gebhart/patrepeval huggingface dataset:
Insight into the Structural Ambiguity of Actinide(IV) Oxalate Sheet Structures: A Case for Alternate Coordination Geometries (2023)

Invited for the cover of this issue is the group of Amy Hixon at the University of Notre Dame. The image depicts the newly identified structure of a Pu<sup>IV</sup> oxalate sheet compared to the historically assumed structure. Read the full text of the article at 10.1002/chem.202301164.
B2.2 - Network Representation of User’s Mechanical Impedance as Design and Evaluation Basis for Task-Specific Haptic Systems (2013)

This paper deals with the representation of the human user of a haptic system in the design process and investigates different fitting algorithms to find network representations and transfer functions. The user, represented by the mechanical impedance, serves as mechanical load to the system and influences the assessment of the quality of the haptic feedback. Due to large inter-personal variances, the mapping from measurements to concentrated network parameters is investigated in this paper.
Voice over ATM using AAL2 and bit dropping: performance and call admission control (1999)

Asynchronous transfer mode (ATM) adaptation layer 2 (AAL2) has been designed for efficient transport of voice, fax, and voiceband data (VBD) traffic over an ATM virtual circuit. The protocol helps achieve low latency and high bandwidth efficiency while applying suitable compression methods on voice/VBD/fax calls and silence elimination on voice calls. We analyze the performance and capacity of an ATM multiplexer based on AAL2 adaptation. We assume that embedded adaptive differential pulse code modulation (ADPCM) is used to compress voice, and silence elimination is used to achieve statistical multiplexing gain. The embedded ADPCM coding scheme allows selective dropping of less significant bits of voice during congestion in the ATM/AAL2 multiplexer. We compare the call capacities of voice multiplexers with and without bit dropping (BD). The performance models and results presented are based on fairly general assumptions and can be used for traffic engineering and call admission control in land-line or wireless ATM systems for a variety of voice/voiceband compression algorithms. A generalized algorithm for call admission control is also described.
Sinusoidal Siemens star spatial frequency response measurement errors due to misidentified target centers (2015)

Numerous methods are available to measure the spatial frequency response (SFR) of an optical system. A recent change to the ISO 12233 photography resolution standard includes a sinusoidal Siemens star test target. We take the sinusoidal Siemens star proposed by the ISO 12233 standard, measure system SFR, and perform an analysis of errors induced by incorrectly identifying the center of a test target. We show a closed-form solution for the radial profile intensity measurement given an incorrectly determined center and describe how this error reduces the measured SFR of the system. Using the closed-form solution, we propose a two-step process by which test target centers are corrected and the measured SFR is restored to the nominal, correctly centered values.
Regiospecific Solid-Phase Synthesis of Branched Oligoribonucleotides That Mimic Intronic Lariat RNA Intermediates (2014)

We have developed new solid phase methods for the synthesis of branched RNAs that mimic intronic lariat RNA intermediates. These methods produce branched oligoribonucleotide sequences of arbitrary length, base composition, and regiochemistry at the branchpoint junction. The methods utilize branching monomers that allow for the growth of each branch regioselectively from any of the hydroxyl positions (5′, 3′, or 2′) at the branch-point junction. The integrity and branchpoint connectivity of the synthetic products have been confirmed by HPLC and MS analysis, and cleavage of the 2′,5′ linkage by recombinant debranching enzyme. Nonhydrolyzable branched RNA analogues containing arabinose instead of ribose at the branchpoint junction were shown to inhibit debranching activity and, hence, represent “decoys” for sequestering RNA binding proteins thought to drive amyotrophic lateral sclerosis (ALS).
An approximation analysis of nonpreemptive EDF scheduling (2005)

Due to recent advances in multimedia technology, a real-time capability is needed to a certain extent even in information systems, in addition to control systems. In general, information systems are classified as soft real-time systems, which keep operating even if a deadline is missed. In soft real-time systems, it is more important to provide statistical guarantees (probabilistic analysis) than absolute guarantees (deadline guarantees). In current real-time systems, real-time scheduling such as EDF (Earliest Deadline First) is used to meet timing constraints. EDF scheduling simply assigns higher priorities in the order of earlier deadlines. It can be applied to aperiodic tasks without prior knowledge of their starting times. In this paper, it is assumed that each attribute of the task follows a probabilistic distribution. The system performance when a nonpreemptive EDF scheduling is applied is then mathematically analyzed. © 2005 Wiley Periodicals, Inc. Electron Comm Jpn Pt 3, 89(2): 13–23, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjc.20177
Tumorgrafts as In Vivo Surrogates for Women with Ovarian Cancer (2014)

Abstract Purpose: Ovarian cancer has a high recurrence and mortality rate. A barrier to improved outcomes includes a lack of accurate models for preclinical testing of novel therapeutics. Experimental Design: Clinically relevant, patient-derived tumorgraft models were generated from sequential patients and the first 168 engrafted models are described. Fresh ovarian, primary peritoneal, and fallopian tube carcinomas were collected at the time of debulking surgery and injected intraperitoneally into severe combined immunodeficient mice. Results: Tumorgrafts demonstrated a 74% engraftment rate with microscopic fidelity of primary tumor characteristics. Low-passage tumorgrafts also showed comparable genomic aberrations with the corresponding primary tumor and exhibit gene set enrichment of multiple ovarian cancer molecular subtypes, similar to patient tumors. Importantly, each of these tumorgraft models is annotated with clinical data and for those that have been tested, response to platinum chemotherapy correlates with the source patient. Conclusions: Presented herein is the largest known living tumor bank of patient-derived, ovarian tumorgraft models that can be applied to the development of personalized cancer treatment. Clin Cancer Res; 20(5); 1288–97. ©2014 AACR.
Population structure and genome-wide association analysis for frost tolerance in oat using continuous SNP array signal intensity ratios (2016)

Infinium SNP data analysed as continuous intensity ratios enabled associating genotypic and phenotypic data from heterogeneous oat samples, showing that association mapping for frost tolerance is a feasible option. Oat is sensitive to freezing temperatures, which restricts the cultivation of fall-sown or winter oats to regions with milder winters. Fall-sown oats have a longer growth cycle, mature earlier, and have a higher productivity than spring-sown oats, therefore improving frost tolerance is an important goal in oat breeding. Our aim was to test the effectiveness of a Genome-Wide Association Study (GWAS) for mapping QTLs related to frost tolerance, using an approach that tolerates continuously distributed signals from SNPs in bulked samples from heterogeneous accessions. A collection of 138 European oat accessions, including landraces, old and modern varieties from 27 countries was genotyped using the Infinium 6K SNP array. The SNP data were analyzed as continuous intensity ratios, rather than converting them into discrete values by genotype calling. PCA and Ward's clustering of genetic similarities revealed the presence of two main groups of accessions, which roughly corresponded to Continental Europe and Mediterranean/Atlantic Europe, although a total of eight subgroups can be distinguished. The accessions were phenotyped for frost tolerance under controlled conditions by measuring fluorescence quantum yield of photosystem II after a freezing stress. GWAS were performed by a linear mixed model approach, comparing different corrections for population structure. All models detected three robust QTLs, two of which co-mapped with QTLs identified earlier in bi-parental mapping populations. The approach used in the present work shows that SNP array data of heterogeneous hexaploid oat samples can be successfully used to determine genetic similarities and to map associations to quantitative phenotypic traits.
Lynch-Syndrom – Chromokoloskopie vs. Standard-Koloskopie (2015)

Studien weisen darauf hin, dass beim Lynch-Syndrom insbesondere kleine bzw. flache Adenome dazu neigen, maligne zu entarten. Eine Standard-Koloskopie ermöglicht nicht immer, solche Adenome zu erkennen. Ist hier die Chromokoloskopie leistungsfähiger?
Photochemistry of phenyl azide: the role of singlet and triplet phenylnitrene as transient intermediates (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPhotochemistry of phenyl azide: the role of singlet and triplet phenylnitrene as transient intermediatesElisa. Leyva, Matthew S. Platz, Gabriele. Persy, and Jakob. WirzCite this: J. Am. Chem. Soc. 1986, 108, 13, 3783–3790Publication Date (Print):June 1, 1986Publication History Published online1 May 2002Published inissue 1 June 1986https://pubs.acs.org/doi/10.1021/ja00273a037https://doi.org/10.1021/ja00273a037research-articleACS PublicationsRequest reuse permissionsArticle Views1917Altmetric-Citations196LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Discrete-time simulation of smart antenna systems in Network Simulator-2 Using MATLAB and Octave (2010)

This paper presents two platforms that exploit the scalability properties of Network Simulator-2 for the discrete-event simulation of a telecommunication network, and the modeling capabilities of two development tools for the discrete-time implementation of adaptive antenna arrays at the physical layer. The two tools are the proprietary MATLAB and the open source Octave, both of which are used to implement the physical antenna system, the beamforming algorithm, the channel coding scheme, and the multipath and fading statistics. The adopted approach enables detailed modeling of the antenna radiation pattern generated by each network node, thus improving the accuracy of the signal-to-interference ratio estimated at the receiver. This study describes the methods that can be adopted to interface MATLAB and Octave with Network Simulator-2, and discusses the advantages and disadvantages that characterize the integration of the two tools with Network Simulator-2. The proposed numerical platforms, which can be interfaced with any wireless network supported by Network Simulator-2, are used to investigate the possibility of exploiting smart antenna systems in a wireless mesh network to enable the coexistence of multiple simultaneous communications.
Table S1 from Metastatic Melanoma Patient–Derived Xenografts Respond to MDM2 Inhibition as a Single Agent or in Combination with BRAF/MEK Inhibition (2023)

&lt;p&gt;Supplementary Table S1. A. NGS Summary.&lt;/p&gt;
Engineering subtilisin YaB: restriction of substrate specificity by the substitution of Gly124 and Gly151 with Ala (1998)

The 3-D structure of subtilisin YaB was computer modelled using the structures of subtilisin BPN', subtilisin Carlsberg and thermitase as templates. Gly124 and Gly151 located on both sides of the waist of the S1 pocket were selected for site-directed mutagenesis based on the modelled structure. The mutated ale genes coding for the mutant subtilisin YaB were expressed in Bacillus subtilis DB104. All of the G124 and G151 series of mutants exhibited an increase of relative catalytic activity for elastin-orcein against casein and myofibrillar proteins. The S1 substrate specificity of G124A, G124V and G151A mutants were assessed using various carbobenzoxy-amino acid-nitrophenyl esters and succinyl-Ala-Ala-(Pro or Val)-(Ala, Phe or Leu)-p-nitroanilide [AA(P/V) (A/F/L)]. While G124A and G124V mutants hydrolyzed only Ala and Gly esters, G151A mutant hydrolyzed Ala, Leu and Gly esters. The G124A and G124V mutants did not hydrolyze AAPF and AAPL. However, these two mutants hydrolyzed AAPA and AAVA with kcat/Km values approximately 3-10-fold higher than those of the wild-type enzyme. The G151A mutant did not hydrolyze AAPF, but hydrolyzed AAPL, AAPA and AAVA with kcat/Km values approximately 1-4-fold higher than those of the wild-type enzyme. These results clearly indicate that the S1 substrate specificity of G124A and G124V mutants was restricted to Ala and Gly, and G151A mutant to Ala, Gly and Leu.
Effect of Glycan Shift on Antibodies against Hepatitis C Virus E2 412–425 Epitope Elicited by Chimeric sHBsAg-Based Virus-Like Particles (2023)

Two of the most important mechanisms of hepatitis C virus (HCV) immune evasion are the high variability of the amino acid sequence and epitope shielding via heavy glycosylation of the envelope (E) proteins. Previously, we showed that chimeric sHBsAg (hepatitis B virus [HBV] small surface antigen)-based virus-like particles (VLPs) carrying highly conserved epitope I from the HCV E2 glycoprotein (sHBsAg_412-425) elicit broadly neutralizing antibodies (bnAbs). However, many reports have identified escape mutations for such bnAbs that shift the N-glycosylation site from N417 to N415. This shift effectively masks the recognition of epitope I by antibodies raised against the wild-type glycoprotein. To investigate if glycan-shift-mediated immune evasion could be overcome by targeted vaccination strategies, we designed sHBsAg-based VLPs carrying epitope I with an N417S change (sHBsAg_N417S). Studies in BALB/c mice revealed that both sHBsAg_412-425 and sHBsAg_N417S VLPs were immunogenic, eliciting antibodies that recognized peptides encompassing epitope I regardless of the N417S change. However, we observed substantial differences in E1E2 glycoprotein binding and cell culture-derived HCV (HCVcc) neutralization between the sera elicited by sHBsAg_412-425 and those elicited by sHBsAg_N417S VLPs. Our results suggest a complex interplay among antibodies targeting epitope I, the E1E2 glycosylation status, and the epitope or global E1E2 conformation. Additionally, we observed striking similarities in the E1E2 glycoprotein binding patterns and HCVcc neutralization between sHBsAg_412-425 sera and AP33, suggesting that the immunization of mice with sHBsAg_412-425 VLPs can elicit AP33-like antibodies. This study emphasizes the role of antibodies against epitope I and represents an initial effort toward designing an antigen that elicits an immune response against epitope I with a glycan shift change. <b>IMPORTANCE</b> Epitope I, located within amino acids 412 to 423 of the HCV E2 glycoprotein, is an important target for an epitope-based HCV vaccine. One interesting feature of epitope I is the N417 glycosylation site, where a single change to S417 or T417 can shift the glycosylation site to position N415. This shift can effectively prevent the binding of broadly neutralizing antibodies targeting epitope I. Aiming to overcome glycan-shift-mediated immune evasion, we constructed sHBsAg_N417S VLPs carrying E2 epitope I, with N417S, and compared them with VLPs carrying wild-type epitope I. We show that antibodies elicited by the sHBsAg-based VLPs presenting two variants of the 412-425 epitope targeted two distinct glycan variants of the HCV E1E2 heterodimer. Our study suggests that due to the conformational flexibility of the E2 glycoprotein and epitope I, future vaccine antigens should elicit antibodies targeting more than one conformation and glycosylation variant of the 412-423 epitope.
Laparoscopic coloanal anastomosis for low rectal cancer. (2003)

Laparoscopic coloanal anastomosis combined with intraanal canal dissection is safe and technically feasible. The oncologic results seem not to be compromised, but need further evaluation.
Impact of genetic testing and smoking on the distribution of risk factors in patients with recurrent acute and chronic pancreatitis (2021)

Genetic testing and a detailed assessment of smoking dose and duration reduce the proportion of patients with alcoholic and idiopathic pancreatitis. Other risk factor(s) for pancreatitis are found in the majority of patients with pancreas divisum further questioning its role as an independent risk factor.1. What is the current knowledge?Approximately 30% of patients with pancreatitis have no clear risk factor(s) and are categorized as having an idiopathic etiology.Pathogenic variant(s) as well as smoking dose and duration are well-established risk factors for recurrent acute and chronic pancreatitis but are not widely recognized or incorporated into clinical practice.2. What is new here?Genetic testing and a detailed assessment of smoking dose and duration reduced the proportion of patients with alcoholic and idiopathic acute recurrent and chronic pancreatitis.Approximately three-fourths of patients with pancreas divisum have a risk factor for pancreatitis.
Optimization for chip stack in 3-D packaging (2005)

We have been developing three-dimensional (3-D) packaging technology for forming through-type electrodes in chips that are then directly connected in stacks. The model examined in this study is defined by its simple structure. The structure was optimized for successful connection in a chip stack without degrading the features of the chips. The use of this structure enabled a stable and rigid connection, and a four-layer chip stack assembled on a ceramic substrate exhibited adequate thermal cycle performance. This paper discusses how the structure of terminals was optimized for chip stacking. A finished package assembled from static random access memory (SRAM) with through-type electrodes was confirmed to operate well and exhibit normal functioning.
Studien zur Synthese, Struktur und Reaktivität heterozyklischer Metallonitridophosphinate (2005)

Abstract Studies on the Synthesis, Structure and Reactivity of Heterocyclic Metallonitridophosphinates t ‐BuP(NH 2 ) 2 reacts with base‐stabilized group 13 trihydrides with adduct formation (THF‐BH 3 ), with reduction to give t ‐BuPH 2 (Me 3 N‐AlH 3 ) and with elimination of H 2 and formation of a metallonitridophosphinate (Me 3 N‐GaH 3 ). In contrast, the reaction with Cp*TiMe 3 proceeds with formation of the four‐membered heterocycle [ t ‐Bu(H)P(NH) 2 Ti(Cp*)Me 2 ]. The aluminonitridophosphinate [ t ‐Bu(H)P(NH) 2 AlMe 2 ] 2 reacts with C‐H acidic reagents such as ROH, H 2 O with protonation of the N atom and subsequent formation of t ‐BuP(NH 2 ) 2 . This general reaction sequence was used for the synthesis of the first alumino(oxo)nitridophosphinate [ t ‐Bu(H)P(NH)OAlMe 2 ] 2 . The compounds were characterized by spectroscopic methods ( 1 H, 13 C, IR, mass spectrometry) and single crystal X‐ray diffraction ([ t ‐Bu(H)P(NH) 2 Ti(Cp*)Me 2 ], [ t ‐Bu(H)P(NH)OAlMe 2 ] 2 ).
Effect of Oat Bran on Lithogenic Index of Bile and Bile Acid Metabolism (1983)

Epidemiological studies lend support to the hypothesis that high-fibre diets might prevent and low-fibre diets might facilitate the formation of cholesterol gall stones. In the present study, the bile compositions after ingestion of oat bran 18 g/day and placebo 18 g/day for 2 X 2 weeks were compared in a randomized, double-blind cross-over study in 6 healthy volunteers. The lithogenic index of bile was not influenced, whereas the following changes (0.05 less than p less than 0.10) occurred: the cholic acid pool was enlarged, the relative proportion of chenodeoxycholate in bile was increased and that of deoxycholate reduced, while cholate remained unchanged. It is concluded that oat bran seems to influence the metabolism of bile acids.
Gastric electrical stimulation: an evidence-based analysis. (2006)

"For use in weight reduction for obese adults with a body mass index greater than 35."The GES device that is licensed by Health Canada for treatment of GP, produces high-frequency GES. Most clinical studies examining GES for GP have used high-frequency (4 times the intrinsic slow wave frequency, i.e., 12 cycles per minute), low energy, short duration pulses. This type of stimulation does not alter gastric muscular contraction and has no effect on slow wave dysrhythmias. The mechanism of action is unclear but it is hypothesized that high-frequency GES may act on sensory fibers directed to the CNS. The GES device licensed by Health Canada for treatment of morbid obesity produces low-frequency GES, which is close to or just above the normal/native gastric slow wave cycle (approximately 3 cycles/min.). This pacing uses low-frequency, high-energy, long-duration pulses to induce propagated slow waves that replace the spontaneous ones. Low-frequency pacing does not invoke muscular contractions. Most studies examining the use of GES for the treatment of morbid obesity use low-frequency GES. Under normal circumstances, the gastric slow wave propagates distally and determines the frequency and propagation direction of gastric peristalsis. Low-frequency GES aims to produce abnormal gastric slow waves that can induce gastric dysrhythmia, disrupt regular propagation of slow waves, cause hypomotility of the stomach, delay gastric emptying, reduce food intake, prolong satiety, and produce weight loss. In the United States, the Enterra Therapy System is a Humanitarian Use Device (HUD), meaning it is a medical device designated by the FDA for use in the treatment of medical conditions that affect fewer than 4,000 individuals per year. The Enterra Therapy System is indicated for "the treatment of chronic, drug- refractory nausea and vomiting secondary to GP of diabetes or idiopathic etiology" (not postsurgical etiologies). GES for morbid obesity has not been approved by the FDA and is for investigational use only in the United States. (ABSTRACT TRUNCATED)
CCR7 ligands CCL19 and CCL21 increase permissiveness of resting memory CD4+ T cells to HIV-1 infection: a novel model of HIV-1 latency (2007)

Latent HIV-1 infection of resting memory CD4(+) T cells represents the major barrier to HIV-1 eradication. To determine whether the CCR7 ligands involved in lymphocyte migration can alter HIV-1 infection of resting CD4(+) T cells, we infected purified resting CD4(+) T cells after incubation with the chemokines CCL19 and CCL21. Incubation with CCL19 or CCL21 did not alter markers of T-cell activation or proliferation. However, after HIV-1 infection of CCL19- or CCL21-treated CD4(+) T-cells, we observed low-level HIV-1 production but high concentrations of integrated HIV-1 DNA, approaching that seen in mitogen-stimulated T-cell blasts. Restimulation of CCL19-treated infected CD4(+) T cells resulted in virus production consistent with establishment of postintegration latency. CCR7 ligands facilitate efficient entry of HIV-1 into resting CD4(+) T cells. These studies demonstrate a unique action of the chemokines CCL19 and CCL21 and provide a novel model with which to study HIV-1 latency in vitro.