gebhart/patrepeval huggingface dataset:
JAMA Oncology—The Year in Review, 2020 (2021)

2020 has been an unprecedented year, not only for the world but also for JAMA Oncology. The coronavirus disease 2019 (COVID-19) pandemic dominated both the news and the medical literature. JAMA Oncology received more than 350 manuscripts related to the COVID-19 pandemic in 2020, including one of the first reports of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission in patients with cancer from Wuhan province, China, which was published on March 25, 2020 (Table ). ][3][4][5][6] I thank our authors, reviewers, and readers for the significant contributions made to the journal this past year, especially surrounding the pandemic. The editorial board, our JAMA Oncology editors, and I are honored to have the opportunity to serve the oncology community by offering original, innovative, and timely scientific content that has a direct impact on researchers, clinicians, and the patients we serve. Most importantly, we rapidly evaluated and published COVID-19related articles to provide needed information for decisionmaking concerning the infection and its implications in patients with cancer and cancer treatment changes during the pandemic. The journal's impact factor of 24.8 places it as one of the highest-ranking oncology journals.
In vitro assessment of biological activity and stability of the ALVAC-HIV vaccine (2018)

The first evidence in humans that a safe and effective preventive vaccine for HIV is possible came from the phase III HIV clinical trial RV144 in Thailand. This trial was based on a prime/boost combination of a recombinant canarypox vaccine and two glycoprotein 120 proteins (ALVAC-HIV and AIDSVAX B/E). A pivotal phase IIb/III trial has recently commenced in the Republic of South Africa, for which the infectious titer assay was applied as the quantitative release test for the ALVAC-HIV vaccine. The infectious titer assay measures the ability of the vaccine vector to infect target permissive cells, but does not indicate if the vaccine transgenes are expressed. We have developed a high-throughput biological activity assay that provides results in agreement with the infectious titer assay. This assay uses flow cytometry to quantify expression of ALVAC-HIV encoded proteins gp120 and p24 in human cells. This transgene expression is detected by two cross-clade-reactive, biologically functional human anti-gp120 monoclonal antibodies isolated from clinical trial participants and a commercial mouse anti-p24 monoclonal antibody. The relative biological activity of the vaccine test sample is calculated by comparison of the test sample dose-response curve against that of a reference standard. We show that the novel biological activity assay is specific, accurate, precise, stability-indicating, and robust. The assay is being used for characterization of ALVAC-HIV (vCP2438) product, the efficacy of which is being evaluated in the pivotal phase IIb/III clinical trial HVTN702. The biological activity assay has the potential to indicate vaccine consistency and quality as a complement to the infectious titer assay.
Mammosphere-forming cells from breast cancer cell lines as a tool for the identification of CSC-like- and early progenitor-targeting drugs (2010)

Here we show that a subpopulation of MCF-7 breast cancer cells which stains pale to Toluidine Blue (Light Cells- LCs), is endowed with features of CSCs. LCs give rise to self-renewing mammospheres and express typical CSC markers; moreover this subpopulation is chemoresistant and highly tumorigenic in vivo. LCs can be identified in several other breast cancer cell lines, irrespectively of their histological origin (luminal vs. mesenchymal vs. basal) and represent an heterogeneous cell population composed mainly of CSC-like and early progenitor cells. By a limited in vitro drug screening assay, we identify compounds which can specifically interfere with the viability of LCs from multiple breast cancer cell lines. Analysis of the Sphere-Forming Efficiency (SFE) and of the distribution of ALDH(bright) cells within the treated cell lines suggest that one of the identified compounds acts in vitro by modulating the CSC phenotype. Interestingly, a subset of the identified compounds is known to affect directly or indirectly the NFkappaB pathway which is emerging as an important modulator of CSC proliferation and chemoresistance.
Magnetic resonance imaging analysis of age‐related changes in the brains of individuals with Down's syndrome (1994)

Neuroanatomic characteristics of the brains of individuals with Down's syndrome (DS) are typically characterized at autopsy. Apparent anatomic differences in brain between DS and normal individuals are observable upon gross inspection of MRIs. Area measurements from coronal MRIs are used in this study to determine quantitative structural differences that may occur in DS and during aging. In DS individuals, a significantly larger parahippocampal gyrus, and smaller hippocampus and neocortex, are reported relative to age-matched controls. We also examine two DS individuals with a clinical diagnosis of dementia who exhibit atrophy similar to that typically observed in Alzheimer's disease. MRI appears to be a useful tool for quantitative anatomic analysis and may be beneficial for determining baseline anatomic measures that can be useful in the diagnosis of changes associated with dementia.
Effect of 3-Dimensional, Virtual Reality Models for Surgical Planning of Robotic Prostatectomy on Trifecta Outcomes: A Randomized Clinical Trial (2022)

This randomized clinical trial demonstrated patients whose surgical planning involved 3D VR models have better oncologic outcomes while maintaining functional outcomes.
Vasoactive agents and splanchnic oxygen uptake (1982)

Many vasoactive agents are known to alter oxygen uptake by splanchnic organs. Data from the literature indicate that, in general, vasodilators increase, whereas vasoconstrictors decrease oxygen uptake. We compare and contrast the effects of vasoactive agents on oxygen uptake observed in vivo, under constant-flow and free-flow conditions, to those observed in vitro. The discrepancies between the in vivo and in vitro data are discussed relative to the effects of vasoactive agents on blood flow, intraorgan blood flow distribution, the countercurrent exchange of oxygen, capillary exchange capacity, and oxidative metabolism. Changes in blood flow, oxidative metabolism, and capillary density appear to be the major mechanisms by which vasoactive agents alter splanchnic oxygen uptake in vivo. Experimental designs are proposed that may help minimize inconsistencies in the data in future studies.
Inhibitor-Sensitive FGFR2 and FGFR3 Mutations in Lung Squamous Cell Carcinoma (2013)

A comprehensive description of genomic alterations in lung squamous cell carcinoma (lung SCC) has recently been reported, enabling the identification of genomic events that contribute to the oncogenesis of this disease. In lung SCC, one of the most frequently altered receptor tyrosine kinase families is the fibroblast growth factor receptor (FGFR) family, with amplification or mutation observed in all four family members. Here, we describe the oncogenic nature of mutations observed in FGFR2 and FGFR3, each of which are observed in 3% of samples, for a mutation rate of 6% across both genes. Using cell culture and xenograft models, we show that several of these mutations drive cellular transformation. Transformation can be reversed by small-molecule FGFR inhibitors currently being developed for clinical use. We also show that mutations in the extracellular domains of FGFR2 lead to constitutive FGFR dimerization. In addition, we report a patient with an FGFR2-mutated oral SCC who responded to the multitargeted tyrosine kinase inhibitor pazopanib. These findings provide new insights into driving oncogenic events in a subset of lung squamous cancers, and recommend future clinical studies with FGFR inhibitors in patients with lung and head and neck SCC.
Sperm proteasome and fertilization (2011)

The omnipresent ubiquitin-proteasome system (UPS) is an ATP-dependent enzymatic machinery that targets substrate proteins for degradation by the 26S proteasome by tagging them with an isopeptide chain composed of covalently linked molecules of ubiquitin, a small chaperone protein. The current knowledge of UPS involvement in the process of sperm penetration through vitelline coat (VC) during human and animal fertilization is reviewed in this study, with attention also being given to sperm capacitation and acrosome reaction/exocytosis. In ascidians, spermatozoa release ubiquitin-activating and conjugating enzymes, proteasomes, and unconjugated ubiquitin to first ubiquitinate and then degrade the sperm receptor on the VC; in echinoderms and mammals, the VC (zona pellucida/ZP in mammals) is ubiquitinated during oogenesis and the sperm receptor degraded during fertilization. Various proteasomal subunits and associated enzymes have been detected in spermatozoa and localized to sperm acrosome and other sperm structures. By using specific fluorometric substrates, proteasome-specific proteolytic and deubiquitinating activities can be measured in live, intact spermatozoa and in sperm protein extracts. The requirement of proteasomal proteolysis during fertilization has been documented by the application of various proteasome-specific inhibitors and antibodies. A similar effect was achieved by depletion of sperm-surface ATP. Degradation of VC/ZP-associated sperm receptor proteins by sperm-borne proteasomes has been demonstrated in ascidians and sea urchins. On the applied side, polyspermy has been ameliorated by modulating sperm-associated deubiquitinating enzymes. Diagnostic and therapeutic applications could emerge in human reproductive medicine. Altogether, the studies on sperm proteasome indicate that animal fertilization is controlled in part by a unique, gamete associated, extracellular UPS.
Survival and Death Signals Can Predict Tumor Response to Therapy After Oncogene Inactivation (2011)

Cancers can exhibit marked tumor regression after oncogene inhibition through a phenomenon called "oncogene addiction." The ability to predict when a tumor will exhibit oncogene addiction would be useful in the development of targeted therapeutics. Oncogene addiction is likely the consequence of many cellular programs. However, we reasoned that many of these inputs may converge on aggregate survival and death signals. To test this, we examined conditional transgenic models of K-ras(G12D)--or MYC-induced lung tumors and lymphoma combined with quantitative imaging and an in situ analysis of biomarkers of proliferation and apoptotic signaling. We then used computational modeling based on ordinary differential equations (ODEs) to show that oncogene addiction could be modeled as differential changes in survival and death intracellular signals. Our mathematical model could be generalized to different imaging methods (computed tomography and bioluminescence imaging), different oncogenes (K-ras(G12D) and MYC), and several tumor types (lung and lymphoma). Our ODE model could predict the differential dynamics of several putative prosurvival and prodeath signaling factors [phosphorylated extracellular signal-regulated kinase 1 and 2, Akt1, Stat3/5 (signal transducer and activator of transcription 3/5), and p38] that contribute to the aggregate survival and death signals after oncogene inactivation. Furthermore, we could predict the influence of specific genetic lesions (p53⁻/⁻, Stat3-d358L, and myr-Akt1) on tumor regression after oncogene inactivation. Then, using machine learning based on support vector machine, we applied quantitative imaging methods to human patients to predict both their EGFR genotype and their progression-free survival after treatment with the targeted therapeutic erlotinib. Hence, the consequences of oncogene inactivation can be accurately modeled on the basis of a relatively small number of parameters that may predict when targeted therapeutics will elicit oncogene addiction after oncogene inactivation and hence tumor regression.
Miniaturized InSb Mid-JR Sensor for Room Temperature Operation (2006)

This paper reports the development and evaluation of an InSb photovoltaic infrared sensor (InSb PVS) operating at room temperature. The InSb PVS consists of 700 InSb p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> -p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> -n <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> photodiodes connected in series, on a semi-insulating GaAs (100) substrate. An Al <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.17</sub> In <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.83</sub> Sb barrier layer between p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> and p <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-</sup> layers was used to reduce diffusion of photo-excited electrons. Cutoff wavelength was 6.8 mum and output signal was linear with incident irradiance. Noise equivalent temperature difference (NETD) of 2.2times10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">-3</sup> degC/Hz <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1/2</sup> was obtained at room temperature, which shows the sensor to be a promising device for human body detection or non-contact thermometry.
Achieving 11.95% efficient Cu2ZnSnSe4 solar cells fabricated by sputtering a Cu–Zn–Sn–Se quaternary compound target with a selenization process (2019)

CZTSe solar cells with 11.95% peak efficiency have been achieved by sputtering a quaternary compound target using the selenization process.
Contextual Language Model Adaptation for Conversational Agents (2018)

Statistical language models (LM) play a key role in Automatic Speech Recognition (ASR) systems used by conversational agents. These ASR systems should provide a high accuracy under a variety of speaking styles, domains, vocabulary and argots. In this paper, we present a DNN-based method to adapt the LM to each user-agent interaction based on generalized contextual information, by predicting an optimal, context-dependent set of LM interpolation weights. We show that this framework for contextual adaptation provides accuracy improvements under different possible mixture LM partitions that are relevant for both (1) Goal-oriented conversational agents where it's natural to partition the data by the requested application and for (2) Non-goal oriented conversational agents where the data can be partitioned using topic labels that come from predictions of a topic classifier. We obtain a relative WER improvement of 3% with a 1-pass decoding strategy and 6% in a 2-pass decoding framework, over an unadapted model. We also show up to a 15% relative improvement in recognizing named entities which is of significant value for conversational ASR systems.
Efficiency Enhancement in Hybrid P3HT/Silicon Nanocrystal Solar Cells (2011)

Abstract Hybrid organic-inorganic solar cells from poly(3-hexylthiophene) (P3HT) and freestanding silicon nanocrystals (Si-ncs) combine the advantages of silicon-based photovoltaics with the cost-efficient solution processing technique. At present, the microwave-plasma synthesis of Si-ncs that allows for a future upscaling to industrial demands is at the expense of the Si-nc surface quality and the number of charge-trapping defects. Here, we present an enhancement of the solar cell performance by identifying the major factors which are limiting the device efficiency. With the help of low-cost post-growth treatments of the Si-ncs and the optimization of various device parameters, P3HT:Si-ncs bulk heterojunction solar cells with an efficiency up to 1.1% are achieved. In particular, etching of the Si-ncs with hydrofluoric acid to remove the surface oxide shells and surface defects has a strong impact on the solar cell performance. An intermediate Si weight ratio of around 60% is found to lead to the highest current densities. For Si-ncs with very small diameters, an additional enhancement of the open circuit voltage was observed. Moreover, we show that the structural order of P3HT has a strong influence on the efficiency, which can be explained by an improved charge carrier separation at the P3HT/Si-ncs interface in combination with an enhanced charge transport in the P3HT phase.
(INVITED)Direct laser writing of visible and near infrared 3D luminescence patterns in glass (2022)

We report the fluorescent properties of 3D localized structure with size near the diffraction limit induced by femtosecond direct laser writing (DLW) in Yb 3+ and silver-containing phosphate glass. The homogenous dispersion of the silver ions and Yb 3+ ions in the glass matrix before DLW was evidenced using photo-luminescent spectroscopy and time-resolved spectroscopy. Using high repetition rate femtosecond DLW, the inscription of 3D visible and near-infrared fluorescent patterns formed by co-localization of silver cluster and Yb 3+ ions was demonstrated. The local refractive index change associated with the formation of silver clusters is dependent on the laser irradiance. Confocal micro-luminescent spectroscopy for excitation wavelength in the visible range shows efficient emission of Yb 3+ only on DLW induced 3D fluorescent patterns. This finding demonstrated the ability to perform thanks to DLW laser a resonant efficient nonradiative energy transfer from silver clusters to Yb 3+ and allows 3D writing of near-infrared luminescence.
Non Contrast-Enhanced MRA versus Ultrasound Blood Vessel Assessment to determine the Choice of Hemodialysis Vascular Access (2013)

The results obtained indicate that extreme caution should be exercised when replacing one diameter measurement modality with the other. A further need exists to improve both vessel mapping protocols to obtain a geometric description of the upper extremity vasculature regardless of acquisition modality.
Spraying Small Water Droplets Acts as a Bacteriocide (2020)

Disinfectants are important for arresting the spread of pathogens in the environment. Frequently used disinfectants are often incompatible with certain surfaces, expensive and can produce hazardous by-products. We report that micron-sized water droplets can act as an effective disinfectant, which were formed by spraying pure bulk water with coaxial nebulizing airflow. Spraying for 20 min onto <i>Escherichia coli</i> and <i>Salmonella typhimurium</i> on stainless-steel discs caused inactivation of over 98% of the bacteria. Control experiments resulted in less than 10% inactivation (water stream only and gas only) and 55% inactivation with 3% hydrogen peroxide. Experiments have shown that cell death results from cell wall destruction. We suggest that the combined action of reactive oxygen species present in water droplets (but not in bulk water) along with the droplet surface charge is responsible for the observed bactericidal activity.
Laparoscopic Treatment of Ureteral Obstruction Secondary to Ovarian Remnant Syndrome (1993)

A case is presented in which an ovarian remnant following total abdominal hysterectomy and bilateral salpingo-oophorectomy resulted in unilateral ureteral obstruction. The obstructing tissue was excised laparoscopically with simultaneous ureteroscopic monitoring.
Enhanced Differential Correlation Method for the Acquisition of Galileo Signals (2006)

In this paper, we analyze an enhanced differential non-coherent integration method for the acquisition stage of a BOC-modulated CDMA signal in the new European Galileo satellite navigation system. This method, denoted by DN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , offers an improved suppression of any temporally uncorrelated interferers. Background noise is naturally the most obvious source of temporally uncorrelated interference, but, for example, in CDMA systems, also a multiaccess interference is inherently very weakly time-correlated. Here, we carry out a comprehensive comparison between DN <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> method, the conventional non-coherent integration, and the traditional differential non-coherent integration methods. The correlation methods are compared and analyzed in fading channels, taking into account both ambiguous BOC and sideband based unambiguous technique (such as Betz&Fishman method). We also propose a combined algorithm, which chooses the best correlation method based on an estimation of the coherence time of the current channel
Analysis of matrix metalloproteinases, especially MMP‐8, in gingival crevicular fluid, mouthrinse and saliva for monitoring periodontal diseases (2015)

Matrix metalloproteinase-8 is a promising candidate biomarker for oral fluid (gingival crevicular fluid, peri-implant sulcular fluid and saliva) and mouthrinse chair-side/point-of-care diagnostics to predict, diagnose and determine the progressive phases of episodic periodontitis and peri-implantitis, as well as to monitor the treatments and medications. Matrix metalloproteinase-8 can be used alone or together with interleukin-1beta and Porphyromonas gingivalis to calculate cumulative risk score at the subject level as a successful diagnostic tool, especially in large-scale public health surveys, in which a thorough periodontal examination is not feasible.
Segmental thoracic lipomatosis of nerve with nerve territory overgrowth (2014)

Lipomatosis of nerve (LN), or fibrolipomatous hamartoma, is a rare condition of fibrofatty enlargement of the peripheral nerves. It is associated with bony and soft tissue overgrowth in approximately one-third to two-thirds of cases. It most commonly affects the median nerve at the carpal tunnel or digital nerves in the hands and feet. The authors describe a patient with previously diagnosed hemihypertrophy of the trunk who had a history of large thoracic lipomas resected during infancy, a thoracic hump due to adipose proliferation within the thoracic paraspinal musculature, and scoliotic deformity. She had fatty infiltration in the thoracic spinal nerves on MRI, identical to findings pathognomonic of LN at better-known sites. Enlargement of the transverse processes at those levels and thickened ribs were also found. This case appears to be directly analogous to other instances of LN with overgrowth, except that this case involved axial nerves rather than the typical appendicular nerves.