gebhart/patrepeval huggingface dataset:
Therapeutic Effects of Bacteriophage Cpl-1 Lysin against Streptococcus pneumoniae Endocarditis in Rats (2005)

Cpl-1, a pneumococcal phage lytic enzyme, was tested in rats with experimental endocarditis due to Streptococcus pneumoniae WB4. High-dose regimen Cpl-1 eliminated pneumococci from blood within 30 min and decreased bacterial titers in vegetations (>4 log10 CFU/g) within 2 h. Rapid bacterial lysis induced by Cpl-1 treatment increased cytokine secretion noticeably.
Serum TNF-alpha levels correlate with disease severity and are reduced by effective therapy in plaque-type psoriasis. (1998)

to analyze the serum TNF-alpha levels in plaque-type psoriatic patients to evaluate the concentrations, correlation with the severity score and behaviour after therapy. The serum TNF-alpha levels of thirty-seven patients (25 females and 12 males; median age: 52.5 years, range 18-81: median PASI score: 11.4, range 3.5-42) and thirty healthy controls (21 females and 9 males, median age: 48.5 years, range 25-77) were compared after measurements obtained employing commercially available ELISA kits. The median serum TNF-alpha levels of the patients were significantly higher than those of controls (p = 0.004). 30/37 patients were followed over time at 2 and 4 weeks of treatment. Twenty one subjects were also observed after 6 weeks. After effective treatments, both the PASI scores and the cytokine levels were significantly and concomitantly reduced (p < 0.001). Significant correlations were found when the TNF-alpha values were plotted against the PASI scores both at the time of patient enrollment and at all the subsequent times (118 observations). A significant correlation was observed between circulating TNF-alpha and sE-selectin in agreement with a possible functional activity of the cytokine. However, no correlation was found between the cytokine levels and other 4 soluble membrane molecules. Our findings indicate that the molecule studied, although non specific for the disease considered, presents a behaviour paralleling that of the disease severity and therefore might have clinical usefulness, particularly in monitoring the therapeutic effects.
Electronic structure of oxygen deficient amorphous oxide semiconductor a‐InGaZnO4–x: Optical analyses and first‐principle calculations (2008)

Abstract Defect states in a representative amorphous oxide semiconductor, a‐InGaZnO 4 , were studied by optical analyses and first‐principle calculations. The optical analyses suggested that the as‐deposited a‐IGZO film have weak subgap absorptions around 0.6 and 2 eV. Local density approximation calculations showed that an oxygen defect works as an electron trap as well as a shallow donor depending on its local structure. It suggests that a large vacancy space remained in an oxygen deficient structure forms a deep levels in the band gap and traps electrons, while if such a large space is annihilated e.g. by a film growth process and post thermal annealing, oxygen deficiency may form a shallow donor level. (© 2008 WILEY‐VCH Verlag GmbH &amp; Co. KGaA, Weinheim)
Steatocystoma multiplex: a quick removal technique. (1999)

A 27-year-old man with multiple lesions located on his chest and neck and diagnosed as steatocystoma multiplex desired removal of these lesions. We report a facile, fast, and successful technique for the removal of lesions of steatocystoma multiplex. Using a no. 11 blade, we incised the domes of numerous lesions and removed the cyst walls with small artery forceps. Within 1 month, the incisions healed without scarring, and after 4 months of follow-up, they had not recurred. This procedure allows the removal of many lesions of steatocystoma in a few office visits.
DIFFERENCE IN EXPRESSION OF THE PLASMINOGEN ACTIVATION SYSTEM IN SYNOVIAL TISSUE OF PATIENTS WITH RHEUMATOID ARTHRITIS AND OSTEOARTHRITIS (1996)

Proteolytic joint destruction in inflammatory and non-inflammatory arthropathy is believed to be mediated, at least in part, by the plasminogen activation (PA) system. To further investigate possible involvement of the PA system, we quantified immunoreactive urokinase-type plasminogen activator (u-PA), tissue-type plasminogen activator (t-PA), both plasminogen activator inhibitors (PAI-1 and PAI-2) and u-PA-receptor (u-PAR) in synovial tissue extracts of 14 patients with rheumatoid arthritis (RA) and 12 with osteoarthritis (OA). u-PA, PAI-1, PAI-2 and u-PAR concentrations were significantly higher in RA than in OA patients. t-PA antigen levels were significantly lower in RA than in OA synovial tissue extracts. Immunohistochemistry was performed to compare the distribution and staining intensity of these components in samples of RA and OA synovial tissue. Intense immunostaining of u-PA, u-PAR, PAI-1 and, to a lesser degree, PAI-2 was observed predominantly in the synovial lining of RA patients. In OA patients, u-PA, PAI-1, PAI-2 and u-PAR were barely detectable. t-PA immunostaining was restricted to the endothelial side of vascular walls in both groups. We conclude that the observed increase of u-PA, u-PAR and PAI expression, distributed mainly in the synovial lining area of proliferative and invasively growing synovial tissue in RA patients, supports a pathogenic role for the PA system in destructive arthritis. Depressed t-PA-mediated plasminogen activation might contribute to delayed intra-articular fibrin removal.
Can we do without ranks in Burrows Wheeler transform compression? (2002)

Compressors based on the Burrows Wheeler transform (1994) convert the transformed text into a string of (move-to-front) ranks. These ranks are then encoded with an Order-0 model, or a hierarchy of such models. Although these rank-based methods perform very well, we believe the transformation to MTF numbers blurs the distinction between individual symbols and is a possible cause of inefficiency. Instead of relying on symbol ranking, we examine the problem of directly encoding the symbols in the BWT text.
Polyclonal Antibody-Induced Serum Sickness in Renal Transplant Recipients: Treatment with Therapeutic Plasma Exchange (2005)

Serum sickness is an immune-complex mediated illness that frequently occurs in patients after polyclonal antibody therapy (ATGAM or thymoglobulin). Serum sickness presents with significant morbidity but is self-limited and resolves with prolonged steroid therapy. We present five renal transplant patients who developed serum sickness after polyclonal antibody treatment with severe symptoms that persisted after being started on systemic steroids. These patients underwent one or two courses of therapeutic plasma exchange (TPE) with subsequent complete resolution of their symptoms. Renal transplant recipients with serum sickness after polyclonal antibody therapy may benefit from TPE by accelerating their time to recovery and thereby reducing overall morbidity.
Guardian Angel: Patient-Centered Health Information Systems (1994)

Introduction 3Part I 4Lifetime Patient-Centered Health Information Systems 4 The “Guardian Angel” Concept 4Architecture for “Guardian Angels” 5Guardian Angel Interactions and Interoperations 6Experimental Guardian Angel Applications 6Example Scenario 6Part II 9Objectives 9Architecture 9Reference Implementation 9Experimental Domains 10Experimental Testing 10Technical Rationale 11Roots of the Problems 11 a. Health information for patients. 11 b. Life-long information 11Domain Modeling 12Architecture 13Special Functionalities 15Generic Functional Modules 15Hardware Realizations 16Information Infrastructures and I-95 16 Prototype Applications 17Insulin-Dependent Juvenile Diabetes 17Chronic Hypertension 18Managing Hypertension Using a GA 19Chronic Anticoagulation 20Other Domains 22Implementation 22Comparison with Ongoing Research 23Performance Evaluation 24Conclusion 26 Schedule 26Part III .28Project Partners 28Previous Accomplishments 29MIT Laboratory for Computer Science 29 Tufts/NEMC 31Children’s Hospital 32Veterans Health Adm.: Boston Dev. Center 32 International Business Machines Corp 33Gensym Corporation 33Results, Products and Transferable Technology 34Bibliography 35
Abstract LB-196: Anti-DLL4 reduces tumor growth and tumorigenicity in B-RAF V600E melanomas including those with acquired resistance to B-RAF inhibitors (2012)

Abstract Melanoma is frequently driven by oncogenic mutation in the B-RAF gene (V600E) and this mutation is found in approximately 60% of patients. These patients are highly sensitive to kinase inhibitors targeting B-RAF. However, recent clinical experience has shown that after an initial response, a high percentage of patients develop resistance to B-RAF inhibitors through various mechanisms. In our studies, we evaluated whether inhibition of DLL4-Notch signaling might be effective in B-RAF mutant melanoma. We utilized two patient-derived melanoma xenografts containing the B-RAFV600E mutation, OMP-M2 and OMP-M8. The OMP-M8 xenograft was derived from a patient who was treated with the B-RAF inhibitor Vemurafenib (PLX-4032) and showed an early response to treatment, but later became resistant. We performed combination efficacy experiments with the B-RAF inhibitor PLX-4720 (doses 20-80 mg/kg, oral gavage, qdx5) and anti-DLL4 antibodies (30 mg/kg, IP once a week), and found that PLX-4720 combined with anti-DLL4 treatment caused a significant inhibition of tumor growth in OMP-M2 tumors. In serial transplant limiting dilution assay (LDA) studies with the OMP-M2 model, PLX-4720 treatment induced a significant enrichment of tumor initiating cells. In contrast, anti-DLL4 reduced the frequency of tumor initiating cells compared to controls, as a single agent and in combination with PLX-4720. We also found that the OMP-M8 tumor xenografted in mice retained the lack of response to the B-RAF kinase inhibitor, showing that the xenografts responded to treatment similarly as the patient in the clinic. Interestingly, the B-RAF inhibitor resistant tumor OMP-M8 was sensitive to anti-DLL4, which inhibited the growth of the primary tumor and significantly reduced the frequency of tumor initiating cells as a single agent and in combination with a chemotherapeutic agent. These findings suggest that DLL4-Notch inhibition can be effective in B-RAF V600E mutant melanoma including patients with acquired resistance to B-RAF kinase inhibitors. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr LB-196. doi:1538-7445.AM2012-LB-196
TERLIPRESSIN AS RESCUE THERAPY FOR INTRACTABLE HYPOTENSION DUE TO SEPTIC SHOCK IN CHILDREN (2005)

Intractable hypotension due to septic shock is associated with high mortality rates in critically ill children worldwide. The use of terlipressin (triglycyl-lysine-vasopressin), an analog of vasopressin with a longer duration of action, recently emerged as a treatment of hypotension not responsive to vasopressors and inotropes. This was a retrospective study set in an 18-bed pediatric critical care department in a tertiary care children's hospital. We reviewed the files of all children with septic shock who were treated with terlipressin between January 2003 and February 2004. Fourteen children (mean age, 5.6 years; range, 4 days to 17.7 years) were treated with terlipressin in 16 septic shock episodes. Significant improvements in respiratory and hemodynamic indices were noted shortly after treatment. Mean arterial blood pressure increased significantly from 54 +/- 3 to 72 +/- 5 mmHg 10 min after terlipressin administration (P = 0.001). Heart rate decreased from 153.0 +/- 6.5 beats/min to 138.0 +/- 7.5 beats/min 12 h after treatment onset (P = 0.003). Epinephrine infusion was decreased or stopped in eight patients after terlipressin administration. Urine output increased from 1.6 +/- 0.5 mL/kg/h to 4.3 +/- 1.2 mL/kg/h 1 h after treatment onset (P = 0.011). PaO2 increased from 95.1 +/- 12.3 mmHg to 110.1 +/- 20.5 mmHg, and the oxygenation index decreased from 10.2 +/- 2.2 to 9.2 +/- 1.7. Terlipressin treatment of hypotension due to septic shock was successful in eight out of 16 episodes. Six of the 14 patients with poor prognosis for survival recovered. We conclude that terlipressin improves hemodynamic indices and renal function in critically ill children. Terlipressin should be considered as a rescue therapy in intractable shock not responsive to catecholamines in children.
Normalization Propagation: A Parametric Technique for Removing Internal Covariate Shift in Deep Networks (2016)

While the authors of Batch Normalization (BN) identify and address an important problem involved in training deep networks-- Internal Covariate Shift-- the current solution has certain drawbacks. Specifically, BN depends on batch statistics for layerwise input normalization during training which makes the estimates of mean and standard deviation of input (distribution) to hidden layers inaccurate for validation due to shifting parameter values (especially during initial training epochs). Also, BN cannot be used with batch-size 1 during training. We address these drawbacks by proposing a non-adaptive normalization technique for removing internal covariate shift, that we call Normalization Propagation. Our approach does not depend on batch statistics, but rather uses a data-independent parametric estimate of mean and standard-deviation in every layer thus being computationally faster compared with BN. We exploit the observation that the pre-activation before Rectified Linear Units follow Gaussian distribution in deep networks, and that once the first and second order statistics of any given dataset are normalized, we can forward propagate this normalization without the need for recalculating the approximate statistics for hidden layers.
Group-based recipe recommendations (2010)

Collaborative filtering recommendations were designed primarily for individual user models and recommendations. However, nowadays more and more scenarios evolve, in which the recommended items are consumed by groups of users rather than by individuals. This raises the need to uncover the most appropriate group-based collaborative filtering recommendation strategy. In this work we investigate the use of aggregated group data in collaborative filtering recipe recommendations. We present results of a study that exploits recipe ratings provided by families of users, in order to evaluate the accuracy of several group recommendation strategies and weighting models, and analyze the impact of switching strategies, data aggregation heuristics, and group characteristics on the performance of recommendations.
Clinical evaluation of the Crystalens AT-45 accommodating intraocular lens (2006)

The Crystalens AT-45 accommodating IOL provided good uncorrected near, intermediate, and distance vision in pseudophakic patients. Contrast sensitivity with the Crystalens AT-45 was not diminished relative to standard monofocal IOLs, and near and intermediate visual performance was significantly better than with standard IOLs.
Methane excretion in man--a study of breath, flatus, and faeces. (1985)

In this paper aspects of the variability of methane producing status have been examined, and a survey of breath methane excretion in various clinical and control populations is reported. Prevalences of methane excretion were 54% in healthy controls, 53% in non-gastrointestinal patients and 32% in gastrointestinal patients. Patients with Crohn's disease, ulcerative colitis, and pneumatosis cystoides intestinalis had significantly lower prevalences of methane excretion (13%, 15%, and 11% respectively). Faecal constituents and in vitro incubation analysis were similar in breath methane excretors and non-excretors. Several patients did not excrete methane in the breath although methane was present in colonic gas. The results indicate that different gastrointestinal patient groups have different prevalences of breath methane excretion and that all healthy subjects may produce methane but only when the production reaches a threshold does it appear in the breath.
Acheon Project: A Novel Vectoring Jet Concept (2012)

This paper presents a general overview of the ACHEON Project (EU FP7 Level 0 - Transport including Aeronautic). This project presents a novel dynamically controllable Coanda jet using two fluid streams to produce the angular deflection of the jet as a function of their momentum. A control system with electrostatic plasma is used to produce an effective and more precise control of the system. This paper presents the general guidelines of the project which is going to start and presents expected results.
Double Multielectrode Mapping Catheters Facilitate Radiofrequency Catheter Ablation of Focal Atrial Fibrillation Originating from Pulmonary Veins (1999)

The technique using double multielectrode mapping catheters is a relatively safe and highly effective method for mapping and ablation of focal AF originating from PVs.
Real-time replanning using 3D environment for humanoid robot (2011)

In this paper, we illustrate experimentally an original real-time replanning scheme and architecture for humanoid robot reactive walking. Based on a dense set of actions, our approach uses a large panel of the humanoid robot capabilities and is particularly well suited for 3D collision avoidance. Indeed A* approaches becomes difficult in such situation, thus the method demonstrated here relies on RRT. Combined with an approximation of the volume swept by the robot body while walking, our method is able to cope with 3D obstacles while maintaining real-time computation. We experimentally validate our approach on the robot HRP-2.
The PDZ Domain of Human Erythrocyte p55 Mediates Its Binding to the Cytoplasmic Carboxyl Terminus of Glycophorin C (1997)

The PDZ domain, also known as the GLGF repeat/DHR domain, is an approximately 90-amino acid motif discovered in a recently identified family of proteins termed MAGUKs (membrane-associated guanylate kinase homologues). Sequence comparison analysis has since identified PDZ domains in over 50 proteins. Like SH2 and SH3 domains, the PDZ domains mediate specific protein-protein interactions, whose specificities appear to be dictated by the primary structure of the PDZ domain as well as its binding target. Using recombinant fusion proteins and a blot overlay assay, we show that a single copy of the PDZ domain in human erythrocyte p55 binds to the carboxyl terminus of the cytoplasmic domain of human erythroid glycophorin C. Deletion mutagenesis of 21 amino acids at the amino terminus of the p55 PDZ domain completely abrogates its binding activity for glycophorin C. Using an alanine scan and surface plasmon resonance technique, we identify residues in the cytoplasmic domain of glycophorin C that are critical for its interaction with the PDZ domain. The recognition specificity of the p55 PDZ domain appears to be unique, since the three PDZ domains of hDlg (human lymphocyte homologue of the Drosophila discs large tumor suppressor) do not bind the cytoplasmic domain of glycophorin C. Taken together with our previous studies, these results complete the identification of interacting domains in the ternary complex between p55, glycophorin C, and protein 4.1. Implications of these findings are discussed in terms of binding specificity and the regulation of cytoskeleton-membrane interactions.
Palladium-Catalyzed Cross Coupling of 7-Iodo-2’-deoxytubercidin with Terminal Alkynes (1996)

The 7-alkynyl-2'-deoxytubercidins (7-deaza-2'-deoxyadenosines) 7-17 have been prepared by the Pd(0)/Cu(I)-catalyzed cross coupling of 7-iodo-2'-deoxytubercidin (2d) with terminal alkynes. The coupling products include 17α-ethynyltestosterone and 17α-ethynylestradiol derivatives (16, 17).
A simple synthesis of dimethyl 2‐pyridone‐4, 5‐dicarboxylate derivatives (1989)

Abstract 1‐Hydroxyphenyl‐2‐pyridone derivatives 8, 10 and 11 were easily prepared by treatment of methyl isocro‐tonate derivatives 6 with base at room temperature in good yields.
Histone Deacetylase Inhibitors In The Treatment Of Cancer: Overview And Perspectives (2012)

Histone deacetylase inhibitors (HDACis) are one of the last frontiers in pharmaceutical research. Several classes of HDACi have been identified. Although more than 20 HDACi are under preclinical and clinical investigation as single agents and in combination therapies against different cancers, just two of them were approved by the US FDA: Zolinza(®) and Istodax(®), both licensed for the treatment of cutaneous T-cell lymphoma, the latter also of peripheral T-cell lymphoma. Since HDAC enzymes act by forming multiprotein complexes (clusters), containing cofactors, the main problem in designing new HDACi is that the inhibition activity evaluated on isolated enzyme isoforms does not match the in vivo outcomes. In the coming years, the research will be oriented toward a better understanding of the functioning of these protein complexes as well as the development of new screening assays, with the final goal to obtain new drug candidates for the treatment of cancer.
HIV infection and lymphoma (2007)

The incidence of lymphoma in patients with HIV infection greatly exceeds that of the general population. The increased risk for lymphoma appears related to multiple factors, including the transforming properties of the retrovirus itself, the immunosuppression and cytokine dysregulation that results from the disease, and, most importantly, opportunistic infections with other lymphotrophic herpes viruses such as Epstein-Barr virus and human herpesvirus 8. Histologically lymphomas fall into three groups: (1) those also occurring in immunocompetent patients; (2) those occurring more specifically in HIV-positive patients; and (3) those also occurring in patients with other forms of immunosuppression. Aggressive lymphomas account for the vast majority cases. They frequently present with advanced stage, bulky disease with high tumour burden and, typically, involve extranodal sites. Clinical outcome appears to be worse than in similar aggressive lymphomas in the general population. However, following the introduction of highly active antiretroviral therapy, the risk for developing lymphoma in the context of HIV infection has decreased and the clinical outcome has improved.
Non-Contact Vital Signs Detection with UAV-Borne Radars (2020)

Airborne radar carried on-board unmanned aerial vehicles (UAV) is serving as the harbinger of new remote sensing applications for security and rescue in inclement environments. The mobility and agility of UAVs along with intelligent on-board sensors (cameras, acoustics, and radar) are more effective during the early stages of disaster response. The ability of radars to penetrate through objects and operate during low visibility conditions enables detection of occluded human subjects on and under debris when other sensing modalities fail. Recently, radars have been deployed on UAVs to measure minute human physiological parameters such as respiratory and heart rates while sensing through clothing and building materials. Aggregating radar measurements with the information from other sensors is broadening the applications of drones in life-critical situations. Signal processing techniques are critical in enabling UAV-borne radars for human vital sign detection (VSD) in multiple operation modes. Novel radar configurations such as in a UAV swarm and tethered UAVs are required to facilitate multi-tasking and high endurance, respectively. This paper provides an overview of recent advances in UAV-borne VSD with a focus on deployment modes and processing methods.