gebhart/patrepeval huggingface dataset:
Improving Usability of Integrated Emergency Response Systems: The SoKNOS Approach (2009)

Implementing systems for emergency response poses various challenges.Information from various sources and systems needs to be integrated, processed, aggregated, and visualized in a dynamic and consistent fashion.Amongst all those challenges, one key issue is the development of an optimal user interface, which allows for intuitive operation with different information as well as supports collaborative work, even in stressful situations.In this paper, we introduce the SoKNOS system, an emergency response system addressing those challenges and putting special emphasis on usability.We illustrate how integration on the user interface level enables both efficient engineering and improved usability for emergency management systems, and how collaborative interaction in emergency situations is supported by SoKNOS.
Replication Origin Region of the Chromosome of Alkaliphilic<i>Bacillus halodurans</i>C-125 (1999)

An 18.5-kb DNA fragment containing the oriC region of the chromosome of the alkaliphilic Bacillus halodurans C-125 was obtained by PCR and sequenced. Sixteen open reading frames (ORFs) were identified in this region. A sequencing similarity search using the BSORF database found that ORF1 to 13 all had significant similarities to gene products of Bacillus subtilis. Three other ORFs (ORF14-16) of unknown function were positioned down-stream of gyrB instead of rrnO, which is found in the same region in the case of B. subtilis. The ORF organization from gidA to gyrA was the same as that of B. subtilis. The gene organization and the location of the DnaA-box region were also similar to those of the chromosomes of other bacteria, such as Escherichia coli and Pseudomonas putida. There were two DnaA-box clusters (Box-region C and R) with a consensus sequence TTATCCACA on both sides of the dnaA gene but another DnaA box cluster (Box-region L) which is found in the region between thdF and jag in B. subtilis was not found in the corresponding region in the case of alkaliphilic Bacillus halodurans C-125.
Global temporal patterns of pancreatic cancer and association with socioeconomic development (2017)

Pancreatic cancer induces a substantial global burden. We examined its global incidence/mortality rates and their correlation with socioeconomic development (Human Development Index [HDI] and Gross Domestic Product [GDP] in 2000 as proxy measures). Data on age-standardized incidence/mortality rates in 2012 were retrieved from the GLOBOCAN database. Temporal patterns in 1998-2007 were assessed for 39 countries according to gender. The Average Annual Percent Change (AAPC) of the incidence/mortality trends was evaluated using joinpoint regression analysis. The age-standardized incidence ranged between 0.8-8.9/100,000. When compared among countries, Brazil (AAPC = 10.4, 95%C.I. = 0.8,21) and France (AAPC = 4.7, 95%C.I. = 3.6,5.9) reported the highest incidence rise in men. The greatest increase in women was reported in Thailand (AAPC = 7, 95%C.I. = 2.1,12.1) and Ecuador (AAPC = 4.3, 95%C.I. = 1.3,7.3). For mortality, the Philippines (APCC = 4.3, 95%C.I. = 2,6.6) and Croatia (AAPC = 2, 95% C.I. = 0,3.9) reported the biggest increase among men. The Philippines (AAPC = 5.8, 95% C.I. 4.5,7.2) and Slovakia (AAPC = 3.1, 95% C.I. 0.9,5.3) showed the most prominent rise among women. Its incidence was positively correlated with HDI (men: r = 0.66; women: r = 0.70) and GDP (men: r = 0.29; women: r = 0.28, all p < 0.05), and similarly for mortality (men: r = 0.67; women: r = 0.72 [HDI]; men: r = 0.23; women: r = 0.28 [GDP]). In summary, the incidence and mortality of pancreatic cancer were rising in many countries, requiring regular surveillance.
Controversies in Acute Kidney Injury (2011)

Acute kidney injury (AKI) is a serious and as yet incompletely understood disorder in which sudden impairment of kidney function occurs secondary to one or more of a variety of underlying conditions. This disorder is very common in (elderly) ICU patients and is associated with very high mortality. Many of those who survive suffer from permanent kidney failure and other long-term morbidities, which may include cardiovascular disease and immune dysfunction. Epidemiologic evidence suggests that AKI is not a single disease, but a syndrome comprised of multiple, often coexisting, etiologies. Being usually part of multiorgan failure syndrome, it calls for multiple organ support therapy. The publication at hand contains sections on prerenal azotemia syndromes, dying 'of' or 'with' AKI, pathophysiology of sepsis-induced acute kidney injury, developments in prevention/treatment/rehabilitation, and renal support. Reporting the latest recommendations from experts, it provides valuable information for those that are interested in understanding the disorder and its treatment options.
Correlating Structure and Energetics in Protein-Ligand Interactions: Paradigms and Paradoxes (2013)

Predicting protein-binding affinities of small molecules, even closely related ones, is a formidable challenge in biomolecular recognition and medicinal chemistry. A thermodynamic approach to optimizing affinity in protein-ligand interactions requires knowledge and understanding of how altering the structure of a small molecule will be manifested in protein-binding enthalpy and entropy changes; however, there is a relative paucity of such detailed information. In this review, we examine two strategies commonly used to increase ligand potency. The first of these involves introducing a cyclic constraint to preorganize a small molecule in its biologically active conformation, and the second entails adding nonpolar groups to a molecule to increase the amount of hydrophobic surface that is buried upon binding. Both of these approaches are motivated by paradigms suggesting that protein-binding entropy changes should become more favorable, but paradoxes can emerge that defy conventional wisdom.
Snellen Equivalent for the Bailey-Lovie Acuity Chart (1989)

<h3>To the Editor.</h3> —Many researchers have used the Bailey-Lovie acuity chart<sup>1</sup>in multicenter clinical investigations, such as the Early Treatment Retinopathy Study and the Prospective Evaluation of Radial Keratotomy, because testing with this chart eliminates many of the inherent problems associated with the standard Snellen acuity chart.<sup>2</sup>Thus far, to our knowledge, no one has reported a method for directly converting the number of letters read correctly from the Bailey-Lovie chart to the denominator of the Snellen fraction for 2 ft. Since the Bailey-Lovie chart is designed to have an equal logarithmic change between lines and there is an equal number of letters per line, a simple exponential equation can be derived to relate these two factors to Snellen acuity as follows: Snellen acuity = 20×10<sup>[(55 - x)/50].</sup>where X is the number of letters read correctly from the Bailey-Lovie chart. For example, if all Bailey-Lovie letters (X = 70) are correctly identified, the score
The indirect effect of peer problems on adolescent depression through nucleus accumbens volume alteration (2020)

Literature suggests that neurobiological factors such as brain structure play an important role in linking social stress with depression in adolescence. We aimed to examine the role of subcortical volumetric alteration in the association between peer problems as one type of social stress and adolescent depression. We hypothesized that there would be indirect effects of peer problems on adolescent depression through subcortical volumetric alteration. Seventy eight adolescents with major depressive disorder (MDD) (age mean [SD] = 14.9 ± 1.5, 56 girls) and 47 healthy controls [14.3 ± 1.4, 26 girls]) participated in this study. High-resolution structural T1 images were collected using the Siemens 3T MR scanner. Subcortical volumes were segmented using the Freesurfer 6.0 package. Peer problems were assessed using the Peer-Victimization Scale and the Bullying-Behavior Scale. There was a significant indirect effect of peer problems on adolescent depression through nucleus accumbens (NAcc) volume alteration, but not through the amygdala and hippocampal volumes. This result supported our model, which stated that peer problems have indirect effects through subcortical volumetric alteration (i.e., increased NAcc volume) on adolescent depression. Our finding suggests that altered NAcc volume may serve as a pathway, through which peer problems as one type of social stressor contribute to adolescent depression.
Harnessing fungal nonribosomal cyclodepsipeptide synthetases for mechanistic insights and tailored engineering (2017)

Nonribosomal peptide synthetases represent potential platforms for the design and engineering of structurally complex peptides. While previous focus has been centred mainly on bacterial systems, fungal synthetases assembling drugs like the antifungal echinocandins, the antibacterial cephalosporins or the anthelmintic cyclodepsipeptide (CDP) PF1022 await in-depth exploitation. As various mechanistic features of fungal CDP biosynthesis are only partly understood, effective engineering of NRPSs has been severely hampered. By combining protein truncation, <i>in trans</i> expression and combinatorial swapping, we assigned important functional segments of fungal CDP synthetases and assessed their <i>in vivo</i> biosynthetic capabilities. Hence, artificial assembly line components comprising of up to three different synthetases were generated. Using <i>Aspergillus niger</i> as a heterologous expression host, we obtained new-to-nature octa-enniatin (4 mg L<sup>-1</sup>) and octa-beauvericin (10.8 mg L<sup>-1</sup>), as well as high titers of the hybrid CDP hexa-bassianolide (1.3 g L<sup>-1</sup>) with an engineered ring size. The hybrid compounds showed up to 12-fold enhanced antiparasitic activity against <i>Leishmania donovani</i> and <i>Trypanosoma cruzi</i> compared to the reference drugs miltefosine and benznidazole, respectively. Our findings thus contribute to a rational engineering of iterative nonribosomal assembly lines.
Development of the antibody repertoire in rabbit: gut‐associated lymphoid tissue, microbes, and selection (2000)

Rabbits generate their antibody repertoire in three stages. First, a neonatal repertoire is generated by B lymphopoiesis in fetal liver and bone marrow and is limited by preferential V(H) gene segment usage. Between 4 and 8 weeks after birth a complex primary antibody repertoire is developed by somatically diversifying the neonatal repertoire through somatic hypermutation and a somatic gene conversion-like mechanism in gut-associated lymphoid tissue (GALT). In rabbits, unlike other species, the development of the primary antibody repertoire through somatic diversification of Ig genes appears to be dependent on intestinal microbial flora. The primary antibody repertoire is subsequently modified during antigen-dependent immune responses in which VDJ genes further diversify both by somatic hypermutation and by a gene conversion-like mechanism (the secondary repertoire). During the various stages of development, the antibody repertoire is modified and shaped by selective processes. In this review, we discuss the roles of GALT, microbes, and B-cell selection in generating antibody diversity in rabbits.
Non-homogeneous extracellular resistivity affects the current-source density profiles of up–down state oscillations (2011)

Rhythmic local field potential (LFP) oscillations observed during deep sleep are the result of synchronized electrical activities of large neuronal ensembles, which consist of alternating periods of activity and silence, termed 'up' and 'down' states, respectively. Current-source density (CSD) analysis indicates that the up states of these slow oscillations are associated with current sources in superficial cortical layers and sinks in deep layers, while the down states display the opposite pattern of source-sink distribution. We show here that a network model of up and down states displays this CSD profile only if a frequency-filtering extracellular medium is assumed. When frequency filtering was modelled as inhomogeneous conductivity, this simple model had considerably more power in slow frequencies, resulting in significant differences in LFP and CSD profiles compared with the constant-resistivity model. These results suggest that the frequency-filtering properties of extracellular media may have important consequences for the interpretation of the results of CSD analysis.
Metrological solutions for an adapted inspection of parts and tools of a sheet-bulk metal forming process (2015)

Processes of the new production technology sheet-bulk metal forming allow a fast and efficient near-net-shape forming of highly complex parts. Thus the need of energy and raw material as well as the production cycle time can be reduced. In order to guarantee these advantages by avoiding scrap and moreover to ensure the parts’ geometrical requirements, production-related metrological solutions for an adapted inspection of parts and tools of sheet-bulk forming processes have to be developed. To fulfill the demands of the differing measuring tasks two prototypical measurement solutions are under development: a multi-scale multi-sensor fringe projection system allows for holistic inspections in feature adapted resolutions, whereas a fiberscopic fringe projection system captures the forming tool partly between forming steps. For the purpose of evaluating the metrological solutions’ capabilities of capturing the geometry of filigree structures a comparison of both systems is presented in this work. To guarantee realistic results, the performed measuring tasks have to be comparable to the areas of applications both systems were designed for. During the development of the measuring systems the emphasis was put on the inspection of small complex geometries. These are most challenging for fast and reliable optical inspection under production-related conditions. By considering measurements of calibrated standards on the one side as well as of measuring tasks resulting out of real sheet-bulk metal forming processes on the other side a realistic comparison is assured. Next to the measuring systems’ performances also an approach for combining the measurement data of both metrological solutions is shown. By combining the advantages of both measuring systems, highly detailed information for further interpretations of the forming processes can be provided.
Androgen receptor SUMOylation regulates bone mass in male mice (2018)

The crucial effects of androgens on the male skeleton are at least partly mediated via the androgen receptor (AR). In addition to hormone binding, the AR activity is regulated by post-translational modifications, including SUMOylation. SUMOylation is a reversible modification in which Small Ubiquitin-related MOdifier proteins (SUMOs) are attached to the AR and thereby regulate the activity of the AR and change its interactions with other proteins. To elucidate the importance of SUMOylation of AR for male bone metabolism, we used a mouse model devoid of the two AR SUMOylation sites (AR<sup>SUM-</sup>; K381R and K500R are substituted). Six-month-old male AR<sup>SUM-</sup> mice displayed significantly reduced trabecular bone volume fraction in the distal metaphyseal region of femur compared with wild type (WT) mice (BV/TV, -19.1 ± 4.9%, P < 0.05). The number of osteoblasts per bone perimeter was substantially reduced (-60.5 ± 7.2%, P < 0.001) while no significant effect was observed on the number of osteoclasts in the trabecular bone of male AR<sup>SUM-</sup> mice. Dynamic histomorphometric analysis of trabecular bone revealed a reduced bone formation rate (-32.6 ± 7.4%, P < 0.05) as a result of reduced mineralizing surface per bone surface in AR<sup>SUM-</sup> mice compared with WT mice (-24.3 ± 3.6%, P < 0.001). Furthermore, cortical bone thickness in the diaphyseal region of femur was reduced in male AR<sup>SUM-</sup> mice compared with WT mice (-7.3 ± 2.0%, P < 0.05). In conclusion, mice devoid of AR SUMOylation have reduced trabecular bone mass as a result of reduced bone formation. We propose that therapies enhancing AR SUMOylation might result in bone-specific anabolic effects with minimal adverse effects in other tissues.
Data from Phase I Trial of Arginine Deprivation Therapy with ADI-PEG 20 Plus Docetaxel in Patients with Advanced Malignant Solid Tumors (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; This phase I study examined the toxicity and tolerability of pegylated arginine deiminase (ADI-PEG 20) in combination with docetaxel in patients with advanced solid malignancies.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; Eligible patients had histologically proven advanced solid malignancies, with any number of prior therapies, Zubrod performance status 0–2, and adequate organ function. Patients received ADI-PEG 20 weekly intramuscular injection ranging from 4.5 to 36 mg/m&lt;sup&gt;2&lt;/sup&gt; and up to 10 doses of docetaxel (75 mg/m&lt;sup&gt;2&lt;/sup&gt;) every 3 weeks. Primary endpoints were safety, toxicity, and a recommended phase II dose. Circulating arginine levels were measured before each cycle. Tumor response was measured as a secondary endpoint every 6 weeks on study.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Eighteen patients received a total of 116 cycles of therapy through four dose levels of ADI-PEG 20. A single dose-limiting toxicity (grade 3 urticarial rash) was observed at the 1st dose level, with no additional dose-limiting toxicities observed. Hematologic toxicities were common with 14 patients experiencing at least one grade 3 to 4 leukopenia. Fatigue was the most prevalent toxicity reported by 16 patients. Arginine was variably suppressed with 10 patients achieving at least a 50% reduction in baseline values. In 14 patients with evaluable disease, four partial responses (including 2 patients with PSA response) were documented, and 7 patients had stable disease.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; ADI-PEG 20 demonstrated reasonable toxicity in combination with docetaxel. Promising clinical activity was noted, and expansion cohorts are now accruing for both castrate-resistant prostate cancer and non–small cell lung cancer at a recommended phase II dose of 36 mg/m&lt;sup&gt;2&lt;/sup&gt;. &lt;i&gt;Clin Cancer Res; 21(11); 2480–6. ©2015 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
A Journey of a Thousand Miles Begins With a Single Step, and Then Another . . . (2015)

Welcome to the second issue of Cellular and Molecular Gastroenterology and Hepatology (CMGH). On behalf of the Board of Editors, the American Gastroenterological Association, and Elsevier, I would like to thank the gastrointestinal, liver, and pancreas research community for their strong support of this enterprise. We began accepting submissions June 1, 2014, and the response has grown each week. Ultimately, 70 original manuscripts were submitted in 2014. On average, we were able to notify authors of editorial decisions within 3 weeks of submission for work that had not been previously reviewed.
Chronotropic Incompetence in Patients with an Implantable Cardioverter Defibrillator: Prevalence and Predicting Factors (2005)

Chronotropic incompetence (CI), which has not been systematically examined in the ICD patient population, may have implications for device programming. A total of 123 ICD patients were classified into three groups: single-chamber ICD with sinus rhythm, dual-chamber ICD with sinus rhythm, and single-chamber ICD with permanent atrial fibrillation. Heart rate response, maximum oxygen uptake, and oxygen uptake at the anaerobic threshold were measured during treadmill exercise testing. In addition, clinical variables such as antiarrhythmic drug therapy, underlying heart disease, and left-ventricular (LV) ejection fraction were recorded. Of the patients studied, 38% were chronotropically incompetent (47/123). Significant predictors of CI were as follows: presence of a coronary disease (P = 0.036), prior cardiac surgery (P = 0.037), chronic drug therapy with beta-blockers (P = 0.032), administration of amiodarone (P = 0.025), and a combination of these two forms of treatment (P = 0.01). Spiroergometry revealed reduced exercise capacity (P = 0.041) and lessened VO2max (P = 0.034) among chronotropically incompetent patients. A large percentage of ICD patients demonstrates CI with subsequently reduced physical stress tolerance. In light of the DAVID study, we believe that a closer examination of rate-adaptive modes for ICD patients is warranted under enhanced conditions: (1) optimized AV interval programming; (2) utilization of new algorithms to reduce ventricular pacing in combination with rate-adaptive atrial pacing, with the goal of addressing CI while minimizing ventricular pacing; and (3) an optimized upper heart-rate limit.
Apparatus for injecting high power laser light into a fiber optic cable (2023)

High intensity laser light is evenly injected into an optical fiber by the combination of a converging lens and a multisegment kinoform (binary optical element). The segments preferably have multi-order gratings on each which are aligned parallel to a radial line emanating from the center of the kinoform and pass through the center of the element. The grating in each segment causes circumferential (lateral) dispersion of the light, thereby avoiding detrimental concentration of light energy within the optical fiber.
Design of Low-Current High-Efficiency Augmented Railguns (2009)

Properly designed augmented railguns (ARGs) can operate at significantly lower currents and higher efficiency than conventional non-ARGs. This paper analyzes the performance of a two-turn and a three-turn ARG showing the design parameters that are needed to achieve low-current high-efficiency operation. The ARG of this paper has a 40-mm square bore and is 820 mm long. Typical operating currents are from 150 to 300 kA with pulsewidths of approximately 6 to 8 ms. Projectile mass is typically in the range of 130 to 400 g. Projectile velocity is variable from 50 to 250 m/s. Experimental performance is compared with the theoretical predictions of the recently developed electromagnetic launcher (EML) equation. There is a good agreement between measured efficiency and theoretical predictions providing further confirmation of the EML equation. Deviations between measured efficiency and theoretical predictions are attributed to a poor sliding contact. The data also provide further evidence of the recently reported velocity-skin-effect in the contact.