gebhart/patrepeval huggingface dataset:
Optimizing Frozen Sample Preparation for Laser Microdissection: Assessment of CryoJane Tape-Transfer System® (2013)

Laser microdissection is an invaluable tool in medical research that facilitates collecting specific cell populations for molecular analysis. Diversity of research targets (e.g., cancerous and precancerous lesions in clinical and animal research, cell pellets, rodent embryos, etc.) and varied scientific objectives, however, present challenges toward establishing standard laser microdissection protocols. Sample preparation is crucial for quality RNA, DNA and protein retrieval, where it often determines the feasibility of a laser microdissection project. The majority of microdissection studies in clinical and animal model research are conducted on frozen tissues containing native nucleic acids, unmodified by fixation. However, the variable morphological quality of frozen sections from tissues containing fat, collagen or delicate cell structures can limit or prevent successful harvest of the desired cell population via laser dissection. The CryoJane Tape-Transfer System®, a commercial device that improves cryosectioning outcomes on glass slides has been reported superior for slide preparation and isolation of high quality osteocyte RNA (frozen bone) during laser dissection. Considering the reported advantages of CryoJane for laser dissection on glass slides, we asked whether the system could also work with the plastic membrane slides used by UV laser based microdissection instruments, as these are better suited for collection of larger target areas. In an attempt to optimize laser microdissection slide preparation for tissues of different RNA stability and cryosectioning difficulty, we evaluated the CryoJane system for use with both glass (laser capture microdissection) and membrane (laser cutting microdissection) slides. We have established a sample preparation protocol for glass and membrane slides including manual coating of membrane slides with CryoJane solutions, cryosectioning, slide staining and dissection procedure, lysis and RNA extraction that facilitated efficient dissection and high quality RNA retrieval from CryoJane preparations. CryoJane technology therefore has the potential to facilitate standardization of laser microdissection slide preparation from frozen tissues.
Certificate path generating protocol (CPGP) for authenticated signaling in ATM networks (2002)

Authenticated signaling is an important security service to be provided by ATM networks to guard against threats of spoofing and impersonation. The ATM Forum specifies public key cryptography to be the default ATM authentication mechanism and directory services like X.509 to be the infrastructure for public key distribution and certification. With public key cryptography, authenticated signaling requires the signaling message to be authenticated with a digital signature signed by the private key of the calling party. To verify the digital signature, the called party needs to obtain the public key of the calling party and a proof of the calling party's ownership to that public key. In X.509, the standard form of such a proof is a chain of public key certificates, called the certificate path between two parties. The certificate exchange protocol (CEP), proposed by the ATM Forum, requires that another bi-directional connection be established between two parties to change public keys and certificate paths before an authenticated connection can be established, which is not an ideal approach. We propose a certificate path generating protocol (CPGP), which is embedded into ATM signaling and routing protocols to generate a certificate path inside a signaling message on-the-fly as the signaling message travels through the ATM network. In CPGP all that a calling party needs to do for authenticated signaling is to put into the signaling message its own public key certificate and the digital signature of the signaling message signed using its private key. The CPGP builds the rest of the certificate path for it. The proposed protocol is embedded into the ATM signaling and routing protocol so that no performance overhead is incurred to establish the certificate path.
Alkali Metal Thermoelectric Conversion (AMTEC) for space nuclear power systems (1985)

Provoking factors for seizures in patients with COVID-19 may include metabolic factors, systemic illness, and possibly direct effects of the virus. In endemic areas with community spread of COVID-19, clinicians should be vigilant for the infection in patients who present with seizures, which may precede respiratory symptoms or prompt presentation to medical care. Early testing, isolation, and contact tracking of these patients can prevent further transmission of the virus.
Emerging therapeutic options for the management of hepatitis C infection (2014)

Until recently the traditional treatment for hepatitis C infection included pegylated interferon and ribavirin combination therapy. The sustained virological response (SVR) seen with this combination is poor and requires lengthy treatment to achieve. Additionally, significant side effects and numerous contraindications prevented many patients from being successfully treated with this therapy. In 2011, two new protease inhibitors, telaprevir and boceprevir, were approved for use with pegylated interferon and ribavirin in the United States by the United States Food and Drug Administration. These agents have significantly improved SVR rates; however significant problems with toxicity remain including severe skin rash and neutropenia. There are a wide range of compounds in late stage development for the future treatment of hepatitis C that exploit many different mechanisms of viral inhibition. Some of these compounds include additional protease inhibitors, like telaprevir and boceprevir, as well as inhibitors of other nonstructural proteins in the viral genome such as NS5A and NS5B, and compounds that target host proteins within the virus. Some of these agents are being developed for oral administration once daily and various combinations are being assessed for use without the need for pegylated interferon and ribavirin. This paper reviews agents in late phase development that may be commercially available within 1-2 years.
A network file system over HTTP: remote access and modification of files and "files" (2000)

The goal of the present HTTPFS project is to enable access to remote files, directories, and other containers through an HTTP pipe. HTTPFS system permits retrieval, creation and modification of these resources as if they were regular files and directories on a local filesystem. The remote host can be any UNIX or Win9x/WinNT box that is capable of running a Perl CGI script and accessible either directly or via a web proxy or a gateway. HTTPFS runs entirely in user space. 
The current implementation fully supports reading as well as creating, writing, appending, and truncating of files on a remote HTTP host. HTTPFS provides an isolation level for concurrent file access stronger than the one mandated by POSIX file system semantics, closer to that of AFS. Both an API with familiar open(), read(), write(), close(), etc. calls, and an interactive interface, via the popular Midnight Commander file browser, are provided.
SentEval: An Evaluation Toolkit for Universal Sentence Representations (2018)

We introduce SentEval, a toolkit for evaluating the quality of universal sentence representations. SentEval encompasses a variety of tasks, including binary and multi-class classification, natural language inference and sentence similarity. The set of tasks was selected based on what appears to be the community consensus regarding the appropriate evaluations for universal sentence representations. The toolkit comes with scripts to download and preprocess datasets, and an easy interface to evaluate sentence encoders. The aim is to provide a fairer, less cumbersome and more centralized way for evaluating sentence representations.
Avalanche phenomena in 4H-SiC p-n diodes fabricated by aluminum or boron implantation (2002)

Characteristics of p-n junction fabricated by aluminum-ion (Al/sup +/) or boron-ion (B/sup +/) implantation and high-dose Al/sup +/-implantation into 4H-SiC (0001) have been investigated. By the combination of high-dose (4/spl times/10/sup 15/ cm/sup -2/) Al/sup +/ implantation at 500/spl deg/C and subsequent annealing at 1700/spl deg/C, a minimum sheet resistance of 3.6 k/spl Omega///spl square/ (p-type) has been obtained. Three types of diodes with planar structure were fabricated by employing Al+ or B+ implantation. B/sup +/-implanted diodes have shown higher breakdown voltages than Al/sup +/-implanted diodes. A SiC p-n diode fabricated by deep B+ implantation has exhibited a high breakdown voltage of 2900 V with a low on-resistance of 8.0 m/spl Omega/cm/sup 2/ at room temperature. The diodes fabricated in this study showed positive temperature coefficients of breakdown voltage, meaning avalanche breakdown. The avalanche breakdown is discussed with observation of luminescence.
Automation of a Fourier transform ion cyclotron resonance mass spectrometer for acquisition, analysis, and e-mailing of high-resolution exact-mass electrospray ionization mass spectral data (1999)

A system has been designed to automatically acquire high-resolution (>50,000 FWHM), exact-mass (mass measurement error ≤3 mmu) electrospray ionization mass spectra with a commercial Fourier transform ion cyclotron resonance mass spectrometer equipped with a high-field (9.4 tesla) superconducting magnet and a commercial autosampler. Upon the injection of each individual sample, the autosampler transmits a contact closure signal to the previously tuned and calibrated mass spectrometer to initiate data acquisition. A software package was designed to run off-line and to accept a sample list with input information for each of the samples. Then for each of the samples, the software automatically processes the acquired data, interprets the exact-mass data by correlating the observed masses with predicted masses computed from proposed elemental formulas, and then finally prints the spectra, peak lists, and exact-mass reports, and e-mails the exact-mass reports to the submitting chemists. With this automation package, large numbers of samples can be run unattended while obtaining exact masses for all the abundant ions in the spectra. Sample turnaround times are reduced with a corresponding increase in sample throughput. The performance of the system was evaluated with nearly 700 samples with a precalibrated instrument, without the presence of an internal standard. The system was found to be reliable and robust with a fitted standard deviation of 0.32 mmu and a small average systematic mass error of −0.28 mmu. Typical data acquired with the system have resolving powers >50,000 (FWHM) and mass errors <1.0 mmu.
A systematic review of prevalence studies of dementia in Parkinson's disease (2005)

Prevalence rates of depressive disorders in Parkinson's disease (PD) vary widely across studies, ranging from 2.7% to more than 90%. The aim of this systematic review was to calculate average prevalences of depressive disorders taking into account the different settings and different diagnostic approaches of studies. Using Medline on Pubmed, a systematic literature search was carried out for studies of depression in Parkinson's disease. A total of 104 articles were included and assessed for quality; 51 articles fulfilled the quality criteria. Multiple publications from the same database were not included in the meta-analysis. In the remaining 36 articles, the weighted prevalence of major depressive disorder was 17% of PD patients, that of minor depression 22% and dysthymia 13%. Clinically significant depressive symptoms, irrespective of the presence of a DSM defined depressive disorder, were present in 35%. In studies using a (semi) structured interview to establish DSM criteria, the reported prevalence of major depressive disorder was 19%, while in studies using DSM criteria without a structured interview, the reported prevalence of major depressive disorder was 7%. Population studies report lower prevalence rates for both major depressive disorder and the clinically significant depressive symptoms than studies in other settings. This systematic review suggests that the average prevalence of major depressive disorder in PD is substantial, but lower than generally assumed.
Robust Processing of Color Target Measurements for Device Characterization. (2003)

Device characterization typically involves generating one or more targets each comprising a number of color patches and making colorimetric measurements of these patches. In order to derive the characterization function, one has to obtain the correspondence between the set of colorimetric measurements and a set of device signals. In the case of output device characterization, the device signals are the CMY(K) values used to create the target; for input device characterization the device signals are the captured RGB values. Establishing the correspondence requires knowledge of the spatial target layout, the order in which the measurement instrument measures the patches, and the order in which the input or output device captures or renders respectively the target patches. Since the measurement process requires human intervention, errors can conceivably be introduced at this step. A common example is misorientation of the target on the measurement stage. This results in an incorrect correspondence between device and colorimetric signals, thus producing an erroneous characterization. This paper presents some practical approaches to detect and correct for measurement errors due to misorientation. One approach reserves a number of patches in the target to encode the target layout and orientation. The measurements from this so-called “patch code” are then decoded to retrieve, and if necessary, correct the orientation. Another approach anticipates common misorientations of the target, and uses a pattern matching approach to select the correct orientation. This is done either automatically with a prior device characterization, or with visual validation by the user. Both techniques are successful in correcting for target misorientation with minimal burden to the user.
Retrospective Analysis of Minimal Residual Disease Testing By High Throughput Immunosequencing Versus High Sensitivity Flow Cytometry in Multiple Myeloma (2021)

Abstract Introduction: Detection of minimal residual disease (MRD) is one of the strongest predictors of outcome in multiple myeloma (MM). Until recently, the most commonly available method to detect MRD in clinical practice has been high sensitivity flow cytometry (FC) which can detect MRD with at 10 -5 sensitivity. In recent years, next-generation sequencing (NGS) has become a viable method to assess the MRD in MM patients with a 10 -6 sensitivity. NGS appears to have some advantages over HC-FC by circumventing subjectivity of analysis. However, real-world comparison between these two methodologies in the literature is limited and is important to inform daily hematopathology and oncology ordering practices. Methods: We retrospectively identified all cases of MM with NGS MRD data from bone marrow specimens at the Moffitt Cancer Center and collated corresponding flow MRD data and clinical data (OS, patient demographics) electronically and via chart review. 10-color flow cytometry was performed on a Gallios System and analyzed on Kaluza (Beckman Coulter, IN). Two million events were collected on all cells. Validated lower limit of detection was at least 0.01%. Antibodies included CD28, CD81, CD56, CD138, CD319, CD20, CD19, CD117, CD38, CD45, CD27, CD200 (BD, Biolegend, Beckman Coulter). clonoSEQ ® (Adaptive Biotechnologies, Seattle, WA) testing was performed which uses multiplex polymerase chain reaction (PCR) and NGS to identify, characterize, and monitor clonotypes of immunoglobulin (Ig) IgH (V-J), IgH (D-J), IgK, and IgL receptor gene sequences, and translocated BCL1/IgH (J) and BCL2/IgH (J) sequences Statistical analysis was performed by Spearman correlation coefficient and Kaplan-Meier analysis. Results: 192 samples from 122 unique patients were identified that had both NGS and FC data performed on the same sample. FC+ values ranged from 1x10 -7 to 0.39. NGS+ values ranged from 2.3 x 10 -7 to 0.15. Spearman correlation coefficient showed moderate concordance between NGS and FC at r=0.67 (p&lt;0.001). Six samples were positive by FC (mean tumor burden (MTB)= 0.0007) but missed by NGS; whereas 59 samples were positive by NGS (MTB= 0.002) but missed by flow cytometry. Two cases by FC were equivocal and these were both definitively designated as MRD+ by NGS. Overall survival was worse for MRD+ (by NGS or FC) vs MRD(-) (Figure 1). Conclusion: Our study confirms the importance of MRD detection in MM and shows the robust utility of NGS for MRD detection in routine hematopathology practice. While both FC and NGS are complementary given that each can potentially detect MRD missed by another method, the data supports the increased sensitivity of NGS over FC. Figure 1 Figure 1. Disclosures Nishihori: Novartis: Research Funding; Karyopharm: Research Funding. Hussaini: Stemeline Therapeutics: Honoraria.
A novel converter topology for switched reluctance motor drives improving efficiency and simplifying control strategy (2002)

There has been a growing demand for switched reluctance motor (SRM) drive systems for diverse applications such as pumps, fans, traction, appliances and aerospace. In response to the needs, this paper proposes a novel converter for switched reluctance motors. Compared to the conventional converter topologies which have switching losses due to voltage choppings to control phase currents, the proposed converter eliminates the switching losses by introducing a buck-converter at the front end. This paper includes the topology descriptions, analysis and system operations and verifies the characteristics experimentally using a laboratory prototype.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
A study of nail changes in various dermatosis in Punjab, India (2012)

Nails act as a window to diagnosis of skin diseases. Various dermatosis affect the nails and the severity of the skin disorder is reflected in the nails. Nail changes are seen in various dermatosis like psoriasis, lichen planus, onychomycosis, collagen vascular disorders, vescicobullous disorders and other papulosquamous disorders. We will discuss in detail regarding nail changes in various dermatosis.
Discrimination of Modes of Action of Antifungal Substances by Use of Metabolic Footprinting (2004)

Diploid cells of Saccharomyces cerevisiae were grown under controlled conditions with a Bioscreen instrument, which permitted the essentially continuous registration of their growth via optical density measurements. Some cultures were exposed to concentrations of a number of antifungal substances with different targets or modes of action (sterol biosynthesis, respiratory chain, amino acid synthesis, and the uncoupler). Culture supernatants were taken and analyzed for their "metabolic footprints" by using direct-injection mass spectrometry. Discriminant function analysis and hierarchical cluster analysis allowed these antifungal compounds to be distinguished and classified according to their modes of action. Genetic programming, a rule-evolving machine learning strategy, allowed respiratory inhibitors to be discriminated from others by using just two masses. Metabolic footprinting thus represents a rapid, convenient, and information-rich method for classifying the modes of action of antifungal substances.
A Novel Flood Forecasting Method Based on Initial State Variable Correction (2017)

The influence of initial state variables on flood forecasting accuracy by using conceptual hydrological models is analyzed in this paper and a novel flood forecasting method based on correction of initial state variables is proposed. The new method is abbreviated as ISVC (Initial State Variable Correction). The ISVC takes the residual between the measured and forecasted flows during the initial period of the flood event as the objective function, and it uses a particle swarm optimization algorithm to correct the initial state variables, which are then used to drive the flood forecasting model. The historical flood events of 11 watersheds in south China are forecasted and verified, and important issues concerning the ISVC application are then discussed. The study results show that the ISVC is effective and applicable in flood forecasting tasks. It can significantly improve the flood forecasting accuracy in most cases.
Preliminary Observations on the Ability of Hyperspectral Imaging to Provide Detection and Visualization of Bloodstain Patterns on Black Fabrics (2012)

The analysis of bloodstain patterns can assist investigators in understanding the circumstances surrounding a violent crime. Bloodstains are routinely subjected to pattern analysis, which is inherently dependent upon the ability of the examiner to locate and visualize bloodstain patterns on items of evidence. Often, the ability to properly visualize bloodstain patterns is challenging, especially when the stain patterns occur on dark and/or patterned substrates. In this study, preliminary research was performed to better understand how near-infrared reflectance hyperspectral imaging (HSI) could be used to observe bloodstain patterns on commonly encountered black fabrics. The ability of HSI to visualize latent bloodstains on several commonly encountered substrates is demonstrated. The images acquired through HSI are of sufficient quality to allow for differentiation between stains produced from an impact mechanism or a transfer mechanism. This study also serves as a proof of concept in the differentiation of multiple staining materials. Because of its ability to generate spectral data, the data provide a preliminary separation of stains where more than one type of stain existed.
Bacillus Calmette-Guérin complications in children born to HIV-1-infected women with a review of the literature. (1995)

This and five other cohort studies indicate that there may be a small increased risk of complications following BCG vaccination among HIV-1-infected children, but the reactions are usually mild and the risk does not outweigh the benefits of BCG vaccination in populations at high risk of tuberculosis during infancy and childhood.
Lymphoproliferative Diseases of Fowl: JM-V Leukemic Lymphoblasts in Cell Culture: Brief Communication2 (1977)

JM-V leukemic lymphoblasts were established in cell culture. The cultured cells (JM-VLC cells) were transplantable in young chicks and produced a disease indistinguishable from JM-V lymphoblastic leukemia as initiated by whole-blood inoculation. JM-VLC cells maintained a normal female karyotype through 13 passages in Rhode Island Red cockerels. With the use of JM-V antisera and antisera from birds with naturally occurring Marek's disease (MD), specific antigens were detected on the surfaces of living cells. Intracellular antigens were detected with anti-MD virus sera after cultivation for at least 1 day at 37 degrees C. In spite of the expression of MD antigens, the presence of herpesvirus particles associated with the cultured cells, and the occurrence of foci of multinucleated cells in kidney cultures from chicks inoculated with cellfree preparations of JM-VLC cells, the pathologic potential of the cultured cells was that of JM-V leukemia.