gebhart/patrepeval huggingface dataset:
Purification and Properties of Extracellular Cytosine Deaminase from Chromobacterium violaceum YK 391 (1999)

The extracellular cytosine deaminase (EC 3.5.4.1) from Chromobacterium violaceum YK 391 was purified 264.7-fold with an overall yield of 14.3%. The enzyme was for the first time homogeneous by the criteria of polyacrylamide gel electrophoresis performed in the absence and in the presence of sodium dodecyl sulfate. The molecular weight of the purified enzyme was estimated to be about 156 kDa, The enzyme consisted of two identical subunits of approximate molecular weight 78 kDa. The isoelectric point of the enzyme was pH 5.55. The enzyme had a pH optimum of 7.5 and a temperature optimum of around 40 to 45°C. Besides cytosine, the enzyme deaminated 5-fluorocytosine, cytidine, 5-methylcytosine, and 6-azacytosine, but not 5-azacytosine. The extracellular cytosine deaminase is believed to be unique because it was active not only on cytosine but also on cytidine. The apparent K m values for cytosine, 5-fluorocytosine, cytidine, and 5-methylcytosine were determined to be 1.55 mM, 5.52 mM, 10.4 mM, and 67.2 mM, respectively. The enzyme activity was strongly inhibited by heavy metal ions such as Fe 2+ , Pb 2+ , Cd 2+ , Zn 2+ , Hg 2+ , and Cu 2+ at I mM, and completely by α,α'-dipyridyl, and p-chloromercuribenzoate at 1 mM, and weakly inhibited by I mM o-phenanthroline. The enzyme activity was not affected by various nucleosides and nucleotides.
NK cell exhaustion: bad news for chronic disease? (2015)

Natural killer (NK) cells are generally considered as the effector arm of nonspecific innate immunity, providing rapid recognition and lysis of virus-infected and tumor cells, but can also play significant regulatory roles in pregnancy, cooperate with T and B cell responses, and even exhibit independent adaptive memory. However, much like other lymphocyte populations, recent burgeoning evidence suggests that in chronic conditions NK cells can become functionally exhausted.
Top‐down particle fabrication: control of size and shape for diagnostic imaging and drug delivery (2009)

This review discusses rational design of particles for use as therapeutic vectors and diagnostic imaging agent carriers. The emerging importance of both particle size and shape is considered, and the adaptation and modification of soft lithography methods to produce nanoparticles are highlighted. To this end, studies utilizing particles made via a process called Particle Replication In Non-wetting Templates are discussed. In addition, insights gained into therapeutic cargo and imaging agent delivery from related types of polymer-based carriers are considered.
Rituximab identified as an independent risk factor for severe PJP: A case-control study (2020)

In conclusion, rituximab, which is prescribed for a wide variety of malignant and inflammatory disorders, was found to be significant risk-factor for PJP. Increased awareness of possible PJP infection in this patient population is warranted.
BubbleStorm: Analysis of Probabilistic Exhaustive Search in a Heterogeneous Peer-to-Peer System (2007)

Exhaustive search in large-scale peer-to-peer systems is complicated by heterogeneity, crashes, node churn, hotspots, and weakly structured data. While existing approaches solve some of these problems, the BubbleStorm system offers a naturally integrated and simple solution based on random multigraphs. The simplicity of this mathematical structure allows us to rigorously analyze even the heterogeneous case. We present a new communication primitive, named bubblecast, which induces subgraphs (bubbles) of controlled size. It can incrementally enlarge a bubble, but operates in parallel. Further, the underlying topology deals easily with crashes and node churn as maintenance operations are local, atomic, and minimally disruptive. In spite of this, it preserves the global random structure of a simple permutation. When combined into the BubbleStorm system, bubblecast on this topology performs exhaustive search with adjustable probabilistic guarantees and no hotspots. If every query must rendezvous with every datum, this approach has optimal per-node bandwidth complexity. Indeed, rather than suffering from heterogeneity, it is exploited fully.
Insights into African swine fever virus immunoevasion strategies (2020)

African swine fever (ASF) is an acute and highly contagious disease that causes severe economic losses to the swine industry. ASF is caused by infection of African swine fever virus (ASFV) in domestic pigs, leading to almost 100% mortality. However, no effective vaccines and pharmacologic treatment against ASF are available. ASF poses a severe threat to the swine industry and the economy. Here we summarize potential virus-host cell interaction mechanisms involving the suppression of innate and adaptive immune responses to ASFV entry and infection. These mechanisms include modulation of apoptosis, inhibition of inflammatory responses, reduction of IFN production, inhibition of autophagy, and suppression of MHC-I expression. Insights into immunoevasion strategies by ASFV may shed light on the development of vaccines, as well as preventive and therapeutic drugs.
Improved sectioning in a slit scanning confocal microscope (2008)

We describe a simple implementation of a slit scanning confocal microscope to obtain an axial resolution better than that of a point-scanning confocal microscope. Under slit illumination, images of a fluorescent object are captured using an array detector instead of a line detector so that out-of-focus light is recorded and then subtracted from the adjacent images. Axial resolution after background subtraction is 2.2 times better than the slit confocal resolution, and out-of-focus image suppression is calculated to attenuate with defocus faster by 1 order of magnitude than in the point confocal case.
Output Energy Estimation of Si-Based Photovoltaic Modules Using Clearness Index and Air Mass (2012)

The output energy estimation of photovoltaic (PV) modules was carried out using contour maps as a function of average photon energy (APE), which is an index of solar spectral irradiance and module temperature (Tmod) in our previous report. This method is useful for not only crystalline Si PV modules but also thin film Si PV modules, which have a narrow spectral response. However, this method requires spectrum measurement to obtain APE using a spectroradiometer, which is not widely installed in various locations. In this study, we used clearness index (Kt) and air mass (AM), which have a strong correlation with APE and Tmod. Kt and AM can be calculated easily from irradiance, time, and location. The comparison between the output energy estimation using Kt and AM and that using APE and Tmod was carried out. Results indicate that the accuracy of the output energy estimation using Kt and AM is as high as that using APE and Tmod. The proposed method using Kt and AM is useful for estimating the output energy of the PV modules.
Experiments In Migration Mapping By Computer (1987)

Migration maps represent patterns of geographical movement by arrows or bands between places, using information arriving in "from-to" tables. In the most interesting cases the tables are of large size, suggesting that computer assistance would be useful in the preparation of the maps. A computer program prepared for this purpose shows that graphical representation is feasible for tables as large as fifty by fifty, and possibly larger. The program contains options for alternate forms of movement depiction, and rules are suggested for the parsing of migration tables prior to the cartographic display, without loss of spatial resolution.
A Novel Method for Measuring Antioxidant Capacity and its Application to Monitoring the Antioxidant Status in Premature Neonates (1993)

1. A new method has been developed for measuring the total antioxidant capacity of body fluids and drug solutions, based on the absorbance of the ABTS.+ radical cation. 2. An automated method for use on a centrifugal analyser, as well as a manual method, is described. 3. The procedure has been applied to physiological antioxidant compounds and radical-scavenging drugs, and an antioxidant ranking was established based on their reactivity relative to a 1.0 mmol/l Trolox standard. 4. The Trolox equivalent antioxidant capacity of plasma from an adult reference population has been measured, and the method optimized and validated. 5. The method has been applied to investigate the total plasma antioxidant capacity of neonates and how this may be compromised in prematurity.
Endoluminal calprotectin measurement in assessment of pouchitis and a new index of disease activity: A pilot study (2016)

Pouchitis is the most common complication following proctocolectomy with ileal pouch-anal anastomosis for ulcerative colitis (UC). To provide a standardized definition of pouchitis clinical, endoscopic and histological markers were grouped and weighted in the pouch disease activity index (PDAI). However, the delay in the assessment of the final score due to the time requested for histological analysis remains the main obstacle to the index implementation in clinical practice so that the use of modified-PDAI (mPDAI) with exclusion of histologic subscore has been proposed. We tested the ability of calprotectin measurement in the pouch endoluminal content to mimic the histologic score as defined in the PDAI, the index that we adopted as gold standard for pouchitis diagnosis. Calprotectin was measured by ELISA in the pouch endoluminal content collected during endoscopy in 40 consecutive patients with J-pouch. In each patient PDAI and mPDAI were calculated and 15% of patients were erroneously classified by mPDAI. ROC analysis of calprotectin values vs. acute histological subscore ≥ 3 identified different calprotectin cut-off values with corresponding sensitivity and specificity allowing the definition and scoring of different range of calprotectin subscores. We incorporated the calprotectin score in the mPDAI obtaining a new score that shows the same specificity as PDAI for diagnosis of pouchitis and higher sensitivity when compared with mPDAI. The use of the proposed new score, once validated in a larger series of patients, might be useful in the early management of patients with symptoms of pouchitis.
Inferring the demographics of search users (2013)

Knowing users' views and demographic traits offers a great potential for personalizing web search results or related services such as query suggestion and query completion. Such signals however are often only available for a small fraction of search users, namely those who log in with their social network account and allow its use for personalization of search results. In this paper, we offer a solution to this problem by showing how user demographic traits such as age and gender, and even political and religious views can be efficiently and accurately inferred based on their search query histories. This is accomplished in two steps; we first train predictive models based on the publically available myPersonality dataset containing users' Facebook Likes and their demographic information. We then match Facebook Likes with search queries using Open Directory Project categories. Finally, we apply the model trained on Facebook Likes to large-scale query logs of a commercial search engine while explicitly taking into account the difference between the traits distribution in both datasets. We find that the accuracy of classifying age and gender, expressed by the area under the ROC curve (AUC), are 77% and 84% respectively for predictions based on Facebook Likes, and only degrade to 74% and 80% when based on search queries. On a US state-by-state basis we find a Pearson correlation of 0.72 for political views between the predicted scores and Gallup data, and 0.54 for affiliation with Judaism between predicted scores and data from the US Religious Landscape Survey. We conclude that it is indeed feasible to infer important demographic data of users from their query history based on labelled Likes data and believe that this approach could provide valuable information for personalization and monetization even in the absence of demographic data.
Hydrierung zur Prävention der Kontrastmittel-induzierten Nephropathie: Ein Update (2006)

Contrast medium-induced nephropathy (CIN) continues to be one of the most common causes of hospital-acquired acute renal failure. Since most of the clinical studies on the prophylactic use of different drugs to prevent CIN produced disappointing results, hydration remains the mainstay of prophylaxis. A number of recent prospective randomized trials provided further evidence of the effectiveness of hydration and relevant information regarding the optimization of hydration protocols. It was shown that a bolus hydration solely during examination is not sufficient to prevent CIN. In addition, isotonic 0.9 % saline was superior to the commonly used half-isotonic 0.45 % saline in another trial. An outpatient hydration protocol including oral hydration before the examination followed by forced intravenous hydration over 6 hrs. beginning 30 to 60 min. prior to examination seems to be comparable to the usual hydration over 24 hrs. Another hydration protocol, which could also be very attractive especially for outpatients, included the infusion of sodium bicarbonate. In a recent trial, hydration with sodium bicarbonate, given as a bolus for 1 hr. prior to examination followed by an infusion for 6 hrs. after examination, was more effective than hydration with sodium chloride for the prophylaxis of CIN. However, there is still a lack of large-scale, multi-center trials comparing different hydration protocols and investigating their influence on clinically relevant endpoints such as mortality or the need for dialysis.
TESTS OF INTEGRIN TRANSMEMBRANE DOMAIN HOMO‐OLIGOMERIZATION DURING INTEGRIN LIGAND BINDING AND SIGNALING (2011)

Integrin transmembrane (TM) and/or cytoplasmic domains play a critical role in integrin bidirectional signaling. Although it has been shown that TM and/or cytoplasmic α and β domains associate in the resting state and separation of these domains is required for both inside‐out and outside‐in signaling, the role of TM homomeric association remains elusive. Formation of TM homo‐oligomers was observed in micelles and bacterial membranes previously, and it has been proposed that homomeric association is important for integrin activation and clustering. This study addresses whether integrin TM domains form homo‐oligomers in mammalian cell membranes using cysteine scanning mutagenesis. Our results show that TM homomeric interaction does not occur before or after soluble ligand binding, or during inside‐out activation. In addition, even though the cysteine mutants and the heterodimeric disulfide‐bounded mutant could form clusters after adhering to immobilized ligand, the integrin TM domains do not form homo‐oligomers, suggesting that integrin TM homomeric association is not critical for integrin clustering or outside‐in signaling. Therefore, integrin TM homo‐oligomerization is not required for integrin activation, ligand binding or signaling.
Changes in the Metabolism of Histamine arid Monoamines After Occlusion of the Middle Cerebral Artery in Rats (1991)

Changes in the levels of histamine, monoamines, and their metabolites in the cerebral cortex and striatum after occlusion of the middle cerebral artery in rats were examined. The water content of the ipsilateral brain regions gradually increased after occlusion. In the ischemic side, 1 h after occlusion, the cortical norepinephrine and striatal 5-hydroxy-tryptamine levels significantly decreased, and striatal 3,4-dihydroxyphenylacetic acid and homovanillic acid levels markedly increased. In contrast, the levels of histamine and tele-methylhistamine in either brain region gradually increased and the changes became pronounced and statistically significant 6-12 h after induction of ischemia. The striatal histamine and tele-methylhistamine reached levels three- and twofold higher, respectively, than those of the contralateral side. In rats treated with alpha-fluoromethylhistidine 1 h before induction of ischemia, elevation of histamine and tele-methylhistamine was not observed. The elevated histamine level in the ipsilateral straitum at 9 h after occlusion was further significantly increased by the treatment with metoprine, an inhibitor of histamine-N-methyltransferase. These results suggest that the histaminergic activity in the brain is gradually enhanced by cerebral ischemia.
Massive training artificial neural network (MTANN) for reduction of false positives in computerized detection of lung nodules in low‐dose computed tomography (2003)

In this study, we investigated a pattern-recognition technique based on an artificial neural network (ANN), which is called a massive training artificial neural network (MTANN), for reduction of false positives in computerized detection of lung nodules in low-dose computed tomography (CT) images. The MTANN consists of a modified multilayer ANN, which is capable of operating on image data directly. The MTANN is trained by use of a large number of subregions extracted from input images together with the teacher images containing the distribution for the "likelihood of being a nodule." The output image is obtained by scanning an input image with the MTANN. The distinction between a nodule and a non-nodule is made by use of a score which is defined from the output image of the trained MTANN. In order to eliminate various types of non-nodules, we extended the capability of a single MTANN, and developed a multiple MTANN (Multi-MTANN). The Multi-MTANN consists of plural MTANNs that are arranged in parallel. Each MTANN is trained by using the same nodules, but with a different type of non-nodule. Each MTANN acts as an expert for a specific type of non-nodule, e.g., five different MTANNs were trained to distinguish nodules from various-sized vessels; four other MTANNs were applied to eliminate some other opacities. The outputs of the MTANNs were combined by using the logical AND operation such that each of the trained MTANNs eliminated none of the nodules, but removed the specific type of non-nodule with which the MTANN was trained, and thus removed various types of non-nodules. The Multi-MTANN consisting of nine MTANNs was trained with 10 typical nodules and 10 non-nodules representing each of nine different non-nodule types (90 training non-nodules overall) in a training set. The trained Multi-MTANN was applied to the reduction of false positives reported by our current computerized scheme for lung nodule detection based on a database of 63 low-dose CT scans (1765 sections), which contained 71 confirmed nodules including 66 biopsy-confirmed primary cancers, from a lung cancer screening program. The Multi-MTANN was applied to 58 true positives (nodules from 54 patients) and 1726 false positives (non-nodules) reported by our current scheme in a validation test; these were different from the training set. The results indicated that 83% (1424/1726) of non-nodules were removed with a reduction of one true positive (nodule), i.e., a classification sensitivity of 98.3% (57 of 58 nodules). By using the Multi-MTANN, the false-positive rate of our current scheme was improved from 0.98 to 0.18 false positives per section (from 27.4 to 4.8 per patient) at an overall sensitivity of 80.3% (57/71).
Gain-of-function mutation of a voltage-gated sodium channel NaV1.7 associated with peripheral pain and impaired limb development (2017)

Dominant mutations in voltage-gated sodium channel Na<sub>V</sub>1.7 cause inherited erythromelalgia, a debilitating pain disorder characterized by severe burning pain and redness of the distal extremities. Na<sub>V</sub>1.7 is preferentially expressed within peripheral sensory and sympathetic neurons. Here, we describe a novel Na<sub>V</sub>1.7 mutation in an 11-year-old male with underdevelopment of the limbs, recurrent attacks of burning pain with erythema, and swelling in his feet and hands. Frequency and duration of the episodes gradually increased with age, and relief by cooling became less effective. The patient's sister had short stature and reported similar complaints of erythema and burning pain, but with less intensity. Genetic analysis revealed a novel missense mutation in Na<sub>V</sub>1.7 (2567G>C; p.Gly856Arg) in both siblings. The G856R mutation, located within the DII/S4-S5 linker of the channel, substitutes a highly conserved non-polar glycine by a positively charged arginine. Voltage-clamp analysis of G856R currents revealed that the mutation hyperpolarized (-11.2 mV) voltage dependence of activation and slowed deactivation but did not affect fast inactivation, compared with wild-type channels. A mutation of Gly-856 to aspartic acid was previously found in a family with limb pain and limb underdevelopment, and its functional assessment showed hyperpolarized activation, depolarized fast inactivation, and increased ramp current. Structural modeling using the Rosetta computational modeling suite provided structural clues to the divergent effects of the substitution of Gly-856 by arginine and aspartic acid. Although the proexcitatory changes in gating properties of G856R contribute to the pathophysiology of inherited erythromelalgia, the link to limb underdevelopment is not well understood.
Ka-band direct digital receiver (2002)

A new direct-conversion wideband (26-28.5 GHz) six-port receiver is proposed for mass-market wireless communications. This six-port receiver is designed to operate without the need for precise power reading and the use of a digital signal processor that is usually required in other receivers. The proposed receiver architecture is chosen to satisfy requirements of hardware receivers used in high-speed QPSK communications. The receiver contains a receiver front-end, QPSK demodulator, and carrier recovery module. A reverse modulation loop was used to provide a rapid carrier recovery. The maximum bit rate is determined solely by the limiting speed of the baseband module. This new hardware receiver is proposed as a robust, rugged, low-cost receiver for use in wide Ka-band wireless mass-market QPSK communications such as local multipoint distribution system services, which is a prime example of communication equipment requiring such receivers. Bit-error-rate results are presented versus the noise and reference signal phase shift.