gebhart/patrepeval huggingface dataset:
Decision Models and Technology Can Help Psychiatry Develop Biomarkers (2021)

Why is psychiatry unable to define clinically useful biomarkers? We explore this question from the vantage of data and decision science and consider biomarkers as a form of phenotypic data that resolves a well-defined clinical decision. We introduce a framework that systematizes different forms of phenotypic data and further introduce the concept of decision model to describe the strategies a clinician uses to seek out, combine, and act on clinical data. Though many medical specialties rely on quantitative clinical data and operationalized decision models, we observe that, in psychiatry, clinical data are gathered and used in idiosyncratic decision models that exist solely in the clinician's mind and therefore are outside empirical evaluation. This, we argue, is a fundamental reason why psychiatry is unable to define clinically useful biomarkers: because psychiatry does not currently quantify clinical data, decision models cannot be operationalized and, in the absence of an operationalized decision model, it is impossible to define how a biomarker might be of use. Here, psychiatry might benefit from digital technologies that have recently emerged specifically to quantify clinically relevant facets of human behavior. We propose that digital tools might help psychiatry in two ways: first, by quantifying data already present in the standard clinical interaction and by allowing decision models to be operationalized and evaluated; second, by testing whether new forms of data might have value within an operationalized decision model. We reference successes from other medical specialties to illustrate how quantitative data and operationalized decision models improve patient care.
Molecular profile of catabolic versus anabolic treatment regimens of parathyroid hormone (PTH) in rat bone: An analysis by DNA microarray (2005)

Teriparatide, human PTH (1-34), a new therapy for osteoporosis, elicits markedly different skeletal responses depending on the treatment regimen. In order to understand potential mechanisms for this dichotomy, the present investigation utilized microarrays to delineate the genes and pathways that are regulated by intermittent (subcutaneous injection of 80 microg/kg/day) and continuous (subcutaneous infusion of 40 microg/kg/day by osmotic mini pump) PTH (1-34) for 1 week in 6-month-old female rats. The effect of each PTH regimen was confirmed by histomorphometric analysis of the proximal tibial metaphysis, and mRNA from the distal femoral metaphysis was analyzed using an Affymetrix microarray. Both PTH paradigms co-regulated 22 genes including known bone formation genes (i.e., collagens, osteocalcin, decorin, and osteonectin) and also uniquely modulated additional genes. Intermittent PTH regulated 19 additional genes while continuous treatment regulated 173 additional genes. This investigation details for the first time the broad profiling of the gene and pathway changes that occur in vivo following treatment of intermittent versus continuous PTH (1-34). These results extend previous observations of gene expression changes and reveal the in vivo regulation of BMP3 and multiple neuronal genes by PTH treatment.
Modeling the Use of Air-Injection for Emissions Reduction in a Direct-Injected Diesel Engine (1995)

&lt;div class="htmlview paragraph"&gt;This study investigates the effect of air-injection during the late combustion period produced by an air-cell on emissions from a direct injected diesel engine. The engine considered is a Caterpillar 3401 test engine which was modeled with an air-cell included as part of the piston geometry.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A version of the KIVA-II code with updated submodels for diesel combustion and emissions was modified to allow for geometries with walls interior to the domain. This modified version of KIVA-II was then used to model an air-cell equipped diesel engine for four different air-cell configurations.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;Of the four air-cell configurations simulated, one proved successful in reducing the predicted engine emissions by more than a factor of two while simultaneously reducing NO&lt;sub&gt;x&lt;/sub&gt; by a slight amount, thus moving the engine off its particulate-NO&lt;sub&gt;x&lt;/sub&gt; tradeoff curve defined by varying the fuel injection timing. This air-cell configuration demonstrates that air-injection during the late combustion period can be effective at reducing engine emissions. The other three air-cell configurations simply moved the engine along its particulate-NO&lt;sub&gt;x&lt;/sub&gt; tradeoff. However, this study highlights potential difficulties for designing an air-cell equipped engine. Namely, the large effect produced by the interaction of the turbulence and the in-cylinder flow in the proximity of the air-cell inlet on the overall operation of the air-cell.&lt;/div&gt;
Ultra-short echo-time 2D time-of-flight MR angiography using a half-pulse excitation (1999)

Flow-related artifacts remain a significant concern for magnetic resonance (MR) angiography because their appearance in angiograms adversely impacts accuracy in evaluation of arterial stenoses. In this paper, a half-pulse excitation scheme for improved two-dimensional time-of-flight (2D TOF) angiography is described. The proposed method eliminates the need for gradient moment nulling (of all orders), providing significant reductions in spin dephasing and consequent artifactual signal loss. Furthermore, because the post-excitation refocusing and flow compensation gradients are obviated, the achievable echo time is dramatically shortened. The half-pulse excitation is employed in conjunction with a fast radial-line acquisition, allowing ultra-short echo times on the order of 250-300 microsec. Radial-line acquisition methods also provide additional benefits for flow imaging: effective mitigation of pulsatile flow artifacts, full k-space coverage, and decreased scan times. The half-pulse excitation/radial-line sequence demonstrated improved performance in initial clinical evaluations of the carotid bifurcation when compared with a conventional 2D TOF sequence.
Frequency dependence of high temperature fatigue strength in a water-quenched Fe-Si-C ferritic alloy (2019)

We focused on dynamic strain aging that can effectively raise the non-propagation limit of a fatigue crack. However, in the supersaturated carbon steel, carbides are formed at high temperature over time, and the content of solute carbon is decreased, thereby reducing the contribution of strain aging and the non-propagation limit of a fatigue crack. From these results we confirmed that increasing the test time with decrease of the frequency produced the deterioration of the fatigue characteristics. In addition, we propose the method to predict the frequency dependence of the fatigue characteristics by a simpler hardness test as an alternative test of a fatigue test. In the fatigue test using Fe-0.016C-1.0Si alloy, it was found that the fatigue strength at a frequency of 30 Hz is higher than the fatigue strength at a frequency of 10 Hz. Next, when Fe-0.016C-1.0Si alloy was pre-strained at 8 % and a hardness test was conducted at 433 K, the hardness increased until 2 hours from the start of the test. In the 0 and 4 % pre-strained materials of the previous research, the hardness starts to decrease 24 hours and 6 hours after the start of the test respectively. From this result, it was found that the time when the hardness starts to decrease is faster as the pre-strain is larger.
QE reduction due to pixel vignetting in CMOS image sensors (2000)

CMOS image sensor designers take advantage of technology scaling either by reducing pixel size or by adding more transistors to the pixel. In both cases, the distance from the chip surface to the photodiode increases relative to the photodiode planar dimensions. As a result, light must ravel through an increasingly deeper and narrower `tunnel' before it reaches the photodiode. This is especially problematic for light incident at oblique angles; the narrow tunnel walls cast a shadow on the photodiode, which in turn severely reduces its effective QE. We refer to this phenomenon as pixel vignetting. The paper presents experimental results from a 640 X 512 CMOS image sensor fabricated using a 0.35(mu) 4-layer metal CMOs process that shows significant QE reduction of up to 50% for off-axis relative to on-axis pixels. Using simple geometric models of the sensor and the imaging optics, we compare the QE for on and off-axis pixels. We find that our analysis results support the hypothesis that the experimentally observed QE reduction is indeed due to pixel vignetting. We show that pixel vignetting becomes more severe as CMOS technology scales, even for a 2-layer metal APS pixel. Finally, we briefly discuss several potential solutions to the pixel vignetting problem.
Toxins of toxin/antitoxin systems are inactivated primarily through promoter mutations (2019)

This study demonstrates toxins of TA systems may be inactivated by mutations that primarily affect the toxin gene promoter instead of the toxin structural gene.
Identifying Areas of Unmet Need Among People with Migraine with an Inadequate Response to Prior Acute Therapies: Results from the MOMENTUM trial (P7-12.009) (2023)

The objective of this study was to characterize the areas of greatest unmet needs regarding acute migraine therapy, as determined by the 4-item Migraine Treatment Optimization Questionnaire (mTOQ-4).
Solution-Processed Mixed-Dimensional Hybrid Perovskite/Carbon Nanotube Electronics (2020)

Benefiting from their extraordinary physical properties, methylammonium lead halide perovskites (PVKs) have attracted significant attention in optoelectronics. However, the PVK-based devices suffer from low carrier mobility and high operation voltage. Here, we utilize sorted semiconducting single-walled carbon nanotubes (95% s-SWCNTs) to enhance the performance of thin-film transistors (TFTs) based on the mixed-cation perovskite (MA<sub>1-<i>x</i></sub>FA<sub><i>x</i></sub>)Pb(I<sub>1-<i>x</i></sub>Br<sub><i>x</i></sub>)<sub>3</sub>, enabling mixed-dimensional solution-processed electronics with high mobility (32.25 cm<sup>2</sup>/(V s)) and low voltage (∼3 V) operation. The resulting mixed-dimensional PVK/SWCNT TFTs possess ON/OFF ratios on the order of 10<sup>7</sup>, enabling the fabrication of high-gain inverters.
Quantitative assessment of hepatic fibrosis in an animal model with magnetic resonance elastography (2007)

Chronic liver disease is a world-wide problem that causes progressive hepatic fibrosis as a hallmark of progressive injury. At present, the gold standard for diagnosing hepatic fibrosis is liver biopsy, which is an invasive method with many limitations, including questionable accuracy and risks of complications. MR elastography (MRE), a phase-contrast MRI technique for quantitatively assessing the mechanical properties of soft tissues, is a potential noninvasive diagnostic method to assess hepatic fibrosis. In this work, MRE was evaluated as a quantitative method to assess the in vivo mechanical properties of the liver tissues in a knockout animal model of liver fibrosis. This work demonstrates that the shear stiffness of liver tissue increases systematically with the extent of hepatic fibrosis, as measured by histology. A linear correlation between liver stiffness and fibrosis extent was well-defined in this animal model. An additional finding of the study was that fat infiltration, commonly present in chronic liver disease, does not significantly correlate with liver stiffness at each fibrosis stage and thus does not appear to interfere with the ability of MRE to assess fibrosis extent. In conclusion, MRE has the potential not only for assessing liver stiffness, but also for monitoring potential therapies for hepatic fibrosis.
Optimizing the Operation Cost for UAV-Aided Mobile Edge Computing (2021)

Mobile edge computing (MEC) is leveraged to reduce the latency for the computation-intensive and latency-critical tasks offloaded from wireless devices and Internet of Things Devices (IoTDs). Unmanned aerial vehicles (UAVs) have attracted much attention from both academia and industry attributed to high mobility, high flexibility, and high maneuverability of UAVs. In this article, a novel UAV-assisted MEC architecture is proposed to provision services to IoTDs, where a UAV provides both communication and computing services or works as a relay node. We then formulate the joint computation offloading, spectrum resource allocation, computation resource allocation, and UAV placement (Joint-CAP) problem in the UAV-MEC network to minimize the operation cost of provisioning IoTDs. Since the Joint-CAP problem is a mixed integer non-linear programming problem and NP-hard, we decompose it into two sub-problems and solve the sub-problems sequentially. Then, we propose a (1+ε)-approximation algorithm, named AA-CAP, to solve the Joint-CAP problem, and the performance of the AA-CAP algorithm is demonstrated to be superior to the baseline algorithms via simulations.
Non-coding RNAs and glioma: Focus on cancer stem cells (2022)

Glioblastoma and gliomas can have a wide range of histopathologic subtypes. These heterogeneous histologic phenotypes originate from tumor cells with the distinct functions of tumorigenesis and self-renewal, called glioma stem cells (GSCs). GSCs are characterized based on multi-layered epigenetic mechanisms, which control the expression of many genes. This epigenetic regulatory mechanism is often based on functional non-coding RNAs (ncRNAs). ncRNAs have become increasingly important in the pathogenesis of human cancer and work as oncogenes or tumor suppressors to regulate carcinogenesis and progression. These RNAs by being involved in chromatin remodeling and modification, transcriptional regulation, and alternative splicing of pre-mRNA, as well as mRNA stability and protein translation, play a key role in tumor development and progression. Numerous studies have been performed to try to understand the dysregulation pattern of these ncRNAs in tumors and cancer stem cells (CSCs), which show robust differentiation and self-regeneration capacity. This review provides recent findings on the role of ncRNAs in glioma development and progression, particularly their effects on CSCs, thus accelerating the clinical implementation of ncRNAs as promising tumor biomarkers and therapeutic targets.
Lensless diffractive imaging using tabletop, coherent, high harmonic soft x- (2007)

We present the first experimental demonstration of lensless imaging using a tabletop, coherent soft-x-rays source. A 29 nm high harmonic beam illuminates an object, and the diffraction is collected on an x-ray CCD camera. High dynamic range diffraction patterns are obtained by taking multiple exposures while blocking small-angle diffraction using beam blocks of varying size. These patterns reconstruct to images with 200 nm resolution. This work demonstrates a
Identification of Novel SHOX Target Genes in the Developing Limb Using a Transgenic Mouse Model (2014)

Deficiency of the human short stature homeobox-containing gene (SHOX) has been identified in several disorders characterized by reduced height and skeletal anomalies such as Turner syndrome, Léri-Weill dyschondrosteosis and Langer mesomelic dysplasia as well as isolated short stature. SHOX acts as a transcription factor during limb development and is expressed in chondrocytes of the growth plates. Although highly conserved in vertebrates, rodents lack a SHOX orthologue. This offers the unique opportunity to analyze the effects of human SHOX expression in transgenic mice. We have generated a mouse expressing the human SHOXa cDNA under the control of a murine Col2a1 promoter and enhancer (Tg(Col2a1-SHOX)). SHOX and marker gene expression as well as skeletal phenotypes were characterized in two transgenic lines. No significant skeletal anomalies were found in transgenic compared to wildtype mice. Quantitative and in situ hybridization analyses revealed that Tg(Col2a1-SHOX), however, affected extracellular matrix gene expression during early limb development, suggesting a role for SHOX in growth plate assembly and extracellular matrix composition during long bone development. For instance, we could show that the connective tissue growth factor gene Ctgf, a gene involved in chondrogenic and angiogenic differentiation, is transcriptionally regulated by SHOX in transgenic mice. This finding was confirmed in human NHDF and U2OS cells and chicken micromass culture, demonstrating the value of the SHOX-transgenic mouse for the characterization of SHOX-dependent genes and pathways in early limb development.
Automatic Discovery of Attribute Words from Web Documents and Criteria for Human Evaluation (2006)

本論文では, 広範な概念クラスの属性語を日本語のWeb文書から獲得する手法を提案する.提案する手法は, Web検索を用いて得られた候補の単語を言語的パターン・HTMLタグ・単語の出現の統計量から計算されるスコアで順位付けする簡単な教師無しの獲得手法である.また, 本論文では, 獲得された属性語を人手で評価するための質問解答可能性に基づく評価手順を提案する.この評価手順に従い22個の概念クラスに関して提案獲得手法を人手で評価し, 提案手法により属性語を高精度で獲得可能であること, また, スコアに用いた各手がかりが実際に性能に貢献していることを確認した.
Detection of Rooftop Cooling Unit Faults Based on Electrical Measurements (2006)

Nonintrusive load monitoring (NILM) is accomplished by sampling voltage and current at high rates and reducing the resulting start transients or harmonic contents to concise “signatures.” Changes in these signatures can be used to detect, and in many cases directly diagnose, equipment and component faults associated with rooftop cooling units. Use of the NILM for fault detection and diagnosis (FDD) is important because (1) it complements other FDD schemes that are based on thermo-fluid sensors and analyses and (2) it is minimally intrusive (one measuring point in the relatively protected confines of the control panel) and therefore inherently reliable. This paper describes changes in the power signatures of fans and compressors that were found, experimentally and theoretically, to be useful for fault detection.
Mass spectral study of substituted allyl aryl and allyl alkyl selenides and some analogous sulfides (1999)

The electron impact (EI) mass spectra of allyl aryl selenides showed abundant molecular ions and many fragment ions containing the selenium atom. alpha-Cleavage is the dominant process in the fragmentation of selenides, and cleavage product ions are characteristic of the substituents. In the case of 3-methyl allyl and related aryl selenides, characteristic delta-hydrogen migration to the selenium atom is observed. A McLafferty-type rearrangement is found in benzyl allyl selenides and substituted alkyl allyl selenides. The charge on the rearrangement products preferably remains on the fragments containing the phenyl group. The [M - SeH](+), [M - CH(3)](+) and [M - C(2)H(4)](+) ions are found only in the EI mass spectrum of allyl phenyl selenide, and are attributed to a Claisen rearrangement in the source of the mass spectrometer. All structurally informative fragmentation processes are supported by collision induced dissociation spectra of molecular ions. The fragmentation patterns found in methane chemical ionization (CI) spectra of the selenides were significantly different from those observed in EI. The EI and CI mass spectra of analogous sulfides showed similar behaviour to that observed in the corresponding selenides. Copyright 1999 John Wiley & Sons, Ltd.
Inhibitors of advanced glycation end‐products prevent loss of enteric neuronal nitric oxide synthase in diabetic rats (2007)

Gastrointestinal dysfunction is common in diabetes, and several studies indicate that loss of neuronal nitrergic inhibition may play an important role in its pathogenesis. However, the mechanisms responsible for this effect remain largely unknown. We have previously shown that advanced glycation end-products (AGEs) formed by non-enzymatic glycation dependent processes, can inhibit the expression of intestinal neuronal nitric oxide synthase (nNOS) in vitro acting via their receptor, receptor for AGEs. We now hypothesized that this effect may also be important in experimental diabetes in vivo. We aimed to evaluate the role of AGEs on duodenal nNOS expression and the effects of aminoguanidine (a drug that prevents AGE formation) and ALT-711 (AGE cross-link breaker) in experimental diabetes. Streptozotocin induced diabetic rats were randomized to no treatment, treatment with aminoguanidine (1 g L(-1) daily through drinking water) at the induction of diabetes, or treatment with ALT-711 (3 mg kg(-1) intraperitoneally), beginning at week 6. A fourth group was used as healthy controls. We performed real time polymerase chain reaction, Western blotting and immunohistochemistry to detect nNOS expression. AGE levels were analysed using sandwich ELISA. Diabetes enhanced accumulation of AGEs in serum, an effect that was prevented by treatment with aminoguanidine and ALT-711. Further, diabetic rats showed a significant reduction in duodenal nNOS expression by mRNA, protein and immunocytochemistry, an effect that was prevented by aminoguanidine. ALT-711 had similar effects on nNOS protein and immunohistochemistry (but not on mRNA levels). The generation of AGEs in diabetes results in loss of intestinal nNOS expression and may be responsible for enteric dysfunction in this condition. This study suggests that treatment directed against AGEs may be useful for the treatment of gastrointestinal complications of diabetes.
Glomerular abundance of complement proteins characterized by proteomic analysis of laser-captured microdissected glomeruli associates with progressive disease in IgA nephropathy (2017)

In conclusion, higher glomerular abundance of complement proteins was associated with a progressive clinical course in IgAN and are candidate biomarkers to predict prognosis.
Severe Aortic Valve Regurgitation in Relapsing Polychondritis (2017)

Rossi, Francesca Wanda MD, PhD; Mercurio, Valentina MD; Rivellese, Felice MD, PhD; Lobasso, Antonio MD; Barbieri, Letizia MD; Tocchetti, Carlo Gabriele MD, PhD, FHFA; de Paulis, Amato MD; Marone, Gianni MD, FRCP Author Information
Multi-channel time digitizing systems (2003)

In this paper we present an overview of a family of Time-to-Digital Converter (TDC) systems developed at HYPRES over the past several years. We have developed three types of RSFQ-based time digitizing systems: an eight-channel multi-hit 30-ps TDC, a two-channel multi-hit 6-ps TDC, and a dual-function multi-hit TDC/ADC. We present results of successful testing of an all-digital TDC up to 33-GHz clock frequency, digitizing at 30-ps time intervals. The eight-channel all-digital TDC chip occupies a 1 cm /spl times/1 cm area with more than 10000 Josephson junctions. For better time resolution, the digital counter-based TDC can be integrated with an analog prescaler. The prescaler improves time resolution to 6 ps and has also been successfully tested. We have also integrated TDC channel with sensitive SQUID to a dual-function ADC/TDC digitizer. An advanced VXI-based interface allows the parallel 8-channel data to be acquired at a read-out clock rate of 100 MHz.