were shown to significantly affect the properties of the final polymer films. A lower content of AGENB results in lower moisture absorption, dielectric constant, modulus and residual stress, but it compromises multilayer capability. High crosslink density lowers the dielectric constant but increases the modulus and residual stress. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 91: 3023–3030, 2004
Nonprotein Based Enrichment Method to Analyze Peptide Cross-Linking in Protein Complexes (2009)

Cross-linking analysis of protein complexes and structures by tandem mass spectrometry (MS/MS) has advantages in speed, sensitivity, specificity, and the capability of handling complicated protein assemblies. However, detection and accurate assignment of the cross-linked peptides are often challenging due to their low abundance and complicated fragmentation behavior in collision-induced dissociation (CID). To simplify the MS analysis and improve the signal-to-noise ratio of the cross-linked peptides, we developed a novel peptide enrichment strategy that utilizes a cross-linker with a cryptic thiol group and using beads modified with a photocleavable cross-linker. The functional cross-linkers were designed to react with the primary amino groups in proteins. Human serum albumin was used as a model protein to detect intra- and intermolecular cross-linkages. Use of this protein-free selective retrieval method eliminates the contamination that can result from avidin-biotin based retrieval systems and simplifies data analysis. These features may make the method suitable to investigate protein-protein interactions in biological samples.
Emerging Terahertz Integrated Systems in Silicon (2021)

Silicon-based terahertz (THz) integrated circuits (ICs) have made rapid progress over the past decade. The demonstrated basic component performance, as well as the maturity of design tools and methodologies, have made it possible to build high-complexity THz integrated systems. Such implementations are undoubtedly highly attractive due to their low cost and high integration capability; however, their unique characteristics, both advantageous and disadvantageous, also call for research investigations into unconventional systematic architectures and novel THz applications. In this paper, we review the current status and future trend of silicon-based THz ICs, with the focus on state-of-the-art THz microsystems for emerging sensing and communication applications in the last few years, such as high-resolution imaging, high medium/long-term stability time keeping, high-speed wireline/wireless communications, and miniaturization of RF tags, as well as THz packaging technologies.
The Role of the Thymus and Recent Thymic Migrants in the Maintenance of the Adult Peripheral Lymphocyte Pool (1998)

The thymus is essential for the initial seeding of T cells to the periphery, but its role in maintaining the adult T cell pool remains poorly defined. We investigated whether changes to the rate of T cell export could form part of the mechanism(s) controlling the homeostatic regulation of the size and composition of the peripheral T cell pool. Using neonatal thymi grafted under the kidney capsule, we found that irrespective of whether the pool was oversupplied (by thymic grafts) or undersupplied (due to neonatal thymectomy), the thymic export rate was constant from both the host and graft thymus, and the periphery remained constant in size. Recent thymic emigrants (RTE) were also tracked to determine the extent of their acceptance into the T cell pool of a normal mouse. As a population, RTE are phenotypically mature, but were distinct from resident T cells in the periphery, being released in a CD4/CD8 ratio approximately twice that of established peripheral T cells. This export ratio is similar to that of T cells in the mature thymic compartment, but soon after entry into the periphery, the ratio falls, indicating separate thymic and peripheral regulation of the CD4/CD8 ratio. RTE may also be preferentially incorporated into the periphery, causing displacement of resident T cells, thus maintaining the size of the peripheral pool. Although not vital for the maintenance of a functional T cell pool, the acceptance of RTE in a "full" peripheral pool would ensure that the T cell receptor repertoire is kept diverse and that the T cell population encompasses a broad range of naive as well as memory T cells.
Engineering of L-amino acid deaminases for the production of α-keto acids from L-amino acids (2019)

α-keto acids are organic compounds that contain an acid group and a ketone group. L-amino acid deaminases are enzymes that catalyze the oxidative deamination of amino acids for the formation of their corresponding α-keto acids and ammonia. α-keto acids are synthesized industrially via chemical processes that are costly and use harsh chemicals. The use of the directed evolution technique, followed by the screening and selection of desirable variants, to evolve enzymes has proven to be an effective way to engineer enzymes with improved performance. This review presents recent studies in which the directed evolution technique was used to evolve enzymes, with an emphasis on L-amino acid deaminases for the whole-cell biocatalysts production of α-keto acids from their corresponding L-amino acids. We discuss and highlight recent cases where the engineered L-amino acid deaminases resulted in an improved production yield of phenylpyruvic acid, α-ketoisocaproate, α-ketoisovaleric acid, α-ketoglutaric acid, α-keto-γ-methylthiobutyric acid, and pyruvate.