gebhart/patrepeval huggingface dataset:
Purification and characterization of the reconstitutively active tricarboxylate transporter from rat liver mitochondria. (1990)

The tricarboxylate transporter has been purified in reconstitutively active form from rat liver mitochondria. The transporter was extracted from mitoplasts with Triton X-114 in the presence of cardiolipin and citrate and was then purified by sequential chromatography on hydroxylapatite, Matrex Gel Orange A, Matrex Gel Blue B, and Affi-Gel 501. Analysis of the purified material via sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated the presence of one main protein band with an apparent molecular mass of 32.5 kDa. Upon incorporation into phospholipid vesicles, the purified transporter catalyzed a 1,2,3-benzenetricarboxylate-sensitive citrate/citrate exchange with a specific transport activity of 3240 nmol/4 min/mg of protein. This value was enhanced 831-fold with respect to the starting material. Substrate competition studies indicated that the reconstituted transport could be substantially inhibited by isocitrate, malate, and phosphoenolpyruvate, but not by alpha-ketoglutarate, succinate, malonate, pyruvate, or inorganic phosphate. Moreover, in addition to 1,2,3-benzenetricarboxylate, the reconstituted exchange was sensitive to the anion transport inhibitor n-butylmalonate but was insensitive to phenylsuccinate, alpha-cyano-4-hydroxycinnamate, and carboxyatractyloside. Finally, studies with covalent modifying agents indicated the purified transporter was inhibited by sulfhydryl reagents and by diethyl pyrocarbonate, 2,3-butanedione, phenylglyoxal, and pyridoxal 5-phosphate. In conclusion, these studies describe the first procedure to yield a highly purified tricarboxylate transport protein that both displays a high specific transport activity and can be obtained in quantities that readily enable further structural as well as functional studies. Based on its substrate specificity and inhibitor sensitivity, the purified 32.5-kDa protein appears to represent the complete tricarboxylate transport system found in rat liver mitochondria. Finally, new information is presented concerning the effect of covalent modifying reagents on the function of this transporter.
Toric ideals of Minkowski sums of unit simplices (2020)

In this paper, we discuss the toric ideals of the Minkowski sums of unit simplices. More precisely, we prove that the toric ideal of the Minkowski sum of unit simplices has a squarefree initial ideal and is generated by quadratic binomials. Moreover, we also prove that the Minkowski sums of unit simplices have the integer decomposition property. Those results are a partial contribution to Oda conjecture and Bøgvad conjecture.
210. Step-down from IV to oral therapy in patients with bacteremia due to Enterobacteriaceae: fluoroquinolones (FQ) vs. ß-lactams (BL) or trimethoprim-sulfamethoxazole (TMP-SMX) (2019)

Abstract Background Patients with Gram-negative bloodstream infection (GN BSI) commonly transition from intravenous (IV) to oral therapy after clinical improvement. Some clinical reports suggest similar outcomes with oral step down to TMP/SMX or BL compared with FQ in uncomplicated GN BSI, despite questionable pharmacodynamic target achievement with oral administration of the former. We sought to compare clinical outcomes in Stanford Health Care (SHC) patients with GN BSI who received step-down therapy with FQ vs. BL or TMP/SMX. Methods This was a retrospective cohort study of patients treated at SHC from 1/2010–December 2018 for Enterobacteriaceae bacteremia with oral stepdown to FQ vs. non-FQ (TMP-SMX, BL) initiated by day 7 of therapy. Preliminary data were obtained from electronic health records (EHR) and analyzed via the GreenButton informatics consult service at SHC. The primary outcome was 30-day mortality. Secondary outcomes included 30 and 90-day recurrent BSI, and 90-day C.difficile infection (CDI). Survival analysis was completed for each outcome using the log-rank test to calculate hazard ratio (HR). Cohorts were compared without adjustment and with basic matching controlling for age, sex, length of EHR record, and number of encounters with SHC. Results Of 529 eligible patients, 414 were in the FQ vs. 115 in the non-FQ oral stepdown cohorts. In unadjusted analysis, 30-day mortality was similar between the FQ and non-FQ groups, (5.8% vs. 6.1%, HR 1.06; 95% CI, 0.46–2.46), P = 0.89. Thirty-day recurrent BSI (1.2% vs. 2.6%, HR 2.20; 95% CI, 0.53–9.20) P = 0.27) and 90-day CDI rates (3.1% vs. 1.7%, HR 0.56; 95% CI 0.13–2.48, P = 0.44) were similar between groups. Ninety-day recurrent BSI was higher in the non-FQ group (1.9% vs. 5.2%, HR 1.38; 95% CI, 0.31–6.15. P = 0.0485).(Table 1) In matched analysis (n = 61), 30-day mortality was similar between groups (5.8% vs. 6.1%; HR 1.06, 95% CI 0.46–2.46, P = 0.89). Matched analysis found no statistically significant differences between groups for all secondary outcomes. (Table 2) Conclusion In this study, 30-day mortality was not different among patients that received oral step down to an FQ vs. non-FQ for the treatment of Enterobacteriaceae bacteremia. Larger, prospective trials are warranted to validate observations and determine optimal dosing of oral antibiotics in this setting. Disclosures All authors: No reported disclosures.
Deleted in liver cancer 1 isoforms are distinctly expressed in human tissues, functionally different and under differential transcriptional regulation in hepatocellular carcinoma (2009)

The results suggested that DLC1 isoforms are differentially expressed in human tissues, have different epigenetic transcriptional regulations and are functionally different. DLC1alpha was underexpressed and clinically relevant in human HCCs.
From Stochastic Dominance to Mean-Risk Models: Semideviations as Risk Measures (1997)

Two methods are frequently used for modeling the choice among uncertain outcomes: stochastic dominance and mean-risk approaches. The former is based on an axiomatic model of risk-averse preferences but does not provide a convenient computational recipe. The latter quantifies the problem in a lucid form of two criteria with possible trade-off analysis, but cannot model all risk-averse preferences. In particular, if variance is used as a measure of risk, the resulting mean-variance (Markowitz) model is, in general, not consistent with stochastic dominance rules. This paper shows that the standard semideviation (square root of the semivariance) as the risk measure makes the mean-risk model consistent with the second degree stochastic dominance, provided that the trade-off coefficient is bounded by a certain constant. Similar results are obtained for the absolute semideviation, and for the absolute and standard deviations in the case of symmetric or bounded distributions. In the analysis we use a new tool, the Outcome-Risk diagram, which appears to be particularly useful for comparing uncertain outcomes.
Risk of bladder tumours after childhood cancer: The British Childhood Cancer Survivor Study (2010)

Although the absolute risk of a bladder tumour within childhood cancer survivors was low, the risk was four times that expected from the general population. Specific groups, e.g. survivors of heritable retinoblastoma and those treated with chemotherapy, were at the highest risk.
Minimum entropy combinatorial optimization problems (2009)

Klaus Ambos-Spies, Benedikt Löwe, and Wolfgang Merkle, editors, Mathematical Theory and Computational Practice
Leukocidins and the Nuclease Nuc Prevent Neutrophil-Mediated Killing of Staphylococcus aureus Biofilms (2020)

Bacterial biofilms are linked with chronic infections and have properties distinct from those of planktonic, single-celled bacteria. The virulence mechanisms associated with <i>Staphylococcus aureus</i> biofilms are becoming better understood. Human neutrophils are critical for the innate immune response to <i>S. aureus</i> infection. Here, we describe two virulence strategies that converge to promote the ability of <i>S. aureus</i> biofilms to evade killing by neutrophils. Specifically, we show that while neutrophils exposed to <i>S. aureus</i> biofilms produce extracellular traps (NETs) and phagocytose bacteria, both mechanisms are inefficient in clearance of the biofilm biomass. This is attributed to the leukocidin LukAB, which promotes <i>S. aureus</i> survival during phagocytosis. We also show that the persistence of biofilm bacteria trapped in NETs is facilitated by <i>S. aureus</i> nuclease (Nuc)-mediated degradation of NET DNA. This study describes key aspects of the interaction between primary human neutrophils and <i>S. aureus</i> biofilms and provides insight into how <i>S. aureus</i> evades the neutrophil response to cause persistent infections.
Same but not alike: Structure, flexibility and energetics of domains in multi-domain proteins are influenced by the presence of other domains (2018)

The majority of the proteins encoded in the genomes of eukaryotes contain more than one domain. Reasons for high prevalence of multi-domain proteins in various organisms have been attributed to higher stability and functional and folding advantages over single-domain proteins. Despite these advantages, many proteins are composed of only one domain while their homologous domains are part of multi-domain proteins. In the study presented here, differences in the properties of protein domains in single-domain and multi-domain systems and their influence on functions are discussed. We studied 20 pairs of identical protein domains, which were crystallized in two forms (a) tethered to other proteins domains and (b) tethered to fewer protein domains than (a) or not tethered to any protein domain. Results suggest that tethering of domains in multi-domain proteins influences the structural, dynamic and energetic properties of the constituent protein domains. 50% of the protein domain pairs show significant structural deviations while 90% of the protein domain pairs show differences in dynamics and 12% of the residues show differences in the energetics. To gain further insights on the influence of tethering on the function of the domains, 4 pairs of homologous protein domains, where one of them is a full-length single-domain protein and the other protein domain is a part of a multi-domain protein, were studied. Analyses showed that identical and structurally equivalent functional residues show differential dynamics in homologous protein domains; though comparable dynamics between in-silico generated chimera protein and multi-domain proteins were observed. From these observations, the differences observed in the functions of homologous proteins could be attributed to the presence of tethered domain. Overall, we conclude that tethered domains in multi-domain proteins not only provide stability or folding advantages but also influence pathways resulting in differences in function or regulatory properties.
Text-Independent Speaker Identification Through Feature Fusion and Deep Neural Network (2020)

Speaker identification refers to the process of recognizing human voice using artificial intelligence techniques. Speaker identification technologies are widely applied in voice authentication, security and surveillance, electronic voice eavesdropping, and identity verification. In the speaker identification process, extracting discriminative and salient features from speaker utterances is an important task to accurately identify speakers. Various features for speaker identification have been recently proposed by researchers. Most studies on speaker identification have utilized short-time features, such as perceptual linear predictive (PLP) coefficients and Mel frequency cepstral coefficients (MFCC), due to their capability to capture the repetitive nature and efficiency of signals. Various studies have shown the effectiveness of MFCC features in correctly identifying speakers. However, the performances of these features degrade on complex speech datasets, and therefore, these features fail to accurately identify speaker characteristics. To address this problem, this study proposes a novel fusion of MFCC and time-based features (MFCCT), which combines the effectiveness of MFCC and time-domain features to improve the accuracy of text-independent speaker identification (SI) systems. The extracted MFCCT features were fed as input to a deep neural network (DNN) to construct the speaker identification model. Results showed that the proposed MFCCT features coupled with DNN outperformed existing baseline MFCC and time-domain features on the LibriSpeech dataset. In addition, DNN obtained better classification results compared with five machine learning algorithms that were recently utilized in speaker recognition. Moreover, this study evaluated the effectiveness of one-level and two-level classification methods for speaker identification. The experimental results showed that two-level classification presented better results than one-level classification. The proposed features and classification model for identifying a speaker can be widely applied to different types of speaker datasets.
Renal function is independently associated with circulating betatrophin (2017)

Our data suggest that circulating levels of betatrophin depend on age, gender, waist circumference, total/HDL cholesterol ratio and renal function. Especially the association to eGFR highlights the importance for future studies to address renal function as possible influence on betatrophin regulation and consider eGFR as potential confounder when analyzing the role of betatrophin in humans.
Demo (2014)

Cognitive MAC schemes are emerging as a prospective solution to efficiently utilize the wireless medium. In order to enable opportunistic access to unused licensed band, a node has to monitor the frequency spectrum and carry out its transmission without causing harmful interference to the primary user. In this work, we demonstrate a decentralized multichannel MAC protocol CogMAC+ which uses a multichannel preamble reservation scheme to achieve parallel transmissions for multiple secondary users. Moreover, CogMAC+ uses an adaptive energy detection scheme to dynamically set the frame detection threshold based on the false positive detection ratio. Our table-top demonstration shows that CogMAC+ enables spectral coexistence and allows nodes to utilize spectrum opportunities efficiently in a dynamic fashion.
Ocular Findings of Acute Cytomegalovirus Infection in an Immunologically Competent Adult (1982)

CYTOMEGALIC inclusion disease is a multiorgan viral infection that in adults is most often identified in immunocompromised hosts. Ocular findings in such patients are typically those of acute necrotizing retinitis with variable involvement of the anterior segment.1 2 3 4 5 6 7 8 9 10 Cytomegalovirus infection is identified much less frequently in immunocompetent adults. Only a few such patients with ocular involvement have been described11 , 12; only one of these patients had retinitis, and neither histologic nor virologic confirmation was documented.11 We report serologically and virologically documented acute cytomegalovirus infection associated with self-limited retinitis and impaired tear secretion in a previously healthy adult.Case ReportA 45-year-old . . .
Carnosine and taurine contents in individual fibres of human vastus lateralis muscle (1998)

Analysis of ATPase characterized type I and type II fibres from biopsy samples of the vastus lateralis muscle of four male subjects showed a selective distribution of carnosine and free taurine similar to that observed in other species. The mean carnosine concentration was twice as high in type II compared with type I muscle fibres (23.2 +/- 17.8 and 10.5 +/- 7.6 mmol . kg -1 dry weight, respectively), while taurine was four times higher in type I compared with type II muscle fibres (39.2 +/- 17.8 and 9.6 +/- 2.6 mmol . kg -1 dw, respectively). Overlap in the concentration of carnosine or taurine between fibre types occurred only once in one subject. There was no overlap between fibre types in the ratio of carnosine to taurine. Higher carnosine concentrations in type II fibres will result in a greater contribution to the buffering of H+ arising from anaerobic metabolism. The contribution in a type II fibre with the highest carnosine content was estimated to equal 28% of that from other sources.
Experimental verification of dispersed fringe sensing as a segment phasing technique using the Keck telescope (2004)

Dispersed fringe sensing (DFS) is an efficient and robust method for coarse phasing of segmented primary mirrors (from one quarter of a wavelength to as much as the depth of focus of a single segment, typically several tens of microns). Unlike phasing techniques currently used for ground-based segmented telescopes, DFS does not require the use of edge sensors in order to sense changes in the relative heights of adjacent segments; this makes it particularly well suited for phasing of space-borne segmented telescopes, such as the James Webb Space Telescope. We validate DFS by using it to measure the piston errors of the segments of one of the Keck telescopes. The results agree with those of the Shack-Hartmann-based phasing scheme currently in use at Keck to within 2% over a range of initial piston errors of +/-16 microm.
Patch use by the greater glider (Petauroides volans) in a fragmented forest ecosystem. I. Home range size and movements (2004)

This paper examines home-range attributes of 40 greater gliders (Petauroides volans) in five patches of remnant eucalypt forest surrounded by stands of radiata pine (Pinus radiata) near Tumut in south-eastern Australia. Fixed-kernel smoothing methods were used to estimate home-range size for P. volans. For males, home-range size varied from 1.38–4.10 ha (mean = 2.6 ± 0.8 ha, n = 12) and was significantly larger (P &lt; 0.05) than for females (1.26–2.97 ha, mean = 2.0 ± 0.6 ha, n = 11). Home-range size increased significantly with increasing patch size and reduced patch population density. Thus, small patches had more animals per unit area with smaller home ranges and greater home-range overlap. Our findings illustrate flexibility in the use of space by P. volans. Such results have not previously been reported for P. volans or any other species of arboreal marsupial. Considerable home-range overlap (at 95th percentile isopleth level) was observed between male and female P. volans. Pairs of females also exhibited home-range overlap. Males tended to maintain home ranges exclusive of other males, although some shared common areas. Contrary to the large variations observed in home-range area, core areas (50th isopleth) remained relatively constant, regardless of patch size, population density or sex. This may indicate that core areas are an essential requirement for individuals and resources they contain cannot be shared with congeners.
Serologically Detectable Human Melanoma-Associated Antigens Are Not Genetically Linked to HLA-A and B Antigens (1979)

Abstract Serologic, structural and immunogenic data accumulated in animal model systems suggest that some tumor-specific antigens are newly expressed or modified histocompatibility antigens (see for review 1). This evidence raises the possibility that in man some tumor-associated antigens may derive from histocompatibility (HLA) antigens. We tested this hypothesis in the human melanoma system by investigating whether human chromosome 6, which carries the major histocompatibility complex region (2, 3), controls the expression of serologically detectable melanoma-associated antigens (sd-MAA). An absence of genetic linkage between sd-MAA and HLA antigens would cast serious doubts on the proposition that sd-MAA are modified HLA antigens. In our studies, we prepared hybrid clones by fusing cultured human melanoma cells with murine fibroblasts. We tested these hybrids for expression of sd-MAA and HLA-A and B antigens after a number of passages in vitro, during which a preferential loss of human chromosomes resulted in cells with a few human chromosomes superimposed on essentially complete murine genomes. Since two genes associatedwith a single human chromosome are lost or retained together in interspecific somatic cell hybrids, the independent segregation of two phenotypic markers in a sufficiently largenumber of independently-derived clones would imply lack ofgenetic linkage. Our data indicate that sd-MAA segregate independentlyfrom HLA antigens in these interspecific somaticcell hybrids, which strongly negates the contention that not all(if any) sd-MAA are modified HLA antigens.
A Static Pruning Study on Sparse Neural Retrievers (2023)

Sparse neural retrievers, such as DeepImpact, uniCOIL and SPLADE, have been introduced recently as an efficient and effective way to perform retrieval with inverted indexes. They aim to learn term importance and, in some cases, document expansions, to provide a more effective document ranking compared to traditional bag-of-words retrieval models such as BM25. However, these sparse neural retrievers have been shown to increase the computational costs and latency of query processing compared to their classical counterparts. To mitigate this, we apply a well-known family of techniques for boosting the efficiency of query processing over inverted indexes: static pruning. We experiment with three static pruning strategies, namely document-centric, term-centric and agnostic pruning, and we assess, over diverse datasets, that these techniques still work with sparse neural retrievers. In particular, static pruning achieves $2\times$ speedup with negligible effectiveness loss ($\leq 2\%$ drop) and, depending on the use case, even $4\times$ speedup with minimal impact on the effectiveness ($\leq 8\%$ drop). Moreover, we show that neural rerankers are robust to candidates from statically pruned indexes.
Quality Control: A Challenge to Interior Design Educators (1986)

There is an increasing need to control the quantity and quality of interior design students entering the profession. A portfolio review initiated at the sophomore level has been introduced in an effort to improve the qualifications of the graduating interior design student at the University of Kentucky. This review is also perceived as a determining factor in making career decisions for the student. A first unofficial Sophomore Portfolio Review established the guidelines for interpreting the categories and presentation methodology for future reviews. Such a review process should impart earlier recognition of professional potential, produce high calibre graduates, and provide an enhanced reputation among design professionals.
Developments in SiAlON Glasses and their Derivatives: Effects of Chemistry on Properties (2008)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.