gebhart/patrepeval huggingface dataset:
Basic Principles of Translational Research (2012)

Translational research turns fundamental new science and innovations into a product that has value to the public. The process is difficult because it combines a variety of diverse disciplines and skills from basic science, clinical medicine, engineering, business, public health, laws and regulations. These areas are so wide apart that it is very difficult to combine. The author has engaged in translational research since the early 1980’s and will describe the processes, pitfalls and rewards through typical examples from his projects that include: development of imaging monitored cryosurgery from concept to treatment of hundreds of thousands of patients, transgenes in food engineering from basic science to a twenty year wait for FDA approval, microelectroporation from basic concept to incorporation of the technology by numerous companies and non-thermal irreversible electroporation from basic concept to current clinical use in over 50 hospitals and over thousand treated patients.
A 25 dBm outphasing power amplifier with novel non-isolated combining network (2014)

This paper presents a 25 dBm outphasing power amplifier designed in a standard 45 nm CMOS process. Instead of using bulky quarter-wave transmission lines or transformers as non-isolated combiners, we propose a new combiner based on lump elements. The elements of the combiner act differently for in-phase and out-of-phase components, which allows additional resonant networks to be formed for improved backoff efficiency. The proposed PA design achieves 55% peak power added efficiency (PAE) at 900 MHz and 45% at 2.4 GHz. For an OFDM signal with 6 dB PAR, the PAE is 32% at 900 MHz and 22% at 2.4 GHz. The linearity of the PA meets WiFi spec without digital predistortion (DPD). With DPD, the linearity of the PA can be improved further to reach -53 dBc, -50 dBc, -42 dBc ACPR for 10 MHz, 20 MHz, and 2-carrier 20 MHz LTE signals.
A Wearable Microneedle‐Based Extended Gate Transistor for Real‐Time Detection of Sodium in Interstitial Fluids (2021)

Sodium is a prominent prognostic biomarker for assessing health status, such as dysnatremia. As of now, detection and monitoring of sodium levels in the human body is carried out by means of laborious and bulky laboratory equipmentand/or by offline analysis of various body fluids. Herein, an innovative stretchable, skin-conformal and fast-response microneedle extended-gate FET biosensor is reported for real-time detection of sodium in interstitial fluids for minimally invasive health monitoring along with high sensitivity, low limit of detection, excellent biocompatibility, and on-body mechanical stability. The integration of the reported device with a wireless-data transmitter and the Internet-of-Things cloud for real-time monitoring and long-term analysis is reported and discussed. This platform would eventually help bringing unlimited possibilities for effecient medical care and accurate clinical decision-making.
Evaluating the efficacy of test-driven development (2006)

This paper discusses software development using the Test Driven Development (TDD) methodology in two different environments (Windows and MSN divisions) at Microsoft. In both these case studies we measure the various context, product and outcome measures to compare and evaluate the efficacy of TDD. We observed a significant increase in quality of the code (greater than two times) for projects developed using TDD compared to similar projects developed in the same organization in a non-TDD fashion. The projects also took at least 15% extra upfront time for writing the tests. Additionally, the unit tests have served as auto documentation for the code when libraries/APIs had to be used as well as for code maintenance.
Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation (2022)

Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover 'new' genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic 'signatures' that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.
Neutral depletion in inductively coupled plasmas using hybrid-type direct simulation Monte Carlo (2008)

Neutral and ion transport phenomena were simulated by a hybrid-type direct simulation Monte Carlo (DSMC) method for a one-dimensional (1D) electrostatic plasma in Ar/N2 mixtures to identify the mechanism of neutral depletion. The results show that gas heating and pressure balance are the main mechanisms of neutral depletion in an inductively coupled plasma. When plasma pressure becomes comparable to neutral pressure in high density plasma sources (Te∼2−5 eV, ne∼1011−1012 cm−3), the total pressure (neutral pressure and plasma pressure) is conserved. Therefore, the finite plasma pressure (mainly electron pressure) reduces the neutral pressure. Neutrals collide with ions that have been accelerated by the ambipolar electric field and with Franck-Condon dissociated atoms, resulting in gas heating. Significant neutral depletion (up to 90%) is found at the typical condition of inductively coupled plasma process reactors. The resulting neutral depletion enhances the plasma transport to the surrounding wall, increases the particle loss, and decreases the plasma density.
CCDC 268447: Experimental Crystal Structure Determination (2006)

An entry from the Cambridge Structural Database, the world’s repository for small molecule crystal structures. The entry contains experimental data from a crystal diffraction study. The deposited dataset for this entry is freely available from the CCDC and typically includes 3D coordinates, cell parameters, space group, experimental conditions and quality measures.
On the Enigma of Chlorophyll Degradation: The Constitution of a Secoporphinoid Catabolite (1991)

The fall colors of leaves is caused by the degradation of the green plant pigment chlorophyll—a complex process about which not much is yet known. Now for the first time with the constitution of the chlorophyll catabolite 1, a 1-formyl-19-oxobilane, a structural pointer has been found which throws light on the degradation of chlorophyll. M⊕ = K⊕.
Guest Editorial Special Issue on Sparsity Driven Methods in Medical Ultrasound (2018)

The fundamentals of ultrasound signal and image processing relied for a long time on the hypothesis of Gaussianity, justified by the central limit theorem and the point-scattering model widely accepted in ultrasound imaging. Assuming a large number of scatterers per resolution cell, the probability distribution function of the backscattered radio frequency (RF) signals converges indeed to a Gaussian law, leading to Rayleigh-distributed envelope images. Over the last three decades, several studies questioned this paradigm, based on observations proving that in several clinical applications, the Gaussian distribution did not fit the data well. Consequently, a wide range of non-Gaussian laws were used to model the backscattered signals in a number of ultrasound imaging applications such as tissue characterization and image segmentation. In the early 2000s, heavy-tailed statistical models were shown to be well adapted to ultrasound images, paving the way to new prospects in ultrasound signal processing and ultimately leading to growing interest in the concept of sparsity for ultrasound imaging. Sparse signals are a special class of signals with a particular structure, i.e., they contain many coefficients equal to or close to zero either in the time domain or when represented in an appropriate basis or dictionary.
Latent pregnancy-associated hypopituitarism accompanied by chronic thyroiditis and limited scleroderma, revealed by the breakout of adrenal insufficiency 42 years after delivery (2013)

Pregnancy-associated hypopituitarism (PAH) has been referred to as Sheehan’s syndrome and lymphocytic hypophysitis, both of which are occasionally disclosed several decades after delivery. We report the rare case of a 70-year-old woman diagnosed with PAH with empty sella 42 years after her second delivery; she had had an episode of hypovolemic shock during her second delivery. She had been referred to our hospital because of the emergence of non-sustained ventricular tachycardia and symptoms of appetite loss and general fatigue accompanied by hyponatremia, hypoglycemia, and hypothyroidism. Hypopituitalism and secondary adrenal insufficiency had been revealed after her hospitalization. She had suffered from Raynaud’s syndrome for the past several decades. Our testing revealed that the patient had autoantibodies for thyroid peroxidase, thyroglobulin, and centromere, indicating the diagnosis of chronic thyroiditis and limited scleroderma. Her series of symptoms had been treated successfully by hydrocortisone and thyroid hormone replacement therapy. To the best of our knowledge, latent PAH accompanied by limited scleroderma have not been described in the international literature to date though quite a few latent cases may exist. We assume that some autoimmune mechanism during the perinatal period may possibly be a common step in the pathogenesis of PAH, chronic thyroiditis and limited scleroderma.
Data from Tumor ENPP1 (CD203a)/Haptoglobin Axis Exploits Myeloid-Derived Suppressor Cells to Promote Post-Radiotherapy Local Recurrence in Breast Cancer (2023)

&lt;div&gt;Abstract&lt;p&gt;Locoregional failure (LRF) in patients with breast cancer post-surgery and post-irradiation is linked to a dismal prognosis. In a refined new model, we identified ectonucleotide pyrophosphatase/phosphodiesterase 1/CD203a (ENPP1) to be closely associated with LRF. ENPP1&lt;sup&gt;hi&lt;/sup&gt; circulating tumor cells (CTC) contribute to relapse by a self-seeding mechanism. This process requires the infiltration of polymorphonuclear myeloid-derived suppressor cells and neutrophil extracellular trap (NET) formation. Genetic and pharmacologic ENPP1 inhibition or NET blockade extends relapse-free survival. Furthermore, in combination with fractionated irradiation, ENPP1 abrogation obliterates LRF. Mechanistically, ENPP1-generated adenosinergic metabolites enhance haptoglobin (HP) expression. This inflammatory mediator elicits myeloid invasiveness and promotes NET formation. Accordingly, a significant increase in ENPP1 and NET formation is detected in relapsed human breast cancer tumors. Moreover, high ENPP1 or HP levels are associated with poor prognosis. These findings unveil the ENPP1/HP axis as an unanticipated mechanism exploited by tumor cells linking inflammation to immune remodeling favoring local relapse.&lt;/p&gt;Significance:&lt;p&gt;CTC exploit the ENPP1/HP axis to promote local recurrence post-surgery and post-irradiation by subduing myeloid suppressor cells in breast tumors. Blocking this axis impairs tumor engraftment, impedes immunosuppression, and obliterates NET formation, unveiling new opportunities for therapeutic intervention to eradicate local relapse and ameliorate patient survival.&lt;/p&gt;&lt;p&gt;&lt;i&gt;This article is highlighted in the In This Issue feature, p. 1171&lt;/i&gt;&lt;/p&gt;&lt;/div&gt;
Autonomous Asteroid Exploration by Rational Agents (2013)

The history of software agent architectures has been driven by the parallel requirements of real-time decision-making and the sophistication of the capabilities the agent can provide. Starting from reactive, rule based, subsumption through to layered and belief-desire-intention architectures, a compromise always has to be reached between the ability to respond to the environment in a timely manner and the provision of capabilities that cope with relatively complex environments. In the spirit of these past developments, this paper is proposing a novel "anthropomorphic" agent architecture that brings together the most desirable features: natural language definitions of agent reasoning and skill descriptions, shared knowledge with operators, the combination of fast reactive as well as long term planning, ability to explain why certain actions are taken by the autonomous agent and finally inherent formal verifiability. With these attributes, the proposed agent architecture can potentially cope with the most demanding autonomous space missions.
THE UTILITY OF PROTEOMICS IN ALGAL TAXONOMY: BOSTRYCHIA RADICANS/B. MORITZIANA (RHODOMELACEAE, RHODOPHYTA) AS A MODEL STUDY1 (2008)

A comparison of the proteome of eight genetically well-characterized isolates of the Bostrychia radicans (Mont.) Mont./B. moritziana (Sond. ex Kütz.) J. Agardh species complex was undertaken to establish if genetic relationships among them can be determined using proteome data. Genetic distances were calculated on the basis of common and distinct spots in two-dimensional gel electrophoresis (2-DE). Proteomes of the male and female plants of each population were compared to analyze the range of genetic difference within an isolate. Haploid male and female plants of the same species had 3.7%-7.1% sex-specific proteins. The degree of similarity of the proteome was consistent with previous DNA sequence data and sexual compatibility studies between the isolates. Two sexually compatible isolates from Venezuela showed a pair-wise distance ranging from 0.14 to 0.21. The isolates from Mexico and Venezuela, which were partially compatible, showed a maximum pair-wise distance of 0.26. A high level of genetic difference was found among isolates that were sexually incompatible. The isolate from Brazil was reproductively isolated from the Mexico and Venezuela isolates and showed a maximum pair-wise distance of 0.65 and 0.58, respectively. Comparative proteomics may be helpful for studying genetic distances among algal samples, if intraisolate variation (gene expression) can be minimized or tested.
Viewpoints on the Integrated Reform of Social Security and Tax Systems: Increased Consumption Tax and Intergenerational Equity 1 (2012)

The current fiscal situation of Japan is the worst among leading industrialized nations, based on both stock and flow, which means that currently active generations receive benefits on the premise of burdens borne by the future generations. In this paper, we discuss the cause of Japan's fiscal deficit and its relation to economic growth, calculate when and to what degree the tax burden will need to be increased to prevent fiscal collapse in Japan, and analyze how this would contribute to greater equity of intergenerational burdens by applying generational accounts. In such Japan's fiscal situations, spending cuts can only have a limited effect in creating financial resources because Japan has the biggest upward pressure on expenditure of social security spending associated with its aging society. Therefore, it is important to increase tax burden for preventing the fiscal deficit from expanding. Our estimation suggests the need to raising consumption tax by 9% (to 14%) in 2015 and further 6% (to 20%) in 2020, assuming that the primary balance (around 6.5% of GDP as of FY2009) will be "reduced to around 6% by FY2015 and below 3% by FY2020". This appears to be quite a large increase in burdens, although generational disparity would not be improved without such increases, so that such policy could have good possibilities such as tax smoothing and reduction of the risk of a sharp increase in interest payments.
AdaptUbiFlow: Selection and Adaptation in Workflows for Ubiquitous Computing (2011)

Ubiquitous environments still suffer from low availability given that any device may fail and it is hard to replace a failed element. In this paper we present AdaptUbiFlow (Adaptive Ubiquitous Workflow), an OpenCOPI´s element that aims to increase the availability of an ubiquitous system. When a device fails, AdaptUbiFlow supports the automatic reconfiguration of the system replacing the failed device (or service) by an equivalent one, this makes the system fault-tolerant without the need of any manual intervention. The replacing of a device/service is chosen taking into account not only the QoS and QoC (Quality of Context) provided but also the application's execution flow to ensure that the best adaptation option will be chosen. AdaptUbiFlow evaluation showed encouraging results.
Image Statistics and Anisotropic Diffusion (2003)

Many sensing techniques and image processing applica-tions are characterized by noisy, or corrupted, image data. Anisotropic diffusion is a popular, and theoretically well understood, technique for denoising such images. Diffu-sion approaches however require the selection of an “edge stopping ” function, the definition of which is typically ad hoc. We exploit and extend recent work on the statistics of natural images to define principled edge stopping func-tions for different types of imagery. We consider a variety of anisotropic diffusion schemes and note that they compute spatial derivatives at fixed scales from which we estimate the appropriate algorithm-specific image statistics. Going beyond traditional work on image statistics, we also model the statistics of the eigenvalues of the local structure tensor. Novel edge-stopping functions are derived from these image statistics giving a principled way of formulating anisotropic diffusion problems in which all edge-stopping parameters are learned from training data. 1
Synthesis, Structure−Activity Relationship, and Pharmacological Profile of Analogs of The ASIC-3 Inhibitor A-317567 (2009)

The synthesis, structure-activity relationship (SAR), and pharmacological evaluation of analogs of the acid-sensing ion channel (ASIC) inhibitor A-317567 are reported. It was found that the compound with an acetylenic linkage was the most potent ASIC-3 channel blocker. This compound reversed mechanical hypersensitivity in the rat iodoacetate model of osteoarthritis pain, although sedation was noted. Sedation was also observed in ASIC-3 knockout mice, questioning whether sedation and antinociception are mediated via a non-ASIC-3 specific mechanism.
Insights into Fenton-like oxidation of oxytetracycline mediated by Fe-doped porous g-C3N4 nanomaterials: synthesis, performance and mechanism (2023)

Fe/PCN nanomaterial synthesized via a one-step self-assembly strategy was proposed to provide guidance for the removal of OTC.
Supplementary Figure 3 from Intranodal Vaccination with Naked Antigen-Encoding RNA Elicits Potent Prophylactic and Therapeutic Antitumoral Immunity (2023)

Supplementary Figure 3 from Intranodal Vaccination with Naked Antigen-Encoding RNA Elicits Potent Prophylactic and Therapeutic Antitumoral Immunity
Biomarker Expression in Multifocal Vulvar High-Grade Squamous Intraepithelial Lesions (2021)

In patients with high-grade squamous intraepithelial lesion (HSIL) of the vulva, the presence of multiple lesions, called multifocal HSIL, is common. The aim of this exploratory study was to investigate biomarker expression profiles in multifocal HSIL. In total, 27 lesions from 12 patients with high-risk human papillomavirus (HPV)-positive multifocal HSIL were tested for HPV genotype, expression of p16<sup>INK4a</sup> and Ki-67, and DNA methylation of six genes. HPV16 was found most commonly in 21 (77.8%) HSILs. In two (16.4%) patients, HPV genotype differed between the lesions. All lesions demonstrated diffuse p16<sup>INK4a</sup> staining, of which three (11.1%) were combined with patchy staining. One patient (8.3%) demonstrated markedly different DNA methylation levels between lesions. Generally, heterogeneity in methylation profiles was observed between different patients, even when other biomarkers showed similar expression. In conclusion, this study is the first to demonstrate heterogeneity of individual lesions in patients with multifocal HSIL. The studied biomarkers have the potential to refine prognostic and predictive diagnostics. Future prospective, longitudinal studies are needed to further explore the potential of a biomarker profile for management of patients with multifocal HSIL.
Scene perception from central to peripheral vision (2017)

Citation: Loschky, L. C., Nuthmann, A., Fortenbaugh, F. C., & Levi, D. M. (2017). Scene perception from central to peripheral vision. Journal of Vision, 17(1), 5. doi:10.1167/17.1.6
Die to Wafer Hybrid Bonding for Chiplet and Heterogeneous Integration: Die Size Effects Evaluation-Small Die Applications (2022)

The Direct Bond Interconnect (DBI®) Ultra technology, a die-to-wafer (D2W) and die-to-die (D2D) hybrid bonding, is a platform technology that offers a hermetically sealed solid Cu-Cu interconnect through room temperature bonding and low temperature anneal. DBI wafer to wafer (W2W) bonding has been in high volume production since 2015. Advancement in D2W hybrid bonding technology in recent years has enabled recent adoption the technology by Sony [1]. AMD [2] and Intel [3]. The DBI Ultra D2W technology offers die-on-tape processing with bonding speeds comparable to mass reflow flip chip assembly. The bonding takes place at room temperature in an ambient environment in a class 1000 cleanroom. A low temperature batch anneal following bonding creates a solid Cu-Cu connection with no solder and no underfill.The value of the DBI Ultra technology can be realized in diverse products ranging from very small die to reticle-size large die. Applications such as RF, sensors and microcontrollers are in the small die domain, while GPUs and FPGAs require bonding of very large die. Ultimate SoC disaggregation implementations may include D2W bonding of mid-large sized memory die (e.g. SRAM in V-Cache) as well as ultra-small die for analog functionalities. In this paper, we present the results of D2W bonding development in die size ranging from 0.4x0.4mm to 3.2x3.0mm. The module build process includes dicing, die preparation on tape, and direct pick & place from a tape frame. The bonding quality is characterized with C-mode scanning acoustic microscopy (CSAM) and cross-section microscopy analysis.