gebhart/patrepeval huggingface dataset:
Immunization with Pneumocystis Cross-Reactive Antigen 1 (Pca1) Protects Mice against Pneumocystis Pneumonia and Generates Antibody to Pneumocystis jirovecii (2016)

<i>Pneumocystis</i> pneumonia (PcP) is a life-threatening infection that affects immunocompromised individuals. Nearly half of all PcP cases occur in those prescribed effective chemoprophylaxis, suggesting that additional preventive methods are needed. To this end, we have identified a unique mouse <i>Pneumocystis</i> surface protein, designated <i>Pneumocystis</i> cross-reactive antigen 1 (Pca1), as a potential vaccine candidate. Mice were immunized with a recombinant fusion protein containing Pca1. Subsequently, CD4<sup>+</sup> T cells were depleted, and the mice were exposed to <i>Pneumocystis murina</i> Pca1 immunization completely protected nearly all mice, similar to immunization with whole <i>Pneumocystis</i> organisms. In contrast, all immunized negative-control mice developed PcP. Unexpectedly, Pca1 immunization generated cross-reactive antibody that recognized <i>Pneumocystis jirovecii</i> and <i>Pneumocystis carinii</i> Potential orthologs of Pca1 have been identified in <i>P. jirovecii</i> Such cross-reactivity is rare, and our findings suggest that Pca1 is a conserved antigen and potential vaccine target. The evaluation of Pca1-elicited antibodies in the prevention of PcP in humans deserves further investigation.
ChemInform Abstract: Aminopyrazoles with High Affinity for the Human Neuropeptide Y5 Receptor. (2001)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Racial Differences in Androgen Receptor (AR) and AR Splice Variants (AR-SVs) Expression in Treatment-Naïve Androgen-Dependent Prostate Cancer (2023)

Androgen receptor splice variants (AR-SVs) contribute to the aggressive growth of castration-resistant prostate cancer (CRPC). AR-SVs, including AR-V7, are expressed in ~30% of CRPC, but minimally in treatment-naïve primary prostate cancer (PCa). Compared to Caucasian American (CA) men, African American (AA) men are more likely to be diagnosed with aggressive/potentially lethal PCa and have shorter disease-free survival. Expression of a truncated AR in an aggressively growing patient-derived xenograft developed with a primary PCa specimen from an AA patient led us to hypothesize that the expression of AR-SVs could be an indicator of aggressive growth both in PCa progression and at the CRPC stage in AA men. Tissue microarrays (TMAs) were created from formalin-fixed paraffin-embedded (FFPE) prostatectomy tumor blocks from 118 AA and 115 CA treatment-naïve PCa patients. TMAs were stained with AR-V7-speicifc antibody and with antibodies binding to the N-terminus domain (NTD) and ligand-binding domain (LBD) of the AR. Since over 20 AR-SVs have been identified, and most AR-SVs do not as yet have a specific antibody, we considered a 2.0-fold or greater difference in the NTD vs. LBD staining as indication of potential AR-SV expression. Two AA, but no CA, patient tumors stained positively for AR-V7. AR staining with NTD and LBD antibodies was robust in most patients, with 21% of patients staining at least 2-fold more for NTD than LBD, indicating that AR-SVs other than AR-V7 are expressed in primary treatment-naïve PCa. About 24% of the patients were AR-negative, and race differences in AR expression were not statistically significant. These results indicate that AR-SVs are not restricted to CRPC, but also are expressed in primary PCa at higher rate than previously reported. Future investigation of the relative expression of NTD vs. LBD AR-SVs could guide the use of newly developed treatments targeting the NTD earlier in the treatment paradigm.
Outer‐Sphere Reactivity Shift of Secondary Phosphine Oxide‐Based Nickel Complexes: From Ethylene Hydrophosphinylation to Oligomerization (2017)

A new dimension for secondary phosphine oxide (SPOs) ligands is described in this article. Demonstrated on original π-allylic nickel structures, these self-assembled complexes trigger catalytic hydrophosphinylation reactions. Addition of a Lewis acid B(C<sub>6</sub> F<sub>5</sub> )<sub>3</sub> switches the reactivity towards migratory insertion and thus ethylene oligomerization through an unprecedented outer-sphere interaction with the coordinated SPO ligand. NMR experiments and X-ray analyses allowed for the observation of the formation of zwitterionic active species as well as their degradation pathway.
Compressive sensing based energy detector (2016)

While most of research in Compressive Sensing (CS) has been focused on reconstruction of the sparse signal from very fewer samples than the ones required by the Shannon-Nyquist sampling theorem, recently there has been a growing interest in performing signal processing directly in the measurement domain. This new area of research is known in the literature as Compressive Signal Processing (CSP). In this paper, we consider the detection problem using a reduced set of measurements focusing on the Energy Detector (ED), which is the optimal Neyman-Pearson (NP) detector for random signals in Gaussian noise. In particular, we provide simple closed form expressions for evaluating the detection performance of ED when considering compressive measurements. The resulting equations reflect the loss due to CS and allow to determine the minimum number of samples to achieve certain detection performance.
Accurately Predicting Case-Time Duration (2019)

Bartek, Matthew A. MD, MPH1; Saxena, Rajeev C. MD, MBA1; Solomon, Stuart MD1; Fong, Christine T. MS1; Lang, John D. MD1; Nair, Bala G. PhD1; Behara, Lakshmana D. MS2; Venigandla, Ravitheja MS2; Velagapudi, Kalyani PhD2 Author Information
ChemInform Abstract: DETERMINATION OF ENANTIOMERIC PURITIES OF ALCOHOLS AND AMINES BY A PHOSPHORUS‐31 NMR TECHNIQUE (1984)

Abstract Der aus PSCI; und l‐Ephedrin erhaltene P‐Heterocyclus (III) ergibt mit chiralen oder racemischen Aminen wie z.B. (II) oder Alkoholen wie z.B. (IV) die Amide (I) bzw. die Ester (V), deren Enantiomerenverteilungen sich durch 31 P‐NMR‐Messungen bestimmen lassen.
Controlling Effective Aspect Ratio and Packing of Clay with pH for Improved Gas Barrier in Nanobrick Wall Thin Films (2014)

Polymer-clay thin films constructed via layer-by-layer (LbL) assembly, with a nanobrick wall structure (i.e., clay nanoplatelets as bricks surrounded by a polyelectrolyte mortar), are known to exhibit a high oxygen barrier. Further barrier improvement can be achieved by lowering the pH of the clay suspension in the polyethylenimine (PEI) and montmorillonite (MMT) system. In this case, the charge of the deposited PEI layer is increased in the clay suspension environment, which causes more clay to be deposited. At pH 4, MMT platelets deposit with near perfect ordering, observed with transmission electron microscopy, enabling a 5× improvement in the gas barrier for a 10 PEI/MMT bilayer thin film (85 nm) relative to the same film made with pH 10 MMT. This improved gas barrier approaches that achieved with much higher aspect ratio vermiculite clay. In essence, lower pH is generating a higher effective aspect ratio for MMT due to greater induced surface charge in the PEI layers, which causes heavier clay deposition. These flexible, transparent nanocoatings have a wide range of possible applications, from food and electronics packaging to pressurized bladders.
An Ethnobotanical Study of Medicinal Plants in the Greek Islands of North Aegean Region (2018)

Greek islands of the North Aegean Region are a group of nine inhabited islands (Lemnos, Agios Efstratios, Lesvos, Chios, Psara, Oinousses, Samos, Ikaria, and Fourni) located in the northern part of the Aegean Sea, close to Asia Minor. Each island of this region can be considered autonomous in terms of culture and biodiversity. With this work we try to evaluate the status of the traditional uses of medicinal plants in this region. Endemic and endangered species such as <i>Sideritis sipylea</i> Boiss., <i>Origanum sipyleum</i> L., <i>Thymus sipyleus</i> Boiss., <i>Pistacia lentiscus</i> L., <i>Verbascum ikaricum</i> Murb., are still used by locals to treat different ailments. Moreover, the use of some species for the treatment of specific diseases has been reported for the first time. We report about 109 wild plants of medicinal importance, from 52 families, listing their uses for therapeutic purposes and galenic preparations provided by local medical doctors and pharmacists. The information we include was derived from literature sources and additionally collected through semi-structured interviews conducted on 200 informants (100 men and 100 women). Additionally, informant consensus factor (FIC) and UV value were calculated for the medicinal plants in the current study in relation with the diseases treated. This research confirms the importance of the medicinal plants and the diffusion of their use in traditional medicine within this region. This ethnopharmacological survey is a fundamental step for the preservation of the local knowledge both for further scientific research and for the protection of endangered and endemic medicinal plants.
Oncology: Adrenal/Renal/Upper Tract/Bladder Fuhrman Grade Provides Higher Prognostic Accuracy Than Nucleolar Grade for Papillary Renal Cell Carcinoma (2010)

Purpose: Recent evidence suggests that nucleolar grade but not Fuhrman grade is applicable to papillary renal cell carcinoma. We tested this hypothesis in an independent large series from a single institution. Materials and Methods: One dedicated uropathologist regraded 158 cases of papillary renal cell carcinoma by nucleolar and Fuhrman grades. The prognostic value and predictive accuracy of these grading systems to predict disease specific survival were analyzed by Cox proportional hazards models and the concordance index. Results: There were 39 papillary renal cell carcinoma related deaths (25%) at a mean followup of 50 months. On univariate analysis nucleolar grade predicted disease specific survival with a concordance index of 67.8% but the survival difference between grades 1 and 2 did not attain statistical significance (p 0.1441). Fuhrman grade predicted disease specific survival significantly better (concordance index 74.7%, p 0.001). Comparison of survival estimates between the grades revealed statistical significance across each grade category (each p 0.05). Fuhrman but not nucleolar grade was retained as an independent prognostic factor on multivariate analysis (p 0.027 and 0.128, respectively). Conclusions: Each grading system performs well but the predictive accuracy of Fuhrman grade is statistically superior to that of nucleolar grade and only Fuhrman grade provides independent prognostic information on patients with papillary renal cell carcinoma. Thus, Fuhrman grade should be the standard grading system for papillary renal cell carcinoma.
Diagnosis and Management of Neuromyelitis Optica (2011)

Background and purpose: Neuromyelitis optica (NMO) or Devic′s disease is a rare inflammatory and demyelinating autoimmune disorder of the central nervous system (CNS) characterized by recurrent attacks of optic neuritis (ON) and longitudinally extensive transverse myelitis (LETM), which is distinct from multiple sclerosis (MS). The guidelines are designed to provide guidance for best clinical practice based on the current state of clinical and scientific knowledge. Search strategy: Evidence was collected from searches of original articles, case reports and meta-analyses in the Medline and Cochrane databases. In addition, clinical practice guidelines of professional neurological and rheumatological organizations were studied. Results: Different diagnostic criteria for NMO diagnosis (Wingerchuk et al. Revised NMO criteria, 2006; Miller et al. NMSS task force criteria, 2008) and features potentially indicative of NMO facilitate the diagnosis. In addition, guidance for the work-up and diagnosis of spatially limited NMO spectrum disorders is provided by the Task Force. Owing to a lack of studies fulfilling the requirement for the highest levels of evidence the Task Force suggests treatment of acute exacerbations and attack prevention based on expert opinion. Conclusions: Studies of diagnosis and management of NMO fulfilling requirements for the highest levels of evidence (class I–III rating) are limited and diagnostic and therapeutic concepts based on expert opinion and consensus of the Task Force members were drawn up for this guideline.
InAsSb photodiodes grown on GaAs substrates for long-wavelength-infrared gas-sensing applications (2021)

Abstract We investigated highly mismatched InAsSb photodiodes (PDs) grown on GaAs substrates working in the long-wavelength-infrared range (8–12 μ m). Because of their low absorption coefficient levels and high Auger recombination rates, InAsSb PDs suffer from several difficulties, including low responsivity and low resistance levels at room temperature. Additionally, the large lattice mismatch between the active layer and substrate material introduces a high density of dislocations and thus degrades performance. In the work described in this report, we realized high-performance InAs 0.13 Sb 0.87 PDs by reducing the density of dislocations as a result of applying a dislocation filter structure, as well as by optimizing interference within the active layer. The resulting device (cut-off wavelength of about 11 μ m) showed, at room temperature, a resistance R 0 of 90 kΩ and responsivity R i of 0.47 mA W −1 at a wavelength of 9.5 μ m, leading to a high detectivity D * of 1.2 × 10 8 cm Hz 1/2 W −1 , which is suitable for detecting alcohol.
Disease-Associated Mutations in Cytoplasmic Loops 1 and 2 of Cystic Fibrosis Transmembrane Conductance Regulator Impede Processing or Opening of the Channel (1997)

Since little is known about the contribution to function of the N-terminal cytoplasmic loops (CL1, residues 139-194; CL2, residues 242-307) of cystic fibrosis transmembrane conductance regulator (CFTR), all nine point mutations identified in CLs 1 and 2 from patients with cystic fibrosis were reconstructed in the expression vector pcDNA3-CFTR and expressed transiently in COS-1 and HEK-293 cells and stably in Chinese hamster ovary (CHO) cells. Four amino acid substitutions retarded production of mature, fully glycosylated CFTR, suggesting that misprocessing of the channel causes the disease symptoms in the affected patients. Protein maturation could not be promoted by cell culture conditions of reduced temperature (26 degrees C). When properly processed mutants were evaluated for functional defects by the iodide efflux method, the G178R- and E193K-CFTR-expressing cell lines showed impaired anion translocation activities. Patch-clamp studies of single channels revealed that E193K variants had a significantly decreased open probability, which resulted from an increase in the mean closed time of the channels. This contrasted with a previous study of disease-associated point mutations in CL3 that mainly affected the mean open time. None of the maturation-competent CL 1 and 2 mutants had altered conductance. Thus, the N-terminal CLs appear not to contribute to the anion translocation pathway of CFTR; rather, mutations in CL1 can impede transition to the open state. Interestingly, the ability of the non-hydrolyzable ATP analogue adenylyl imidodiphosphate (AMP-PNP) to lock the channel into open bursts was abolished by the I148T and G178R amino acid substitutions.
237 A novel algorithm for VF detection from subcutaneously implanted leads (2005)

Absence of any sensation 1 Aware of a sensation 2 Tingling sensation 3 Slightly uncomfortable 4 Moderately uncomfortable 5 Veldt uncomfortable or painful Results: The HVLIC IMP at implant was slightly lower when compared to the implant HV IMP (33.4±4.7U vs. 38±3.1U,p<0.01).However, the HVLIC IMP at PD was very close to the implant HV IMP (38.6±5.0U vs. 38±3.1U,p=0.71).The pts reported a mean SS of 1.4 as compared to a placebo SS of 0 (p<0.09).The SS obtained at the CHR follow-up visit (mean 53±23 days) did not significantly change from PD (1.77±1.64 vs. 1.45±1.63,p= 0.64). Conclusion:The HVLIC IMP at PD is a strong correlate to the HV IMP measured at ICD implant.The HVLIC feature performs painless measurements, which are only slightly perceptible by pts.
Monte Carlo simulation of region-of-interest reconstruction for real-time tumor tracking by OpenPET (2013)

We are developing the OpenPET which can provide an open space to make the patient observable and accessible during PET measurements. In addition, we have proposed a real-time imaging system for the OpenPET which is expected to be used in PET-guided tumor tracking radiation therapy. We conducted a feasibility study on tumor tracking using 18F-FDG by Monte Carlo simulation of a human body-sized OpenPET and showed that the tumor tracking is feasible with a time window of 0.5 s if the tumor contains sufficient radioactivity. Although we have demonstrated real-time tumor tracking using a small OpenPET prototype, the delay was 2 s. On a human body scale, the image matrix size become huge compared to the body size of the small prototype and delay can be increased. Therefore, further improvement of the reconstruction speed is essential. From this viewpoint, image reconstruction of the entire field-of-view (FOV) is time consuming and not required for the purpose of tumor tracking. In this study, we developed a region-of-interest (ROI) reconstruction method for the OpenPET and evaluated the tumor tracking accuracy. Although conventional wisdom states that the ROI reconstruction requires a priori information of a small region inside the ROI and 180° scanning without angular truncation for accurate image reconstruction, the computer simulation showed that the ROI reconstruction method without any a priori information had equivalent accuracy in terms of tumor tracking compared with the case reconstructing the entire region. The ROI reconstruction method was more than 10 times faster than the entire FOV reconstruction method.
High-Performance Binary Protein Interaction Screening in a Microfluidic Format (2012)

The standard procedure to increase microfluidic chip performance is to grow the number of parallel test systems on the chip. This process is accompanied by miniaturizing biochemical workflows and micromechanical elements, which is often a major challenge for both engineering fields. In this work, we show that it is possible to substantially increase the runtime performance of a microfluidic affinity assay for protein interactions by simultaneously engineering fluid logics and assay chemistry. For this, synergistic effects between the micro- and chemical architecture of the chip are exploited. The presented strategy of reducing the runtime rather than size and volume of the mechanical elements and biological reagent compartments will, in general, be of importance for future analytical test systems on microfluidic chips to overcome performance barriers.
Shared idiotypes are expressed on mouse and human anti-DNA autoantibodies. (1985)

The expression of common idiotypes on human and mouse anti-DNA monoclonal autoantibodies made by hybridomas was examined by their competitive binding to anti-idiotype antibodies. Some murine autoantibodies inhibited the binding of a human anti-DNA autoantibody 16/6 to monoclonal or polyclonal anti-idiotypic antibodies. Another human antibody (134) was not inhibited in its binding to homologous anti-idiotypic antibodies. The expression of the human 16/6 idiotype on mouse antibodies was restricted to those that had a specificity similar to the 16/6 antibody itself, their major properties being that they reacted more strongly with single stranded DNA (ssDNA) than double stranded DNA (dsDNA). One mouse antibody expressing the 16/6 idiotype also bound weakly to RNA. The results imply structural similarities between the binding sites of the antibodies in the two species, and are consistent with evolutionary conservation of V genes coding for primitive ancestral antibodies that react with DNA and become diversified through somatic mutation.
Direct Bonding of Chitosan Biomaterials to Tissues Using Transglutaminase for Surgical Repair or Device Implantation (2016)

Natural biomaterials, such as chitosan and collagen, are useful for biomedical applications because they are biocompatible, mechanically robust, and biodegradable, but it is difficult to rapidly and tightly bond them to living tissues. In this study, we demonstrate that the microbial transglutaminase (mTG), can be used to rapidly (<5 min) bond chitosan and collagen biomaterials to the surfaces of hepatic, cardiac, and dermal tissues, as well as to functionalized polydimethylsiloxane (PDMS) materials that are used in medical products. The mTG-bonded chitosan patches effectively sealed intestinal perforations, and a newly developed two-component mTG-bonded chitosan spray effectively repaired ruptures in a breathing lung when tested ex vivo. The mechanical strength of mTG-catalyzed chitosan adhesive bonds were comparable to those generated by commonly used surgical glues. These results suggest that mTG preparations may be broadly employed to bond various types of organic materials, including polysaccharides, proteins, and functionalized inorganic polymers to living tissues, which may open new avenues for biomedical engineering, medical device integration, and tissue repair.
Effect of Age and Disc Size on Rim Order Rules by Heidelberg Retina Tomograph (2013)

The ISNT rule does not apply to neuroretinal rim area as measured by HRT, as only 18% of the eyes complied with the ISNT rule in this normative database. Although the ISNT rule may be more applicable to normal eyes with a smaller disc area, the IS and IST rules seem to better represent the normative database.
Migration of cells in a social context (2012)

In multicellular organisms and complex ecosystems, cells migrate in a social context. Whereas this is essential for the basic processes of life, the influence of neighboring cells on the individual remains poorly understood. Previous work on isolated cells has observed a stereotypical migratory behavior characterized by short-time directional persistence with long-time random movement. We discovered a much richer dynamic in the social context, with significant variations in directionality, displacement, and speed, which are all modulated by local cell density. We developed a mathematical model based on the experimentally identified "cellular traffic rules" and basic physics that revealed that these emergent behaviors are caused by the interplay of single-cell properties and intercellular interactions, the latter being dominated by a pseudopod formation bias mediated by secreted chemicals and pseudopod collapse following collisions. The model demonstrates how aspects of complex biology can be explained by simple rules of physics and constitutes a rapid test bed for future studies of collective migration of individual cells.