gebhart/patrepeval huggingface dataset:
Feasibility of a new bariatric fully endoscopic duodenal-jejunal bypass: a pilot study in adult obese pigs (2022)

This study assessed a new natural orifice transluminal endoscopic surgery (NOTES) bariatric endoscopic procedure in obese adult pigs. This 14-week prospective study compared 6 adult male Yucatan test pigs with baseline mean age 1.5 years to 2 control pigs. The test pigs received a fully endoscopic NOTES-based duodenal-jejunal bypass including measurement of the bypassed limb and creation of a gastrojejunal anastomosis (GJA) using a gastrojejunal lumen-apposing metal stent (GJ-LAMS) at Week 0, placement of a duodenal exclusion device (DED) at Week 2, and endoscopic examinations at Weeks 6 and 10. At Week 14, the pigs were sacrificed for necropsy. All endoscopic procedures were technically successful. By Week 14, the controls had gained a mean 1.1 ± 2.1 kg (+ 1.6%) while the intervention animals lost a mean 6.8 ± 3.9 kg (- 10.5%) since baseline. GJ-LAMS migrations occurred in 3 pigs, two of which also had DED migration and/or partial dislocation. Two other pigs died, one with aberrant splenic vein positioning near the GJA and the other from an unknown cause. An endoscopic bariatric bypass procedure with controlled bypass length was technically successful in all the cases and led to weight loss in test animals. Safety concerns must be further addressed.
Jackson's intrasacral fixation in the management of high-grade isthmic spondylolisthesis (2007)

The aim of this study is to describe a surgical procedure proposed for high-grade isthmic spondylolisthesis, with intraoperative reduction using Jackson's intrasacral fixation. The procedure is performed using a single posterior approach. The intraoperative correction of the deformity is obtained by sacral dome resection and reduction of the lumbosacral kyphosis using Jackson's fixation to rotate the sacrum. After sagittal balance restoration, L4-S1 circumferential fusion is performed with interbody cages. The technique is effective in the restoration of spinal and pelvic parameters of sagittal balance, and optimal conditions for fusion are obtained. The use of Jackson's intrasacral fixation provides the strong stability needed to correct the lumbosacral deformity, with little neurological risk during intraoperative reduction.
On the Impacts of Phase Shifting Design and Eavesdropping Uncertainty on Secrecy Metrics of RIS-aided Systems (2022)

This paper investigates the secrecy outage probability (SOP), the lower bound of SOP, and the probability of non-zero secrecy capacity (PNZ) of reconfigurable intelligent surface (RIS)-assisted systems from an information-theoretic perspective. In particular, we consider the impacts of eavesdroppers' location uncertainty and the phase adjustment uncertainty, namely imperfect coherent phase shifting and discrete phase shifting on RIS. More specifically, analytical and simulation results are presented to show that (i) the SOP gain due to the increase of the RIS reflecting elements number gradually decreases; and (ii) both phase shifting designs demonstrate the same PNZ secrecy performance, in other words, the random discrete phase shifting outperforms the imperfect coherent phase shifting design with reduced complexity.
The intermediate filament vimentin regulates chondrogenesis of adult human bone marrow‐derived multipotent progenitor cells (2009)

Cytoskeletal proteins play important regulatory roles in a variety of cellular processes, including proliferation, migration, and differentiation. However, whereas actin and tubulin have established roles regulating developmental chondrogenesis, there is no evidence supporting a function for the intermediate filament vimentin in embryonic cartilage formation. We hypothesized that vimentin may regulate the chondrogenic differentiation of adult multipotent progenitor cells (MPCs), such as those involved in cartilage formation during bone fracture repair. As our model of adult progenitor cell chondrogenesis, we employed high-density pellet cultures of human bone marrow-derived MPCs. siRNA-mediated knockdown of vimentin mRNA and protein triggered a reduction in the extent of MPC cartilage formation, as evidenced by depressed accumulation of mRNAs for the cartilage-specific marker genes aggrecan and collagen type II, as well as reduced levels of Alcian blue-stainable proteoglycan and collagen II protein in the extracellular matrix. Moreover, mRNA and protein levels for the chondro-regulatory transcription factors SOX5, SOX6, and SOX9 were diminished by vimentin knockdown. Depleted cellular vimentin also induced a drastic reduction in PKA phosphorylation levels but did not affect the phosphorylation of multiple other chondro-regulatory kinases and transcription factors, including ERK1/2, p38, Smad2, and Smad1/5/8. Importantly, siRNA-mediated knockdown of PKA C-alpha mRNA and protein mimicked the reduction in chondrogenesis caused by diminished cellular vimentin. Finally, overexpression of vimentin in MPCs significantly enhanced the activity of a transfected collagen II promoter-luciferase reporter gene. In conclusion, we describe a novel role for the intermediate filament vimentin as a positive regulator of adult human bone marrow-derived MPC chondrogenesis.
Single-cell transcriptional atlas of the Chinese horseshoe bat ( Rhinolophus sinicus ) provides insight into the cellular mechanisms which enable bats to be viral reservoirs (2020)

Abstract Bats are a major “viral reservoir” in nature and there is a great interest in not only the cell biology of their innate and adaptive immune systems, but also in the expression patterns of receptors used for cellular entry by viruses with potential cross-species transmission. To address this and other questions, we created a single-cell transcriptomic atlas of the Chinese horseshoe bat ( Rhinolophus sinicus ) which comprises 82,924 cells from 19 organs and tissues. This atlas provides a molecular characterization of numerous cell types from a variety of anatomical sites, and we used it to identify clusters of transcription features that define cell types across all of the surveyed organs. Analysis of viral entry receptor genes for known zoonotic viruses showed cell distribution patterns similar to that of humans, with higher expression levels in bat intestine epithelial cells. In terms of the immune system, CD8+ T cells are in high proportion with tissue-resident memory T cells, and long-lived effector memory nature killer (NK) T-like cells ( KLRG1 , GZMA and ITGA4 genes) are broadly distributed across the organs. Isolated lung primary bat pulmonary fibroblast (BPF) cells were used to evaluate innate immunity, and they showed a weak response to interferon β and tumor necrosis factor-α compared to their human counterparts, consistent with our transcriptional analysis. This compendium of transcriptome data provides a molecular foundation for understanding the cell identities, functions and cellular receptor characteristics for viral reservoirs and zoonotic transmission.
Algorithmic problems in right-angled Artin groups: complexity and\n applications (2018)

In this paper we consider several classical and novel algorithmic problems\nfor right-angled Artin groups, some of which are closely related to graph\ntheoretic problems, and study their computational complexity. We study these\nproblems with a view towards applications to cryptography.\n
Role of the Programmed Death-1 Pathway in Regulation of Alloimmune Responses In Vivo (2005)

Programmed death-1 (PD-1), an inhibitory receptor up-regulated on activated T cells, has been shown to play a critical immunoregulatory role in peripheral tolerance, but its role in alloimmune responses is poorly understood. Using a novel alloreactive TCR-transgenic model system, we examined the functions of this pathway in the regulation of alloreactive CD4+ T cell responses in vivo. PD-L1, but not PD-1 or PD-L2, blockade accelerated MHC class II-mismatched skin graft (bm12 (I-Abm12) into B6 (I-Ab)) rejection in a similar manner to CTLA-4 blockade. In an adoptive transfer model system using the recently described anti-bm12 (ABM) TCR-transgenic mice directly reactive to I-Abm12, PD-1 and PD-L1 blockade enhanced T cell proliferation early in the immune response. In contrast, at a later time point preceding accelerated allograft rejection, only PD-L1 blockade enhanced T cell proliferation. In addition, PD-L1 blockade enhanced alloreactive Th1 cell differentiation. Apoptosis of alloantigen-specific T cells was inhibited significantly by PD-L1 but not PD-1 blockade, indicating that PD-1 may not be the receptor for the apoptotic effect of the PD-L1-signaling pathway. Interestingly, the effect of PD-L1 blockade was dependent on the presence of CD4+ CD25+ regulatory T cells in vivo. These data demonstrate a critical role for the PD-1 pathway, particularly PD-1/PD-L1 interactions, in the regulation of alloimmune responses in vivo.
Substrate Specificity of Rat DESC4, a Type II Transmembrane Serine Protease (2009)

Type II transmembrane serine proteases (TTSPs) are involved in important physiological processes, such as pro-hormone processing, cellular signaling, host immune defense, and cancer development. The diversity of functions is reflected by the multidomain architecture of these proteases, which are composed of a variety of functional domains in addition to the catalytic domain. Recently, we identified rat DESC4, a member of the HAT/DESC1-like subfamily of TTSPs. Intriguingly, DESC4 gene expression is confined to few tissues including gustatory papillae. In the current publication we present the purification of the catalytic domain of recombinant rat DESC4. Subsequently, the catalytic domain was subjected to a refolding procedure. During refolding we observed endogenous catalytic activity leading to smaller fragments, which were analyzed by peptide sequencing. The identified cleavage-sites are typical for trypsin-like serine proteases. For further analyses a homology-based model of the DESC4 catalytic domain was generated enabling us to investigate protease-substrate interaction in more detail.
Fabrication of metallic nanoslit waveguides with sharp bends (2008)

Metallic nanoslit waveguides are promising candidates for ultrahigh-density optical interconnections. A variety of devices based on metallic nanoslit waveguides have already been proposed that show a great superiority over conventional photonic devices for compactness. However very few two-dimensional devices have been experimentally demonstrated with in-plane geometries due to fabrication difficulties. In this article, a feasible process is presented using traditional semiconductor fabrication technologies such as mix-and-match lithography and electroplating, which is cable of fabricating complicated 100 nm wide, 800 nm deep gold slit waveguides with multiple sharp right-angle corners. The process can be extended to volume production manufacturing with minor modifications, thus enabling the fabrication of nanoslit photonic circuits and networks.
Corrected Confidence Bands for Functional Data Using Principal Components (2012)

Functional principal components (FPC) analysis is widely used to decompose and express functional observations. Curve estimates implicitly condition on basis functions and other quantities derived from FPC decompositions; however these objects are unknown in practice. In this article, we propose a method for obtaining correct curve estimates by accounting for uncertainty in FPC decompositions. Additionally, pointwise and simultaneous confidence intervals that account for both model- and decomposition-based variability are constructed. Standard mixed model representations of functional expansions are used to construct curve estimates and variances conditional on a specific decomposition. Iterated expectation and variance formulas combine model-based conditional estimates across the distribution of decompositions. A bootstrap procedure is implemented to understand the uncertainty in principal component decomposition quantities. Our method compares favorably to competing approaches in simulation studies that include both densely and sparsely observed functions. We apply our method to sparse observations of CD4 cell counts and to dense white-matter tract profiles. Code for the analyses and simulations is publicly available, and our method is implemented in the R package refund on CRAN.
Phage‐Inducible Chromosomal Islands as a Diagnostic Platform to Capture and Detect Bacterial Pathogens (2023)

Phage-inducible chromosomal islands (PICIs) are a family of phage satellites that hijack phage components to facilitate their mobility and spread. Recently, these genetic constructs are repurposed as antibacterial drones, enabling a new toolbox for unorthodox applications in biotechnology. To illustrate a new suite of functions, the authors have developed a user-friendly diagnostic system, based upon PICI transduction to selectively enrich bacteria, allowing the detection and sequential recovery of Escherichia coli and Staphylococcus aureus. The system enables high transfer rates and sensitivities in comparison with phages, with detection down to ≈50 CFU mL<sup>-1</sup> . In contrast to conventional detection strategies, which often rely on nucleic acid molecular assays, and cannot differentiate between dead and live organisms, this approach enables visual sensing of viable pathogens only, through the expression of a reporter gene encoded in the PICI. The approach extends diagnostic sensing mechanisms beyond cell-free synthetic biology strategies, enabling new synthetic biology/biosensing toolkits.
A caching model of operating system kernel functionality (1994)

Operating system research has endeavored to develop micro-kernels that provide modularity, reliability and security improvements over conventional monolithic kernels. However, the resulting kernels have been slower, larger and more error-prone than desired. These efforts have also failed to provide sufficient application control of resource management required by sophisticated applications.This paper describes a caching model of operating system functionality as implemented in the Cache Kernel, the supervisor-mode component of the V++ operating system. The Cache Kernel caches operating system objects such as threads and address spaces just as conventional hardware caches memory data. User-mode application kernels handle the loading and writeback of these objects, implementing application-specific management policies and mechanisms. Experience with implementing the Cache Kernel and measurements of its performance on a multiprocessor suggest that the caching model can provide competitive performance with conventional monolithic operating systems, yet provides application-level control of system resources, better modularity, better scalability, smaller size and a basis for fault containment.
Observation of radon mitigation in MicroBooNE by a liquid argon filtration system (2022)

Abstract The MicroBooNE liquid argon time projection chamber (LArTPC) maintains a high level of liquid argon purity through the use of a filtration system that removes electronegative contaminants in continuously-circulated liquid, recondensed boil off, and externally supplied argon gas. We use the MicroBooNE LArTPC to reconstruct MeV-scale radiological decays. Using this technique we measure the liquid argon filtration system's efficacy at removing radon. This is studied by placing a 500 kBq 222 Rn source upstream of the filters and searching for a time-dependent increase in the number of radiological decays in the LArTPC. In the context of two models for radon mitigation via a liquid argon filtration system, a slowing mechanism and a trapping mechanism, MicroBooNE data supports a radon reduction factor of greater than 97% or 99.999%, respectively. Furthermore, a radiological survey of the filters found that the copper-based filter material was the primary medium that removed the 222 Rn. This is the first observation of radon mitigation in liquid argon with a large-scale copper-based filter and could offer a radon mitigation solution for future large LArTPCs.
ACQUIRED SYSTEMIC TOLERANCE TO RAT CARDIAC ALLOGRAFTS INDUCED BY INTRATHYMIC INOCULATION OF SYNTHETIC POLYMORPHIC MHC CLASS I ALLOPEPTIDES1,2 (1996)

This study extends the finding that intrathymic (IT) injection of 3M KC1 extracts of T cells induces transplant tolerance to the use of well defined polymorphic MHC class I allopeptides derived from the hypervariable domain of RT1.Au (WF MHC class I). While three of the six synthetic RT1.Au peptides were immunogenic, three others were nonimmunogenic when tested in ACI responders. In our initial studies, we examined the effects of IT injection of a mixture of equal concentrations of the three nonimmunogenic RT1.Au peptides on WF cardiac allograft survival in ACI recipients. The results showed that a single IT injection of 100 and 300 microg class I MHC allopeptides on day -7 relative to cardiac transplant did not significantly prolong graft survival in naive ACI recipients (MST of 9.8, and 12.3 days vs. 10.5 days in controls). In contrast, 600 microg allopeptides injected IT resulted in modest prolongation of graft to an MST of 19.5 days. However, IT injection of 600 microg allopeptides combined with 0.5 ml ALS on day -7 led to permanent acceptance (>200 days) of cardiac allografts in 7/9 ACI recipients compared with survival of 24.2 days in ALS alone treated controls. In contrast, similar treatment led to acute rejection of third party (Lewis) cardiac allografts. Intravenous injection of 600 microg allopeptides combined with ALS did not result in prolonged graft survival (26.8 days). The long-term unresponsive ACI recipients (>100 days) challenged with second-set cardiac grafts accepted permanently donor-type (WF) grafts while rejecting the third party (Lewis) grafts, a finding that confirms acquired systemic tolerance. These findings confirm the role of IT injection of synthetic polymorphic allopeptides in the induction of acquired thymic tolerance and provide the rationale for testing this strategy in large animals and eventually in man.
Thermoresponsive Micellar Assembly Constructed from a Hexameric Hemoprotein Modified with Poly(N-isopropylacrylamide) toward an Artificial Light-Harvesting System (2020)

Artificial protein assemblies inspired by nature have significant potential in development of emergent functional materials. In order to construct an artificial protein assembly, we employed a mutant of a thermostable hemoprotein, hexameric tyrosine-coordinated heme protein (HTHP), as a building block. The HTHP mutant which has cysteine residues introduced on the bottom surface of its columnar structure was reacted with maleimide-tethering thermoresponsive poly(<i>N</i>-isopropylacrylamide), PNIPAAm, to generate the protein assembly upon heating. The site-specific modification of the cysteine residues with PNIPAAm on the protein surface was confirmed by SDS-PAGE and analytical size exclusion chromatography (SEC). The PNIPAAm-modified HTHP (PNIPAAm-HTHP) is found to provide a 43 nm spherical structure at 60 °C, and the structural changes observed between the assembled and the disassembled forms were duplicated at least five times. High-speed atomic force microscopic measurements of the micellar assembly supported by cross-linkage with glutaraldehyde indicate that the protein matrices are located on the surface of the sphere and cover the inner PNIPAAm core. Furthermore, substitution of heme with a photosensitizer, Zn protoporphyrin IX (ZnPP), in the micellar assembly provides an artificial light-harvesting system. Photochemical measurements of the ZnPP-substituted micellar assembly demonstrate that energy migration among the arrayed ZnPP molecules occurs within the range of several tens of picoseconds. Our present work represents the first example of an artificial light-harvesting system based on an assembled hemoprotein oligomer structure to replicate natural light-harvesting systems.
Fluorous Techniques for the Synthesis of Organic Molecules: A Unified Strategy for Reaction and Separation (2005)

Abstract For Abstract see ChemInform Abstract in Full Text.
Endogenous Retroviruses as Targets for Antitumor Immunity in Renal Cell Cancer and Other Tumors (2013)

Human endogenous retroviruses (HERVs), remnants of ancient germ-line infections with exogenous retroviruses, are estimated to comprise up to 8% of human genome. Most HERVs have accumulated mutations and deletions that prevent their expression as an infectious virus. Nevertheless, a growing number of HERV genes and proteins have been found to be expressed in different cancers, raising the possibility that HERV-derived antigens might represent excellent targets for tumor immunotherapy. Here, we review data showing HERV-encoded antigens are capable of eliciting humoral and T-cells specific antitumor immunity. We also describe a novel HERV-E that was recently found to be selectively expressed in over 80% of clear cell kidney cancer but not in normal tissues. Remarkably, the restricted expression of HERV-E in kidney tumors was found to occur as a consequence of inactivation of the von Hippel-Lindau tumor suppressor. Importantly, antigens derived from this provirus are immunogenic, stimulating cytotoxic T-cells that kill kidney cancer cells in vitro and in vivo. Taken altogether, these data suggest efforts aimed at boosting human immunity against HERV-derived antigens could be used as a strategy to treat advanced tumors including kidney cancer.
Kinetic analysis of guanosine 5'-O-(3-thiotriphosphate) effects on phosphatidylinositol turnover in NRK cell homogenates (1987)

Addition of the guanine nucleotide analogue guanosine 5'-O-(3-thiotriphosphate) (GTP gamma S) to [3H]inositol-labeled NRK cell homogenates resulted in rapid breakdown of cellular polyphosphoinositides. GTP gamma S stimulated phospholipase C, resulting in a more than 4-fold increase in the hydrolysis rates of phosphatidylinositol 4-phosphate (PIP) and phosphatidylinositol 4,5-bis(phosphate) (PIP2). No significant effect of GTP gamma S on direct phosphatidylinositol (PI) hydrolysis was detected. There was an increase in water-soluble inositols, with inositol tris(phosphate) (IP3) levels increasing at least 10 times over the decrease seen in PIP2, indicating that PIP kinase activity was also accelerated following GTP gamma S addition. Inositol 1,4,5-tris(phosphate) peaked rapidly after GTP gamma S addition (less than 2 min) while inositol 1,3,4-tris-(phosphate) was produced more slowly and leveled off after approximately 10 min. The differential equations describing conversion between intermediates in the PI turnover pathway were solved and fitted to data obtained from both [3H]inositol and [32P]phosphate fluxes by nonlinear least-squares analysis. GTP gamma S effects on the pseudo-first-order rate constants for the lipase, kinase, and phosphatase steps were determined from the analysis. From these measurements it can be estimated that, in the presence of GTP gamma S and calcium buffered to 130 nM, hydrolysis of PIP2 accounts for at least 10 times as much diacylglycerol as direct PI breakdown despite the 100-fold excess of PI over PIP2. From the kinetic model it is predicted that small changes in the activities of PI and PIP kinases can have large but different effects on the level of IP3 and diacylglycerol following GTP gamma S addition. These results argue that regulation of PI and PIP kinases may be important for determining both cellular IP3 and diacylglycerol levels.