gebhart/patrepeval huggingface dataset:
9q32-q33.1 amplification as a prognostic factor for overall survival in metastatic germ cell tumors. (2011)

4652 Background: Germ cell tumors (GCTs) are the most common malignancy in young men. Recently, our group has reported the development of human nonseminoma (NSE) after orthotopic nude mice implantation and demonstrated acquisition of specific chromosomal imbalances after becoming cisplatin (CDDP) resistant in vivo (Piulats et al, ASCO 2009; abstr e16143). Gain of 9q32-q33.1 was present in 3 of 4 tumors explored and contains genes that could be related to CDDP resistance. Methods: To gain insight into the clinical relevance of these results we next investigate the gains at 9q32-q33.1 by FISH analysis in a retrospective cohort of 75 male patients with metastatic CGTs treated at our hospital from August 1989 to November 2004. NSE represents 84% of the tumors analyzed and 32% were resistant to CDDP based chemotherapy. Four patients with extragonadal GCTs were included. Forty-four patients were considered good prognosis, 14 intermediate and 16 bad according to the IGCCCG prognostic classification. Results: 9q32-q33.1 amplification was identified in 18 out 75 (24%) cases. This amplification was present in 37.5% of resistant and 17.6% of sensitive cases (p=0.06). Overall survival (OS) analysis showed that amplification at 9q32-q33.1 is associated with an increased risk of death in patients with GCTs (HR=2.84; 95% CI 1.14-7.09; p=0.033). In the group of patients with NSE (n=63) the risk of death was increased (HR=3.03; 95% CI 1.18-7.76; p=0.026). The higher risk of death was identified among the group of patients with NSE and good/intermediate prognosis (HR=5.16; 95% CI 1.47-18.12; p=0.014), whereas risk was not modified in patients with bad prognosis disease. When progression-free survival was evaluated, the same pattern was found. Conclusions: We have identified amplification at 9q32-q33.1 as a prognostic factor for OS in metastatic NSE GCTs, being to date the only molecular prognostic marker in this disease.
Genomics of injury (2015)

From the Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, Massachusetts. Classifications: organ dysfunction, nosocomial infection, inflammation, mortality, shock, trauma, intensivist, evidence-based medicine. ClinicalTrials.gov numbers: NCT00257231 and NCT00257244. Address for reprints: Ronald G. Tompkins, MD, ScD, Harvard Medical School Director, Center for Surgery, Innovation & Bioengineering Massachusetts General Hospital, 55 Fruit St, GRB 1401 Boston, MA 02114–2696; email: [email protected].
Ambulatory Glucose Profile (AGP) Report in Daily Care of Patients with Diabetes: Practical Tips and Recommendations (2022)

The ambulatory glucose profile (AGP) is now established as the standardised, practical one-page report for graphically presenting a summary of glycaemic control status in patients with diabetes who use continuous glucose monitoring (CGM) systems as part of their daily diabetes care. The AGP report provides both a visual and a statistical summary of the glucose metrics that, as agreed in the 2019 international consensus for assessing glycaemic control, should be analysed in all people with diabetes who are using CGM systems. The AGP report can be analysed in a systematic fashion to understand current glycaemic control and to monitor, in real time, the impact of adjustments to therapy in both type 1 diabetes and type 2 diabetes. Here we provide a practical guide to the glycaemic measures that are summarised in the AGP Report and illustrate the essential components of an AGP review in a series of hypothetical, real-world, patient-centred case studies (see Supplementary Materials).
Preparation of monodisperse multilayer vesicles of controlled size and high encapsulationratio. (1993)

The effect of shear on lyotropic lamellar phases is studied by light scattering and microscopic observations. We found that in a certain range of shear rate the lamellar phase organizes itself into spherical multilayer vesicles of well controlled size. The size is shown to vary as the inverse of the square root of the shear rate. A simple explanation in terms of a balance between shear stress and elastic forces is given.
Modeling of spiking-bursting neural behavior using two-dimensional map (2002)

A simple model that replicates the dynamics of spiking and spiking-bursting activity of real biological neurons is proposed. The model is a two-dimensional map that contains one fast and one slow variable. The mechanisms behind generation of spikes, bursts of spikes, and restructuring of the map behavior are explained using phase portrait analysis. The dynamics of two coupled maps that model the behavior of two electrically coupled neurons is discussed. Synchronization regimes for spiking and bursting activities of these maps are studied as a function of coupling strength. It is demonstrated that the results of this model are in agreement with the synchronization of chaotic spiking-bursting behavior experimentally found in real biological neurons.
Submolecular Plasticization Induced by Photons in Azobenzene Materials (2015)

We demonstrate experimentally for the first time that the illumination of azobenzene derivatives leads to changes in molecular environment similar to those observed on heating but that are highly heterogeneous at the submolecular scale. This localized photoplasticization, which can be associated with a free volume gradient, helps to understand the puzzling phenomenon of photoinduced macroscopic material flow and photoexpansion upon illumination far below the glass transition temperature (T(g)). The findings stem from the correlation of infrared (IR) spectral band shifts measured upon illumination with those measured at controlled temperatures for two amorphous DR1-functionalized azo derivatives, a polymer, pDR1A, and a molecular glass, gDR1. This new approach reveals that IR spectroscopy can be used as an efficient label-free molecular-scale thermometer that allows the assignment of an effective temperature (T(eff)) to each moiety in these compounds when irradiated. While no band shift is observed upon illumination for the vibrational modes assigned to backbone moieties of pDR1A and gDR1 and a small band shift is found for the spacer moiety, dramatic band shifts are recorded for the azo moiety, corresponding to an increase in T(eff) of up to nearly 200 °C and a molecular environment that is equivalent to thermal heating well above the bulk T(g) of the material. An irradiated azo-containing material thus combines characteristic properties of amorphous materials both below and above its bulk T(g). The direct measurement of T(eff) is a powerful probe of the local environment at the submolecular scale, paving the way toward better rationalization of photoexpansion and the athermal malleability of azo-containing materials upon illumination below their T(g).
Surface morphology evolution in silicon during ion beam processing (1999)

The Semiconductor Industry Association (SIA) projects that the semiconductor chips used in personal computers and scientific workstations will reach five times the speed and ten times the memory capacity of the current pentium-class processor by the year 2007. However, 1 GHz on-chip clock speeds and 64 Gbits/Chip DRAM technology will not come easy and without a price. Such technologies will require scaling the minimum feature size of CMOS devices (the transistors in the silicon chip) down to below 100nm from the current 180 to 250 nm. This requirement has profound implications for device manufacturing. Existing processing techniques must increasingly be understood quantitatively and modeled with unprecedented precision. Indeed, revolutionary advances in the development of physics-based process simulation tools will be required to achieve the goals for cost efficient manufacturing, and to satisfy the needs of the defense industrial base. These advances will necessitate a fundamental improvement in our basic understanding of microstructure evolution during processing. In order to cut development time and costs, the semiconductor industry makes extensive use of simple models of dopant implantation, and of phenomenological models of defect annealing and diffusion. However, the production of a single device often requires more than 200 processing steps, and the cumulative effects of the various steps are far too complex to be treated with these models. The lack of accurate process modeling simulators is proving to be a serious impediment to the development of next generation devices. New atomic-level models are required to describe the point defect distributions produced by the implantation process, and the defect and dopant diffusion resulting from rapid thermal annealing steps. In this LDRD project, we investigated the migration kinetics of defects and dopants in silicon both experimentally and theoretically to provide a fundamental database for use in the development of predictive process simulators. The results were then used to develop kinetic Monte Carlo simulations that, when coupled to molecular dynamics studies, could be used to study and compare the long time and length scale behavior of ion implanted silicon to the predictions of experiments. The results of these kinetic Monte Carlo simulations were validated with experimental data and then used to predict boron activation fractions during annealing of ion implanted silicon under conditions similar to those encountered in the semiconductor manufacturing environment. The success of the work and promise of the approach are reflected in the number of publication and in the fact that following completion of the project we signed a funds-in CRADA with Intel corporation and Applied Materials Corporation to continue the research.
Amrinone Enhances Myocardial Contractility and Improves Left Ventricular Diastolic Function in Conscious and Anesthetized Chronically Instrumented Dogs (1993)

Amrinone produced positive inotropic and lusitropic effects in both conscious and anesthetized dogs with autonomic nervous system blockade. These results indicate that amrinone-induced improvement of left ventricular performance are related to actions in diastole, as well as systole.
Optical spectroscopy enhancing acrylamide sensing in French fries production increasing food safety (2022)

Carcinogenic contaminants in food are typically detected using sample-based and time-consuming chemical analysis. To offer a nondestructive alternative, we investigate the use of optical sensing methods for food safety evaluation, particularly considering broadband diffuse reflection spectroscopy and spatially resolved spectroscopy. As a case-study, the acrylamide sensing during potato processing is considered. For both spectroscopic methods, the broadband spectra (400-1700 nm) are recorded for different potato batches, showing acrylamide concentrations between 200 ppb and 2000 ppb, covering levels below and above the European regulation of 500 ppb. First, the raw spectra are evaluated enabling to identify the key spectral regions, being 400-525 nm, 750-1000 nm, 1220 nm, and 1440 nm, corresponding to different potato constituents such as riboflavin, starch, reducing sugar and water. Following, different data processing algorithms were applied maximizing the classification performance of the different batches. When considering the reflection spectroscopic data, a classification performance exceeding 92% could be obtained using Linear Discriminant Analysis, while with spatially resolved spectroscopy, a classification performance around 75% was obtained when considering the ratios of the diffuse and specular reflected light. Both techniques show a harvest-independent result, while coping with the large natural variation by considering the combined effect of different acrylamide precursors. In general, our results demonstrate that optical spectroscopy enables a successful acrylamide precursor sensing, allowing an accurate exclusion of potatoes unsuited for French fries production, complying with the European regulations.
DolphinAtack: Inaudible Voice Commands (2017)

Speech recognition (SR) systems such as Siri or Google Now have become an increasingly popular human-computer interaction method, and have turned various systems into voice controllable systems(VCS). Prior work on attacking VCS shows that the hidden voice commands that are incomprehensible to people can control the systems. Hidden voice commands, though hidden, are nonetheless audible. In this work, we design a completely inaudible attack, DolphinAttack, that modulates voice commands on ultrasonic carriers (e.g., f &gt; 20 kHz) to achieve inaudibility. By leveraging the nonlinearity of the microphone circuits, the modulated low frequency audio commands can be successfully demodulated, recovered, and more importantly interpreted by the speech recognition systems. We validate DolphinAttack on popular speech recognition systems, including Siri, Google Now, Samsung S Voice, Huawei HiVoice, Cortana and Alexa. By injecting a sequence of inaudible voice commands, we show a few proof-of-concept attacks, which include activating Siri to initiate a FaceTime call on iPhone, activating Google Now to switch the phone to the airplane mode, and even manipulating the navigation system in an Audi automobile. We propose hardware and software defense solutions. We validate that it is feasible to detect DolphinAttack by classifying the audios using supported vector machine (SVM), and suggest to re-design voice controllable systems to be resilient to inaudible voice command attacks.
Furovirus Isolation and RNA Extraction (1998)

The Furovirus (fungus-transmitted rod-shaped) group, whose type member is soil-borne wheat mosaic virus (SBWMV) (), is a very heterogeneous group infecting a wide variety of hosts. The group consists of viruses that are naturally transmitted by soil-borne fungal vectors, generally of the family Plasmodiophorales. Virions are rigid rods and contain two or more genome components consisting of positive-sense RNA. Furoviruses typically infect roots, but can also invade, or be inoculated to, leaves. As sequence data for different furoviruses has become available, it has become clear that there are significant differences in genetic organization within the group (,). We find it convenient to divide the viruses into two major subgroups (Fig. 1), which are distinguished by the nature of the protein(s) putatively involved in cell-to-cell movement. Subgroup 1 consists of SBWMV, which appears to have a movement protein (MP) of the type characterized by the 30-kDa protein of tobacco mosaic virus (TMV) (). Subgroup 2 furoviruses (beet necrotic yellow vein virus [BNYVV], peanut clump virus [PCV], and potato moptop virus [PMTV]) do not have a TMV type MP but instead possess a cluster of three slightly overlapping genes known as the triple gene block (TGB), which has been shown for BNYVV (), and is presumed for the other viruses (, , ) to mediate viral cell-to-cell movement. Open image in new window Fig 1. Genetic organization of characterized members of the furovirus group. RNA1 of PMTV has not yet been sequenced, but presumably encodes the viral replicase. ORFs are represented as hollow rectangles. Asterisks indicate suppressible termination codons. TGB, tripe gene block; Cys-rich, cysteine rich protein; C P, coat protein; mvt, putative movement protein of SBWMV; AA, poly(A) tail; black rectangle, consensus core polymerase motif ().
Dorsal inlay inner preputial graft for primary hypospadias repair (2014)

Primary dorsal inlay inner preputial graft urethroplasty successfully fulfills all traditional hypospadias repair criteria. It offers a viable, safe, rapid and easy option in the management of proximal hypospadias with a narrow urethral plate.
Morphology‐Performance Relationships in High‐Efficiency All‐Polymer Solar Cells (2013)

Careful selection of processing solvents to tune optimal active layer morphology in a donor-acceptor copolymer blend [PTB7:P(NDI2OD-T2)] yields bulk heterojunction microstructures with intradomain percolative pathways and enhanced charge transport. Such microstructures afford all-polymer solar cells with power conversion efficiencies as high as 2.7%. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Variation of Y-chromosome DNA markers in Chinook salmon (Oncorhynchus tshawytscha) populations (2005)

Two Y-chromosome DNA markers (a repetitive sequence, OtY1, and a single-copy marker, GH-Y) tightly linked to the sex-determination locus have been examined for their association with sexual development among 55 populations of Chinook salmon (Oncorhynchus tshawytscha) from the Yukon, British Columbia, Washington, Oregon, and Idaho. Normal linkage has been observed in 96.7% of 2478 individuals examined. Only five males (0.44%) were found lacking both markers (none from Canadian systems), and 14 females (1.04%) from US populations and two females (0.15%) from Canadian populations were found to possess both markers. Variants identified included weakly amplifying alleles for GH-Y and OtY1 and structural variants identified by Southern-blot analysis. The frequency of variants in males was more than 2-fold that in females, and males deficient in GH-Y were more common (3.6%) than males deficient in the repetitive OtY1 sequence (0.7%). Some individuals (of both sexes) possessed fewer copies of the OtY1 repeat than normal males, revealing molecular dynamics that alter Y-chromosome structure within and among populations. A population (Hanford Reach) previously reported as having a high incidence of females possessing the OtY1 marker, and suspected of being sex-reversed, was found to have normal sex-marker genotypes in the present study.
Deep learning for classification of pediatric chest radiographs by WHO’s standardized methodology (2021)

A deep learning model can classify pneumonia CXR images in children at a performance comparable to human readers. Our method lays a strong foundation for the potential inclusion of computer-aided readings of pediatric CXRs in vaccine trials and epidemiology studies.
A Comparison of Health Care Systems: South Africa vs. Canada (2010)

Canada and South Africa have two very different health care systems.  The principles of universal health care are the cornerstone of the Canadian system.  This is also the basis of South Africa’s public sector.  However, the well-funded private system is contributing to a lack of resources, medical professionals, and adequate facilities in the public system.  This article compares common medical issues and follows thier management in each Country's system, illustrating the different challenges that each faces.  In conclusion, the disparity in the two-tiered system is severely impeding accessibility and quality of care in South Africa’s medical system.  While the Canadian system is not perfect, it stands as an example of a relatively successful model of universal health care.
2-Amino-1-azetines, a new class of strained amidines (1980)

The reaction of amide chlorides with N-benzhydrylimines yields azetidin-2-iminium salts, which, upon hydrogenolysis and treatment with base, are converted into 2-amino-1-azetines.
Fast Optical Humidity Sensor Based on Hydrogel Thin Film Expansion for Harsh Environment (2019)

With the application of a recently developed deposition method called initiated chemical vapor deposition (iCVD), responsive hydrogel thin films in the order of a few hundred nanometers were created. When in contact with humid air, the hydrogel layer increases its thickness considerably. The measurement of the thickness change was realized interferometrically with a laser and a broadband light source in two different implementations. The relative change in thickness with respect to humidity can be described with the Flory⁻Huggins theory. The required Flory⁻Huggins interaction parameter was determined for the actual hydrogel composition. The setup was designed without electric components in the vicinity of the active sensor layer and is therefore applicable in harsh environments such as explosive or corrosive ones. The implemented sensor prototype delivered reproducible relative humidity ( R H ) values and the achieved response time for an abrupt change of the humidity τ 63 ≤ 2.5 s was about three times faster compared to one of the fastest commercially available sensors on the market.
Chemical Assay for the Detection of Vertebrate Fecal Metabolites in Adult Blow Flies (Diptera: Calliphoridae) (2018)

Filth flies are commonly implicated in pathogen transmission routes due to their affinity for vertebrate waste and their synanthropic associations. However, solidifying the link between flies and infected feces in the wild can be difficult, as interpretations made solely from microbial culturing or sequencing methods may represent an incomplete picture of pathogen acquisition. We present an analytical assay using high performance liquid chromatography tandem mass spectrometry (HPLC MS/MS) to detect vertebrate fecal metabolites (urobilinoids) in adult blow fly guts. Proof of concept experiments consisted of controlled feeding in which flies were grouped into three treatments (unfed, exposure to beef liver tissue, and exposure to canine feces; N = 20/treatment) using the black blow fly Phormia regina Meigen (Diptera: Calliphoridae). It was revealed that only feces-related samples exhibited peaks with an m/z of 591 and MS/MS spectra consistent with urobilinoids. These peaks were not seen for beef liver tissue, flies exposed to beef liver tissue, or unfed flies. Samples taken directly from beef liver tissue and from feces of several animals were also tested. To test this assay in wild flies, 216 flies were additionally analyzed to determine whether they had ingested vertebrate feces. About 13% of the wild flies exhibited these same peaks, providing a baseline measure of blow flies collected in urban and residential areas consuming feces from the environment. Overall, this assay can be used for P. regina collected in an applied setting and its integration with microbial culturing and sequencing methods will help to improve its use.
A unified framework for self-healing in wireless networks (2012)

Future wireless networks will be Heterogeneous Networks (HetNet), as they will comprise multiple Radio Access Technologies (RAT) and network architectures. The complexity of managing and operating such networks is forcing operators to find new strategies if they want to remain competitive. In this context, Self-Organizing Networks (SON) have arisen as one of the key technologies for enhancing operation and minimizing costs in future networks. SON functionalities can be classified as self-configuration, self-optimization, and self-healing. Although the first two categories have received considerable attention in the last years, the studies devoted to self-healing have been scarce. In addition, existing references use different terminology and concepts and they focus only on partial aspects of self-healing for a particular RAT. This article unifies previous research and proposes a reference model for self-healing in which terms and functions are unambiguously defined. In addition, this article presents a survey on the state of the art, in which the main references on self-healing are outlined. Finally, the main research challenges in self-healing that will have to be faced in the near future are summarized.