gebhart/patrepeval huggingface dataset:
Antibodies and Lentiviruses That Specifically Recognize a T Cell Epitope Derived from HIV-1 Nef Protein and Presented by HLA-C (2010)

HIV selectively downregulates HLA-A and -B from the surfaces of infected cells to avoid detection by the immune system. In contrast, the HLA-C molecules are highly resistant to this downregulation. High expression level of HLA-C on the cell surface, which correlates with a single nucleotide polymorphism, is also associated with lower viral loads and slower progression to AIDS. These findings strongly suggest that HIV-1-derived peptides are efficiently presented by HLA-C and trigger the elimination of infected cells. Accordingly, the ability to detect these HLA-C-peptide complexes may be used for therapeutic targeting of HIV-1-infected cells and for measuring effective presentation of vaccine candidates after immunization with HIV-1-related proteins or genes. However, low level of HLA-C expression on the cell surface has impeded the development of such complex-recognizing reagents. In this study, we describe the development of a high-affinity human Ab that specifically interacts, at low pM concentrations, with a conserved viral T cell epitope derived from HIV-1 Nef protein and presented by HLA-C. The human Ab selectively detects this complex on different cells and does not interact with a control complex that differed only in the presented peptide. Engineering lentiviruses to display this Ab endowed them with the same specificity as the Ab, whereas coexpressing the Ab and Fas ligand enables the lentiviruses to kill specifically Nef-presenting cells. Abs and pseudoviruses with such specificity are likely to be highly valuable as building blocks for specific targeting and killing of HIV-1-infected cells.
Diagnosis and mode of treatment for ‘pseudo’‐class III patients and its effects on masticatory movements (1996)

This paper describes the treatment and functional analysis of 18 'pseudo'-class III patients. Clinical examination revealed IC-RC discrepancies, aesthetic aberrations and functional disturbances. The improvement of these parameters upon treatment was followed by sirognathographic recordings.
Personalized medicine in rheumatoid arthritis: methotrexate polyglutamylation revisited (2018)

For many decades, the folate antagonist methotrexate (MTX) is being used as first-line chemotherapeutic agent for the treatment of (pediatric) leukemia [1] and also constitutes the cornerstone in t...
Deep Task-Based Analog-to-Digital Conversion (2022)

Analog-to-digital converters (ADCs) allow physical signals to be processed using digital hardware. Their conversion consists of two stages: Sampling, which maps a continuous-time signal into discrete-time, and quantization, i.e., representing the continuous-amplitude quantities using a finite number of bits. ADCs typically implement generic uniform conversion mappings that are ignorant of the task for which the signal is acquired, and can be costly when operating in high rates and fine resolutions. In this work we design task-oriented ADCs which learn from data how to map an analog signal into a digital representation such that the system task can be efficiently carried out. We propose a model for sampling and quantization that facilitates the learning of non-uniform mappings from data. Based on this learnable ADC mapping, we present a mechanism for optimizing a hybrid acquisition system comprised of analog combining, tunable ADCs with fixed rates, and digital processing, by jointly learning its components end-to-end. Then, we show how one can exploit the representation of hybrid acquisition systems as deep networks to optimize the sampling and quantization rates given the task by utilizing Bayesian meta-learning techniques. We evaluate the proposed deep task-based ADC in two case studies: the first considers synthetic multi-variate symbol detection, where multiple analog signals are simultaneously acquired in order to recover a set of discrete symbols. The second application is beamforming of analog channel data acquired in ultrasound imaging. Our numerical results demonstrate that the proposed approach achieves performance which is comparable to operating with high sampling rates and fine resolution quantization, while operating with reduced overall bit rate. For instance, we demonstrate that deep task-based ADCs enable accurate reconstruction of ultrasound images while using <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"><tex-math notation="LaTeX">$12.5\%$</tex-math></inline-formula> of the overall number of bits used by conventional ADCs.
Reduction of BMPR2 mRNA Expression in Peripheral Blood of Pulmonary Arterial Hypertension Patients: A Marker for Disease Severity? (2022)

Pulmonary arterial hypertension (PAH) can be caused by pathogenic variants in the gene bone morphogenetic protein receptor 2 (BMPR2). While BMPR2 protein expression levels are known to be reduced in the lung tissue of heritable PAH (HPAH) patients, a systematic study evaluating expression in more easily accessible blood samples and its clinical relevance is lacking. Thus, we analyzed the BMPR2 mRNA expression in idiopathic/HPAH patients and healthy controls in blood by quantitative polymerase chain reaction and protein expression by enzyme-linked immunosorbent assay. Clinical parameters included right heart catherization, echocardiography, six-minute walking test and laboratory tests. BMPR2 variant-carriers (n = 23) showed significantly lower BMPR2 mRNA expression in comparison to non-carriers (n = 56) and healthy controls (n = 30; p < 0.0001). No difference in BMPR2 protein expression was detected. Lower BMPR2 mRNA expression correlated significantly with greater systolic pulmonary artery pressure and pulmonary vascular resistance. Higher BMPR2 mRNA expression correlated with greater glomerular filtration rate, cardiac index and six-minute walking distance. We demonstrated the feasibility to assess BMPR2 expression in blood and, for the first time, that BMPR2 mRNA expression levels are significantly reduced in variant carriers and correlated with clinical parameters. Further studies may evaluate the usefulness of BMPR2 mRNA expression in blood as a new marker for disease severity.
Computerized Clinical Protocols in an Intensive Care Unit: How Well Are They Followed? (1990)

Abstract
Computerized protocols were created to direct the management of arterial hypoxemia in critically ill patients with adult respiratory distress syndrome (ARDS) and have now been applied routinely, 24 hours a day, in the care of 36 such patients. We evaluated the performance of the protocols by measuring how often the clinical staff followed protocol instructions. Since compliance with the protocols could also vary depending on the type of therapy, we assessed compliance with the protocols as a function of 1) the method of artificially ventilating the patients, 2) whether the protocol instruction was to increase or decrease the intensity of therapy or to wait for an interval of time and 3) whether the computer instruction was “correct” or “incorrect.” A total of 7,663 instructions were evaluated. The clinical staff followed protocol instructions 63.8% of the time in the first 8 patients and 90.8% of the time in the subsequent patients. Instructions to wait were more likely to be followed than instructions to change therapy. There was no difference in compliance between instructions to increase and those to decrease the intensity of therapy. “Incorrect” instructions were followed 27% of the time. These instructions may not have been clinically important. The mode of ventilation therapy did not affect compliance with protocol instructions. We conclude that protocols can direct the clinical care of critically ill patients in a manner that is acceptable to experienced clinicians.
The Effect of Human Muscle-Derived Stem Cells (MDSC) and Glycine-Isoleucine-Lysine-Valine-Alanine-Valine (GIKVAV) on the Cryo-Injured Bladder of Nude Mouse (2009)

Purpose: In neurogenic bladder, both smooth muscle contraction and nerve regeneration are very important for functional improvement. Glycineisoleucine-lysine-valine-alanine-valine (GIKVAV) is a peptide that can induce nerve regeneration in vivo. In this study, we evaluated bladder function after injection of muscle-derived stem cells (MDSCs) and GIKVAV into the cryo-injured bladder of nude mice. Materials and Methods: Human muscle samples were obtained from the rectus abdominis muscle of 12 patients who underwent laparotomy. The purpose and entire method of the study were explained to the patients, and all subjects who participated in this study provided written informed consent. The MDSCs were isolated by a modified preplate technique, and only CD34+ human MDSC were extracted by use of Mini-MACS kits. The nude mice were subdivided into 5 groups (n=40): normal group (N, n=8), saline injection group after cryo-injury (S, n=8), GIKVAV injection group after cryo-injury (G, n=8), human MDSC injection group after cryo-injury (M, n=8), and GIKVAV and human MDSC injection group after cryo-injury (GM, n=8). At 2 weeks after injection, we compared the contractility of a bladder muscle strip of each group by organ bath and polygraph by using electronic field stimulation (EFS). Nerve regeneration was evaluated by choline acetyl transferase (ChAT) immunostaining. Results: The contractile powers of the N, S, G, M, and GM groups were 3.58±0.27, 1.54±0.25, 1.54±0.31, 2.49±0.36, and 2.44±0.34 mN/mg, respectively, by EFS. The contractility of the bladder muscle strip in the S and G groups was lower than that in the N group. The contractile powers of the M and GM groups were lower than those of the N group but greater than those of the S and G groups. In ChAT immunohistochemical staining, nerve regeneration was increased in the G and GM groups compared with the S and M groups. Conclusions: Nerve regeneration was induced by GIKVAV injection regardless of human MDSC injection. There was no direct effect of GIKVAV on bladder muscle contractility. (Korean J Urol 2009;50:480-485) 󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏󰠏
Enhancing the management of quality of VGI: contributions from context and task modelling (2016)

This chapter presents contributions to managing the quality of Volunteered Geographical Information (VGI) and of crowd sourced geographical information (CSGI) brought by the representation of specific knowledge items: task and context. Task and context modelling have been studied in different communities. We propose an approach for integrating their results with the perspective of improving the quality management of VGI and CSGI.
Osmosensing Properties of the Histidine Protein Kinase MtrB from (2007)

The MtrB-MtrA two component system of Corynebacterium glutamicum was recently shown to be in involved in the osmostress response as well as cell wall metabolism. To address the question of whether the histidine protein kinase MtrB is an osmosensor, the kinase was purified and reconstituted into liposomes in a functionally active form. The activity regulation was investigated by varying systematically physicochemical parameters, which are putative stimuli that could be used by the bacterial cell to detect osmotic conditions. Membrane shrinkage was ruled out as a stimulus for activation of MtrB. Instead, MtrB was shown to be activated upon the addition of various chemical compounds, like sugars, amino acids, and polyethylene glycols. Because of the different chemical nature of the solutes, it seems unlikely that they bind to a specific binding site. Instead, they are proposed to act via a change of the hydration state of the protein shifting MtrB into the active state. For MtrB activation it was essential that these solutes were added at the same side as the cytoplasmic domains of the kinase were located, indicating that hypertonicity is sensed by MtrB via cytoplasmatically located protein domains. This was confirmed by the analysis of two MtrB mutants in which either the large periplasmic loop or the HAMP domain was deleted. These mutants were regulated similar to wild type MtrB. Thus, we postulate that MtrB belongs to a class of histidine protein kinases that sense environmental changes at cytoplasmatic protein domains independently of the periplasmic loop and the cytoplasmic HAMP domain.
HDAC6 is a target for protection and regeneration following injury in the nervous system (2009)

Central nervous system (CNS) trauma can result in tissue disruption, neuronal and axonal degeneration, and neurological dysfunction. The limited spontaneous CNS repair in adulthood and aging is often insufficient to overcome disability. Several investigations have demonstrated that targeting HDAC activity can protect neurons and glia and improve outcomes in CNS injury and disease models. However, the enthusiasm for pan-HDAC inhibition in treating neurological conditions is tempered by their toxicity toward a host of CNS cell types -a biological extension of their anticancer properties. Identification of the HDAC isoform, or isoforms, that specifically mediate the beneficial effects of pan-HDAC inhibition could overcome this concern. Here, we show that pan-HDAC inhibition not only promotes neuronal protection against oxidative stress, a common mediator of injury in many neurological conditions, but also promotes neurite growth on myelin-associated glycoprotein and chondroitin sulfate proteoglycan substrates. Real-time PCR revealed a robust and selective increase in HDAC6 expression due to injury in neurons. Accordingly, we have used pharmacological and genetic approaches to demonstrate that inhibition of HDAC6 can promote survival and regeneration of neurons. Consistent with a cytoplasmic localization, the biological effects of HDAC6 inhibition appear transcription-independent. Notably, we find that selective inhibition of HDAC6 avoids cell death associated with pan-HDAC inhibition. Together, these findings define HDAC6 as a potential nontoxic therapeutic target for ameliorating CNS injury characterized by oxidative stress-induced neurodegeneration and insufficient axonal regeneration.
Introduction of single mutation changes arylmalonate decarboxylase to racemase (2006)

The introduction of only one mutation based on the estimated reaction mechanism endowed arylmalonate decarboxylase with a racemase activity, which catalyses racemisation of alpha-arylpropionates.
Bariatric Surgery and Long-term Durability of Weight Loss (2016)

Patients in the Veterans Administration health care system lost substantially more weight than nonsurgical matches and sustained most of this weight loss in the long term. Roux-en-Y gastric bypass induced significantly greater weight loss among veterans than SG or AGB at 4 years. These results provide further evidence of the beneficial association between surgery and long-term weight loss that has been demonstrated in shorter-term studies of younger, predominantly female populations.
Ultrasensitive molecular fluorescence spectroscopy in levitated microdroplets (1990)

The extreme sensitivity of fluorescence spectrophotometry results from the fact that a molecule can undergo many excitation-emission cycles before destruction by photochemical degradation. For example, Rhodamine 6G (R6G) can emit in excess of 10{sup 5} photons before photolysis takes place. The fraction of emitted photons collected and converted to countable pulses can be as high as 10{sup {minus}3}, although 10{sup {minus}4} is more readily attainable. Therefore, sufficient signal exists for single molecules to be detectable. Detection limits for molecules in solution have been limited by background signal from solvent Raman scattering and fluorescence. This background signal adds noise to the measurement and has effectively restricted the detectable concentration to about 10{sup {minus}13} M. Over the past decade, advances in detection of fewer molecules have all been made by reducing the measurement volume and/or increasing the measuring time. Given the above concentration detection limit a reduction of the measurement volume to 1 pL leads to a minimum observable quantity of {approx}1 molecule. The ability to detect a single molecule in condensed phase could have many important applications in addition to being an interesting problem. The obvious application of this approach is to situations where small quantities of material are available for analysis. The capability to reliably detect a single fluorophore might also allow the screening and/or sorting of a collection of molecules. Such abilities would have application to many biological problems such as DNA sequencing and detection of DNA adducts.
Cover Feature: Chemoselective Kumada‐Type Iron Catalysis with Alkyl Grignard Reagents: Reductive Cyclization and Cyclomethylation (Asian J. Org. Chem. 9/2019) (2019)

The delicate reactivities of iron(II) salts and alkyl Grignard reagents were presented in reductive cyclizations and cyclomethylation of alkyl halides having alkynes or allenes. A reduced iron complex promoted single-electron-transfer to afford alkyl(sp3)-radical intermediates, which were cyclized to form various alkenyl(sp2)-radical intermediates, which is completed by hydrogen transfer from iron hydride (Fe–H) complex or methyl coupling with Fe–Me species. The cyclomethylation reaction was found to be the effective late-stage functionalization to provide a synergetic exploration in iron-radical chemistry. More information can be found in the Communication by Eun Joo Kang et al. on page 1648 in Issue 9, 2019 (DOI: 10.1002/ajoc.201900359).
DOPADY HOSPODÁRSKEJ KRÍZY NA AUTOMOBILOVÝ PRIEMYSEL V RÁMCI TRHOV SEVERNEJ AMERIKY, EURÓPSKEJ ÚNIE A SLOVENSKA V ROKOCH 2008 AŽ 2010 (2010)

Obsahom prvej casti tejto prace je vplyv a dopady svetovej hospodarskej krizy na
najvýznamnejsich producentov osobných automobilov v priebehu rokov 2008, 2009 a
2010. Na porovnanie týchto spolocnosti je využita metoda strategických skupin, ktoru
vypracoval Michael Porter v knihe Competitive strategy.
Use of a Clinical Video Teleconference (CVT) Technology Model to Implement Patient Self-Management to Prevent Stroke (2014)

Purpose: Pooled V-STOP Program data were used to evaluate a nurse practitioner led, patient-centered stroke-risk reduction program delivered to veterans at risk for stroke living in rural areas via clinical video teleconferencing technology. Data Sources: Originally a formative evaluation was completed based on a pilot, open trial, pretest/posttest design in 2 community based outpatient clinics. Veterans at risk for stroke completed questionnaires on stroke risk, self-management behaviors, self-efficacy, and quality of life. Conclusions: Participants (N=37) showed improvement in their stroke risk knowledge (t=5.95, p<.001) over time; they had increases in their physical (t=2.15, p=.039) and emotional (t=1.99, p=.055) quality of life. Moreover, program participants had improvement in their self-management behavior of communication with health care providers at both 12 weeks (t= 2.6, p.014) and 18 weeks (t= 3.2, p=.003) post intervention. Implications for Practice: The V-STOP Program not only promotes nurse-led, patient-centered care but also utilizes clinical video teleconferencing technology and partners with community clinics in rural areas to increase knowledge of stroke risk. The use of technology and community partnerships in this program allowed nurse practitioner providers to effectively deliver selfmanagement support and stroke-risk reduction education among a population of rural veterans at risk for stroke.
Intra- and Intermolecular Reactivity of Triplet Sumanenetrione (2015)

Abstract The intra- and intermolecular reactivity of triplet sumanenetrione 31, which contains a curved π-system, were investigated to characterize the triplet aromatic ketone. The lowest ππ* triplet energy and lifetime were determined from phosphorescence measurements at 77 K to be 196 kJ mol−1 and 9.5 ms in methylcyclohexane, respectively. The transient ππ* triplet state 31 was detected by laser flash photolysis at 293 K and found to be significantly short-lived, e.g., 53.9 µs in degassed benzene, compared to a planar ππ* triplet ketone such as fluorenone triplet (500 µs). The fast intersystem crossing process (ISC) of 31 was attributed to the curved structure of the sumanenetrione, which enhances spin-orbit coupling (SOC). The ππ* character was proven by its negligible quenching by isopropanol, i.e., kq &amp;lt; 4.50 × 103 M−1 s−1, although the quenching rate constants for molecular oxygen and triethylamine in benzene were high: 1.0 × 109 M−1 s−1 and 4.0 × 108 M−1 s−1. The ππ* character of the triplet state was also proven by the relatively small electron spin resonance zero-field splitting parameter, |D|/hc, in toluene at 78 K, which was found to be 0.0621 cm−1. The |E|/hc parameter was determined to be 0.0071 cm−1.
Measurement of Crystallinity in Polymers Using Modulated Temperature Differential Scanning Calorimetry (2001)

Some time ago a proposal was made [1] for an approach to calculating the initial crystallinity for polymers using MTDSC, i.e., the crystallinity of the sample before the start of the experiment. The essence of the technique is that it attempts to estimate the contribution from the vibrational heat capacity to the total enthalpy absorbed by the sample over the temperature range where crystallization, rearrangement and melting occur. This estimate is made from the reversing signal by using interpolation to subtract any contributions to this signal from crystallisation rearrangement or melting processes. The difference between the total enthalpy and the estimate of the vibrational heat capacity contribution must then be a measure of the enthalpy of melting of any initial crystallinity. The thermodynamic basis of this approach is presented in this article together with examples of its application to both simple and complex systems. There are alternatives to this procedure and the advantages and disadvantages of the various possible approaches are discussed.
Frequency stabilization in nonlinear micromechanical oscillators (2012)

Mechanical oscillators are present in almost every electronic device. They mainly consist of a resonating element providing an oscillating output with a specific frequency. Their ability to maintain a determined frequency in a specified period of time is the most important parameter limiting their implementation. Historically, quartz crystals have almost exclusively been used as the resonating element, but micromechanical resonators are increasingly being considered to replace them. These resonators are easier to miniaturize and allow for monolithic integration with electronics. However, as their dimensions shrink to the microscale, most mechanical resonators exhibit nonlinearities that considerably degrade the frequency stability of the oscillator. Here we demonstrate that, by coupling two different vibrational modes through an internal resonance, it is possible to stabilize the oscillation frequency of nonlinear self-sustaining micromechanical resonators. Our findings provide a new strategy for engineering low-frequency noise oscillators capitalizing on the intrinsic nonlinear phenomena of micromechanical resonators.