gebhart/patrepeval huggingface dataset:
Advantage of pancreaticogastrostomy in detecting recurrent intraductal papillary mucinous carcinoma in the remnant pancreas: A case of successful re-resection after pancreaticoduodenectomy (2006)

Recently there has been an increase in the number of case reports detailing the recurrence of cancer in the pancreatic remnants following surgical resection of intraductal papillary mucinous carcinoma (IPMC) of the pancreas. A case is presented here to indicate the advantage of pancreaticogastrostomy (PG) in terms of postoperative follow-up after pancreaticoduodenectomy (PD) for IPMC. A 68-year-old man underwent PD for IPMC of the pancreatic head, and the cut margin of the pancreatic duct was diagnosed as having no cancer but moderately dysplastic epithelium by an intraoperative frozen section of histology. Thus, we decided to proceed with a PG rather than pancreaticojejunostomy (PJ) in order to facilitate easier postoperative examinations. Eight years and 6 months later, during a routine follow-up examination, duct dilation of the remnant pancreas was detected by magnetic resonance imaging (MRI). Upon examination by endoscopic gastroscopy, the anastomotic site was found to be covered with a large amount of mucin from which we easily obtained both cytologic and biopsied specimens, which subsequently proved positive for cancer. In line with our diagnosis of recurrent IPMC, the patient underwent a second surgery (resection of the remnant pancreas, total pancreatectomy) and postoperative histology confirmed that indeed the patient had experienced recurrent IPMC with no nodal involvement or invasion beyond the pancreatic confines. Based on this experience, we decided to recommend PG for all patients deemed to be at high risk for the recurrence of cancer in the pancreatic remnants following PD for IPMC of the pancreatic head.
A structural basis for the activity of retro-Diels–Alder catalytic antibodies: Evidence for a catalytic aromatic residue (2002)

The nitroxyl synthase catalytic antibodies 10F11, 9D9, and 27C5 catalyze the release of nitroxyl from a bicyclic pro-drug by accelerating a retro-Diels-Alder reaction. The Fabs (antigen-binding fragments) of these three catalytic antibodies were cloned and sequenced. Fab 9D9 was crystallized in the apo-form and in complex with one transition state analogue of the reaction. Crystal structures of Fab 10F11 in complex with ligands mimicking substrate, transition state, and product have been determined at resolutions ranging from 1.8 to 2.3 A. Antibodies 9D9 and 10F11 show increased shape complementarity (as quantified by the program sc) to the hapten and to a modeled transition state as compared with substrate and product. The shape complementarity is mediated to a large extent by an aromatic residue (tyrosine or tryptophan) at the bottom of the hydrophobic active pocket, which undergoes pi-stacking interactions with the aromatic rings of the ligands. Another factor contributing to the different reactivity of the regioisomers probably arises because of hydrogen-bonding interactions between the nitroxyl bridge and the backbone amide of PheH101 and possibly a conserved water molecule.
Molecular assembling technology for electrochemical and optical enzyme-sensing films (2002)

Several different molecular film technologies have been developed for fabricating biosensors, including electrochemical codeposition of nonconductive polymer film and enzyme; electrochemical fabrication making a molecular interface of conductive polymer for an enzyme; and protein LB film fabrication. A microenzyme sensor for glucose was fabricated by electrochemical codeposition. An amperometric enzyme sensor was fabricated by incorporating the alcohol dehydrogenase-NAD-mediator system in a conductive polymer membrane. The protein LB film fabrication was used to produce an optical enzyme sensor for triglyceride.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Kinetic Recognition of AT‐Rich DNA by Ruthenium Complexes (2007)

AT erkannt: Eine hohe Selektivität für lange AT-Sequenzen lässt sich durch kinetisch kontrollierte Intercalierung von zweikernigen Ruthenium(II)-Komplexen in DNA erreichen (siehe Bild). Die Einlagerungsgeschwindigkeit korreliert stark mit der Zahl aufeinander folgender AT-Basenpaare und ist bis zu 2500-mal höher mit poly(dAdT)2 als mit DNA mit gemischter Sequenz. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2001/2007/z604294_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Polymeric waveguide Fabry Perot resonators (2014)

Optical microcavities are used in variety of applications ranging from sensors to lasers and signal routing in high volume communication networks. Achieving a high quality factor (Q) is necessary for achieving the higher sensitivity in sensing applications and for narrow linewidth light emission in most lasing applications. In this work, we propose a new way for achieving a higher quality factor in thin film, Fabry-Perot polymeric optical resonators. We show that lateral photon confinement in a vertical Fabry-Perot microcavities can be achieved by optical writing of a refractive index profile utilizing our UV-sensitive polymer. This method can improve the quality factor by one or more orders of magnitudes. In order to demonstrate this improvement, the device has been fabricated. The fabricated device consists of two dielectric Bragg reflectors with a layer of 100 μm thick polymer layer between them. The polymer is a thiol-ene/methacrylate photopolymer whose optical index can be modified utilizing standard photo-lithography processes. The refractive index of this polymer can be modified utilizing standard photo-lithography processes. The measured finesse of the fabricated device was 692 and the quality factor was 55000. The achieved finesse combined with the flexible polymer layer allows this device to be used as an ultrasound detector in optical micromachined ultrasound transducers (OMUT).
Efficacy and safety of empagliflozin, a sodium glucose cotransporter 2 ( SGLT2 ) inhibitor, as add‐on to metformin in type 2 diabetes with mild hyperglycaemia (2013)

Once daily empagliflozin as add-on therapy to metformin was well tolerated except for increased genital infections and resulted in reductions in HbA1c, fasting plasma glucose and body weight in patients with type 2 diabetes inadequately controlled on metformin monotherapy.
Translational control of maturation-protein synthesis in phage MS2: a role for the kinetics of RNA folding? (1995)

The gene for the maturation (A) protein of the single-stranded RNA coliphage MS2 is preceded by an untranslated leader of 130 nt. Secondary structure of the leader was deduced by phylogenetic comparison and by probing with enzymes and chemicals. The RNA folds into a cloverleaf, i.e., three stem-loop structures enclosed by a long-distance interaction (LDI). This LDI is essential for translational control. Its 3'moiety contains the Shine-Dalgarno region of the A-protein gene, whereas its complement is located 80 nt upstream, i.e., about 30 nt from the 5'-terminus of the RNA chain. Mutational analysis shows that this base pairing represses expression of the A-protein gene. We present a model in which translational starts can only take place on nonequilibrated RNA, in which base pairing between the complementary regions has not yet taken place. We suggest that this pairing is kinetically delayed by the intervening sequence, which contains the three hairpins of the cloverleaf. The model is mainly based on the observation that reducing the length of the intervening sequence reduces expression, whereas increasing the length has the opposite effect. In addition, further stabilization of the LDI by a stronger base pair does not lead to a decrease in A-protein synthesis. Such a decrease is predicted to occur if translation would be controlled by the equilibrium structure of the leader RNA. These and other observations fit a kinetic model of translational control by RNA folding.
Effect of thermal residual stress on mechanical properties of SiC/TiC composites (1991)

Des composites denses de SiC renforces de particules de TiC, avec 5% de Al-B-C comme additif de frittage, ont ete presses a 1800°C sous 30 MPa. La tenacite augmente proportionnellement a la teneur en TiC. On propose un mecanisme de renforcement lie a la deflexion par les particules de TiC des fissures provoquees par les contraintes thermiques residuelles dues aux differences des coefficients de dilatation thermique de SiC et TiC. Cependant, la resistance a la flexion des composites decroit quand la temperature d'essai augmente, ce qu'on pense etre le resultat d'une relaxation des contraintes a plus haute temperature.
Phased Array Ultrasonic Sound Field Mapping in Cast Austenitic Stainless Steel (2014)

This study maps the phased array-generated acoustic sound fields through three types of CASS microstructure in four specimens to quantitatively assess the beam formation effectiveness in these materials.
Dualisms (1970)

Dualist doctrines are those which, in holding that the body is material and the mind spiritual, accord to man a dual nature. Dualists retain the first two of our four propositions, and must therefore reject either the third or fourth. So there are two main types of Dualism, one affirming and the other denying the interaction of mind and body.
How to retrieve the encrypted data on the blockchain (2019)

Searchable symmetric encryption (SSE) scheme can perform search on encrypted data directly without revealing the plain data and keywords. At present, many constructive SSE schemes were proposed. However, they cannot really resist the malicious adversary, because it (i.e., the cloud server) may delete some important data. As a result, it is very likely that the returned search results are incorrect. In order to better guarantee the integrity of outsourcing data, and ensure the correction of returned search results at the same time, in this paper, we combine SSE with blockchain (BC), and propose a SSE-on-BC framework model. We then construct two concrete schemes based on the size of the data, which can better provide privacy protection and integrity verification for data. Lastly, we present their security and performance analyses, which show that they are secure and feasible.
An amplified chromosomal sequence that includes the gene for dihydrofolate reductase initiates replication within specific restriction fragments. (1982)

We have developed a methotrexate-resistant Chinese hamster ovary cell line (CHOC 400) containing a 500-fold amplification of a 135-kilobase chromosomal DNA sequence. This sequence includes the gene for dihydrofolate reductase (tetrahydrofolate dehydrogenase, 5,6,7,8-tetrahydrofolate: NADP+ oxidoreductase, EC 1.5.1.3). The high copy number of the amplified sequence permits it to be visualized as a distinct series of restriction fragments in genomic digests separated on ethidium bromide-stained agarose gels. Initiation of DNA replication in the amplified sequence was studied by radiolabeling DNA synthesized during the onset of S phase in synchronized CHOC 400 cells. Autoradiography of Southern blots of labeled genomic digests shows that DNA synthesis initiates in a small subset of the EcoRI fragments derived from the amplified units. These early labeled fragments are not synthesized at later times during S phase, when different subsets of fragments are synthesized. Regardless of the drug used to collect cells at the beginning of S phase, the replication pattern observed remains the same. These data suggest that replication of the amplified sequence initiates at specific sites within each repeated unit and proceeds in nonrandom order throughout the remainder of the sequence--i.e., that initiation of DNA synthesis in the chromosomes of mammalian cells is sequence specific.
Using Galaxy to Perform Large‐Scale Interactive Data Analyses (2012)

Abstract Innovations in biomedical research technologies continue to provide experimental biologists with novel and increasingly large genomic and high‐throughput data resources to be analyzed. As creating and obtaining data has become easier, the key decision faced by many researchers is a practical one: where and how should an analysis be performed? Datasets are large and analysis tool set‐up and use is riddled with complexities outside of the scope of core research activities. The authors believe that Galaxy provides a powerful solution that simplifies data acquisition and analysis in an intuitive Web application, granting all researchers access to key informatics tools previously only available to computational specialists working in Unix‐based environments. We will demonstrate through a series of biomedically relevant protocols how Galaxy specifically brings together (1) data retrieval from public and private sources, for example, UCSC's Eukaryote and Microbial Genome Browsers, (2) custom tools (wrapped Unix functions, format standardization/conversions, interval operations), and 3rd‐party analysis tools. Curr. Protoc. Bioinform . 38:10.5.1‐10.5.47. © 2012 by John Wiley &amp; Sons, Inc.
Estimation of Speed Differentials on Rural Highways using Multilevel Models (2010)

Large speed differentials between highway segments are associated with an increase in accidents. Traditional speed differential measures, derived from single level linear regression models, suffer from serious deficiencies: underestimating the speed differential (due to intra-correlated data), and inflating the adequacy of the model’s explanation (due to aggregate data). High quality speed differential predictions are highly desirable right from the initial design phase, but the estimation process is not straightforward, and decision makers must recognize that speed differential predictions are subject to considerable uncertainty. This paper compares four models: two single level models, a conventional multilevel model, and a Bayes multilevel model. The results show empirically that multilevel models increase the accuracy and precision of speed differentials estimates, possibly with less data. The final part of this paper introduces a new, easy to interpret speed consistency measure that simply represents the probability that a vehicle exceeds a certain speed differential. This measure is calculated using a multilevel model and takes into account the uncertainty in the estimates of speed differentials. Overall, the authors show that a multilevel modeling approach can improve the quality of decision making that makes use of speed differential information in road design and road safety.
Analysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features (2021)

Abstract CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.
Charged Particle Induced Etching and Functionalization of Two-Dimensional Materials (2022)

Focused electron beam induced deposition and etching (FEBID and FEBIE) are direct-write nanofabrication techniques in which an electron beam is used to achieve nanostructure functionalization, etching or deposition. Either alone or in combination with in situ plasmas, these techniques can also be used to accelerate reactions that occur in ambient environment, with simultaneous high-resolution imaging. Here, we describe our recent work on etching, functionalization and directed assembly of a range of nano- and two-dimensional materials using temperature-dependent FEBIE experiments in an environmental scanning electron microscope (ESEM). As examples of the application of these techniques, we demonstrate processes for assembling arrays of nanodiamonds that can be used as magnetic field sensors, as well as for controlled etching of hexagonal boron nitride (hBN) and black phosphorus (BP).
Pasireotide treatment significantly improves clinical signs and symptoms in patients with Cushing's disease: results from a Phase III study (2014)

In the largest Phase III study of medical therapy in Cushing's disease, significant improvements in signs and symptoms were seen during 12 months of pasireotide treatment, as UFC levels decreased.
Towards force feedback in laparoscopic surgical tools (2002)

There has been a phenomenal rise in the number of minimally invasive surgery procedures over the last few years. The inherent drawback of this technique is the removal of the surgeon from the actual site of surgery, thus limiting his/her perception of tool-tissue interaction. In this study, we measured the forces acting at the tip and handle of a pair of instrumented laparoscopic forceps, and thereby investigated the need for force feedback. During the study, we also developed force coefficients that could be used to enhance "feeling" during laparoscopic procedures. Using these coefficients, it is possible to differentiate between objects of varying hardness. The scope of this investigation can be widened by the application of this concept to other surgical tools as well.
A Transmembrane Domain GGxxG Motif in CD4 Contributes to Its Lck-Independent Function but Does Not Mediate CD4 Dimerization (2015)

CD4 interactions with class II major histocompatibility complex (MHC) molecules are essential for CD4+ T cell development, activation, and effector functions. While its association with p56lck (Lck), a Src kinase, is important for these functions CD4 also has an Lck-independent role in TCR signaling that is incompletely understood. Here, we identify a conserved GGxxG motif in the CD4 transmembrane domain that is related to the previously described GxxxG motifs of other proteins and predicted to form a flat glycine patch in a transmembrane helix. In other proteins, these patches have been reported to mediate dimerization of transmembrane domains. Here we show that introducing bulky side-chains into this patch (GGxxG to GVxxL) impairs the Lck-independent role of CD4 in T cell activation upon TCR engagement of agonist and weak agonist stimulation. However, using Forster's Resonance Energy Transfer (FRET), we saw no evidence that these mutations decreased CD4 dimerization either in the unliganded state or upon engagement of pMHC concomitantly with the TCR. This suggests that the CD4 transmembrane domain is either mediating interactions with an unidentified partner, or mediating some other function such as membrane domain localization that is important for its role in T cell activation.
MMIC and fiber optic delay line hybrid transversal filter (2002)

Microwave transversal filters suffer from bandwidth limitations and the inability to provide long time delays due to losses and dispersion in the microstrip delay line. Purely optical transversal filter disadvantages include inaccurate weighting and the inability to provide negative weighting coefficients. Therefore, a novel hybrid transversal filter configuration that utilizes the optical fiber as a delay mechanism, with negligible loss and wide bandwidth, and an existing monolithic microwave integrated circuit (MMIC) transversal filter to provide the necessary accurate positive and negative weighting is presented. The noise performance, dispersion due to the delay line, and a comparison of frequency responses of the existing MMIC advanced transversal filter, the hybrid transversal filter and an ideal filter are reported. The optimum hybrid filter configuration is determined from an analysis of various configurations.
Economic Insights from Internet Auctions: A Survey (2003)

This paper surveys recent studies of Internet auctions. Four main areas of research are summarized.
Commentary on the Interactions ofHIVand Alcohol in the Central Nervous System (2013)

This commentary is to highlight the relevance and public interest of the review published by Silverstein and Kumar, which focuses on the mechanisms by which alcohol and HIV ‐1 infection cause increased in central nervous system (CNS) damage. The overall review is based on previous literature with cell culture systems and animal models that have demonstrated that exposure to alcohol and HIV infection or HIV viral proteins result in synergistic up‐regulation of pro‐inflammatory cytokines and oxidative stress. The authors discuss the effects of alcohol on cells in the CNS , followed by a brief discussion on the impact of HIV ‐1 and HIV proteins on the CNS , and the final section focuses on the combined effects of HIV and alcohol on the CNS as determined by in vitro, in vivo, and clinical studies.
DNA.Land: A digital biobank using a massive crowdsourcing approach (2017)

Abstract Precision medicine necessitates large scale collections of genomes and phenomes. Despite decreases in the costs of genomic technologies, collecting these types of information at scale is still a daunting task that poses logistical challenges and requires consortium-scale resources. Here, we describe DNA.Land, a digital biobank to collect genome and phenomes with a fraction of the resources of traditional studies at the same scale. Our approach relies on crowd-sourcing data from the rapidly growing number of individuals that have access to their own genomic datasets through Direct-to-Consumer (DTC) companies. To recruit participants, we developed a series of automatic return-of-results features in DNA.Land that increase users’ engagement while stratifying human subject research protection. So far, DNA.Land has collected over 43,000 genomes in 20 months of operation, orders of magnitude higher than previous digital attempts by academic groups. We report lessons learned in running a digital biobank, our technical framework, and our approach regarding ethical, legal, and social implications.