gebhart/patrepeval huggingface dataset:
Cations, oxidants, light as causative agents in senile cataracts. (1993)

Lens transparency is a function of regular cell shape, regular cell volume, minimal extracellular space, and minimal scatter elements. The cellular structure and molecular structure of the lens is reviewed. The importance of the cytoarchitecture especially the sutures, is discussed. The high cholesterol: phospholipid ratio of the lens fiber cell membranes is related to the functions of low permeability, low fluidity, and mechanical stability. Also reviewed are the contributions of the lens crystallins to lens clarity and to lens refractive index. The importance of intracellular and extracellular cation and water concentrations are reviewed. Finally the effects of systemic diseases, oxidation, and light on lens clarity are discussed relative to changes in lens fiber cell cation concentrations.
Discovery of INCB8761/PF-4136309, a Potent, Selective, and Orally Bioavailable CCR2 Antagonist (2011)

We report the discovery of a new (S)-3-aminopyrrolidine series of CCR2 antagonists. Structure-activity relationship studies on this new series led to the identification of 17 (INCB8761/PF-4136309) that exhibited potent CCR2 antagonistic activity, high selectivity, weak hERG activity, and an excellent in vitro and in vivo ADMET profile. INCB8761/PF-4136309 has entered human clinical trials.
Priming and Activation of Human Ovarian and Breast Cancer-specific CD8+ T Cells by Polyvalent Listeria monocytogenes-based Vaccines (2009)

Immunotherapeutic vaccine is potentially an effective strategy to combat cancer. Essential components of an effective vaccine must include antigens that are processed by the major histocompatibility complex class I pathway, presented by the tumor major histocompatibility complex molecules, and an effective antigen delivery platform that is capable of breaking self-tolerance. In this study, we characterized a set of ovarian cancer-specific T-cell epitopes delivered by live-attenuated recombinant Listeria monocytogenes (Lm DeltaactADeltainlB) as a vaccine vector. We present data that peptide-specific T cells recognize the human monocytic cell line THP-1 infected with recombinant Lm DeltaactADeltainlB encoding the epitopes. Furthermore, we demonstrate that recombinant L. monocytogenes (Lm)-infected antigen-presenting cells can prime and expand epitope-specific CD8 T cells in vitro and such CD8 T cells recognize not only peptide-loaded targets but also ovarian and breast tumor cells presenting endogenous epitopes. Finally, peptide-specific T cells generated using peripheral blood mononuclear cell from ovarian cancer patients recognize target cells infected with recombinant Lm DeltaactADeltainlB encoding the epitopes. Our results demonstrate that live-attenuated recombinant Lm can be used effectively as a vehicle to deliver cancer peptide antigens singly or as a multiepitope construct. Thus, the use of recombinant live-attenuated Lm strains encoding endogenously processed and presented tumor epitopes/antigens represents an attractive strategy for active cancer immunotherapy in a clinical setting.
Pancreatic polypeptide in dorsal vagal complex stimulates gastric acid secretion and motility in rats (1993)

High concentrations of receptors for pancreatic polypeptide (PP), a pancreatic hormone, were recently discovered in the dorsomedial region of the dorsal vagal complex (DVC). We hypothesized that gastric acid secretion and motility, digestive functions strongly influenced by vagovagal reflexes organized within the DVC, would be affected by PP applied directly to this vagal sensorimotor integration area. After urethan-anesthetized rats were prepared for antral motility recording or titrometric analysis of gastric acid output, phosphate-buffered saline or various doses of PP in phosphate-buffered saline were micropressure injected into the medial DVC. Injections of PP into the DVC produced significant, long-lasting, and dose-dependent increases in gastric acid secretion and antral motility. These gastric responses were blocked by bilateral cervical vagotomy and by atropine, suggesting that intramedullary PP stimulates vagal cholinergic pathways, resulting in enhanced gastric functions. Because PP is not synthesized within the central nervous system, these results point to a new mechanism whereby the digestive tract may modulate its own autonomic control: direct humoral action on vagovagal reflex circuits within the brain stem.
Specific Detection of His-Tagged Proteins with Recombinant Anti-His Tag scFv-Phosphatase or scFv-Phage Fusions (1997)

Using a cell-bound immunogen, we have generated a monoclonal antibody, 3D5, that recognizes carboxy-terminal oligo-histidine tags (His tags) on a wide variety of proteins. From this monoclonal antibody, we have generated a single-chain fragment of the variable domains (scFv), a dimeric scFv-alkaline phosphatase fusion and an oligovalent scFv-display phage. The antibody in its various formats is an effective tool used in fluorescence-activated cell sorting analysis, the BIAcore method, Western blots and enzyme-linked immunosorbent assay (ELISA). Western blots and ELISAs can be developed directly by using crude extracts of E.coli cells that produce the scFv-alkaline phosphatase fusion, thus providing an inexhaustable and convenient supply of detection reagent. Alternatively, oligovalent scFv-displaying phage can be used directly from culture supernatants for this purpose. The dissociation constants, KD of the peptide KGGHHHHH (KD = 4 x 10(-7) M) and of imidazole (KD = 4 x 10(-4) M) were determined. Molecular modeling of the Fv fragment suggests the occurrence of two salt bridges between the protonated histidine side chains of the peptide and the acidic groups in the antibody, explaining why the antibody or the substrate may be eluted under mildly basic conditions.
Inhibition of human platelet glycoprotein IIB/IIIA binding to fibrinogen by tumor cell membrane proteins. (1993)

Immunochemical and functional characteristics of tumor cell membrane proteins and human platelet glycoproteins were studied. Immunoblotting revealed that membrane proteins of a cultured breast tumor cell line (BT-20) had three protein bands, which were each recognized by monoclonal antibodies to human platelet glycoprotein Ib, IIb, and IIIa, suggesting some immunochemical similarities between the tumor cell membrane proteins and platelet glycoproteins. The monoclonal antibodies failed to bind to an extract of a lung tumor cell line (A549). Neither tumor extract induced platelet aggregation. However, tumor-associated antigens isolated from the breast tumor cells markedly inhibited platelet glycoprotein IIb/IIIa binding to fibrinogen. In contrast, tumor-associated antigens from the lung tumor cells had no effect. These results suggest that tumor cells which have immunological and/or structural similarities to platelets may affect hemostasis and coagulation in vivo.
Mesenchymal Regulation of Alveolar Repair in Pulmonary Fibrosis (2000)

Induction of alveolar epithelial cell phenotypes via mesenchymal signaling regulates pneumocyte differentiation not only during lung development (1, 2) but also during the response to a myriad of injuries inciting fibrogenesis (3). Signals generated in the epithelium and the mesenchyme regulate critical functions of cells in both compartments reciprocally, with transduction mediated by soluble growth factors, membrane-anchored receptors, and extracellular matrix proteins (4). Such epithelial‐mesenchymal interactions characterize remodeling in a variety of tissues, including airways and lung parenchyma (3, 5, 6). Transition from injury to the repair phase in alveolar remodeling requires epithelialization to regenerate pneumocyte populations and the epithelial component of the alveolar barrier. Ordered layering of type I and type II pneumocytes, basement membranes, and capillary endothelial cells establishes compartmentalization that normalizes communication among cells and extracellular matrix components in distinct epithelial and mesenchymal layers. Restoration of alveolar quiescence reverses ventilation‐perfusion defects to equilibrate gas exchange. By contrast, unrelenting signaling between the compartments leads to continued invasion of fibroblasts and excessive deposition of matrix proteins, causing intra-alveolar fibrosis and the loss of surface area, which defines the pathophysiology of pulmonary fibrosis (3). Epithelial cells differentiate into subpopulations, which reconstruct a protective barrier and regulate clearance of alveolar exudates. Type II cells differentiate from cuboidal progenitor cells at septal intersections into thin type I cells that line approximately 90% of the alveolar unit. Subpopulations of type II pneumocytes synthesize surfactants needed to reduce alveolar surface tension and also produce matrix constituents such as fibronectin, collagen IV, and proteoglycan, essential for remodeling. Other type II cells help resorb proteinaceous exudates by releasing fibrinolytic proteases or by upregulating expression of water and ion channels. Some type II pneumocytes also serve as stem cells to replenish the type II epithelial cell population itself (3). Failure of the alveolar epithelium to perform these functions results both in the unchecked migration of fibroblasts onto the provisional matrix and the continued matrix protein deposition, which propagate fibrogenesis. Premature demise of the epithelial cell population may result from apoptosis due to incessant injury or from apoptotic signals arising from the mesenchyme (7). Thus, epithelial dysfunction permits sequential flooding and increased surface tension in the alveolar space, apposition and fusion of exposed basement membranes, and irreversible collapse and fibrosis—all of which diminish effective alveolar surface area (3).
Mammalian Nitric Oxide Synthases (1992)

This chapter contains sections titled: Introduction Nitric Oxide Synthase Isoforms: Characterization and Tissue and Subcellular Distribution Purification and Properties Physiological and Pharmacological Regulation Studies of Mechanism Conclusion and Perspective
SWISS‐MODEL and the Swiss‐Pdb Viewer: An environment for comparative protein modeling (1997)

Comparative protein modeling is increasingly gaining interest since it is of great assistance during the rational design of mutagenesis experiments. The availability of this method, and the resulting models, has however been restricted by the availability of expensive computer hardware and software. To overcome these limitations, we have developed an environment for comparative protein modeling that consists of SWISS-MODEL, a server for automated comparative protein modeling and of the SWISS-PdbViewer, a sequence to structure workbench. The Swiss-PdbViewer not only acts as a client for SWISS-MODEL, but also provides a large selection of structure analysis and display tools. In addition, we provide the SWISS-MODEL Repository, a database containing more than 3500 automatically generated protein models. By making such tools freely available to the scientific community, we hope to increase the use of protein structures and models in the process of experiment design.
Reduction of butyrate- and methane-producing microorganisms in patients with Irritable Bowel Syndrome (2015)

The pathophysiology of irritable bowel syndrome (IBS) remains unclear. Here we investigated the microbiome of a large cohort of patients to identify specific signatures for IBS subtypes. We examined the microbiome of 113 patients with IBS and 66 healthy controls. A subset of these participants provided two samples one month apart. We analyzed a total of 273 fecal samples, generating more than 20 million 16S rRNA sequences. In patients with IBS, a significantly lower microbial diversity was associated with a lower relative abundance of butyrate-producing bacteria (P = 0.002; q < 0.06), in particular in patients with IBS-D and IBS-M. IBS patients who did not receive any treatment harboured a lower abundance of Methanobacteria compared to healthy controls (P = 0.005; q = 0.05). Furthermore, significant correlations were observed between several bacterial taxa and sensation of flatulence and abdominal pain (P < 0.05). Altogether, our findings showed that IBS-M and IBS-D patients are characterized by a reduction of butyrate producing bacteria, known to improve intestinal barrier function, and a reduction of methane producing microorganisms a major mechanism of hydrogen disposal in the human colon, which could explain excess of abdominal gas in IBS.
[The inhibition of proteolytic enzyme activity by humic acids]. (1991)

The inhibitory effect of peat humic acids on the hydrolysis of N-acetyl-L-tyrosine ethyl ester and N-benzoyl-L-leucine methyl ester by alpha-chymotrypsin and subtilism has been studied. Samples of humic acids with M(W) approximately 18,000 have been used in experiments. The results of kinetic studies indicates the mixed type of inhibition of proteinase activity by humic acids. The meanings of inhibition constants under the action of humic acids on alpha-chymotrypsin and subtilism have been calculated.
Effect of antimicrobial treatment on chronic reactive arthritis. (1993)

In a double-blind study comprising 36 patients the effect of a three-month course of ciprofloxacin on chronic reactive arthritis was evaluated. At the end of the follow-up period 6 months after stopping the therapy, arthralgia, pain at movement and morning stiffness had decreased significantly compared to the values before the treatment in the ciprofloxacin group, whereas the Ritchie index and ESR showed a significant decrease in the control group. We conclude that further studies are necessary before the value of prolonged ciprofloxacin treatment of chronic reactive arthritis can be established.
SOI technology for the GHz era (2002)

Silicon-on-insulator (SOI) CMOS offers a 20–35% performance gain over bulk CMOS. High-performance microprocessors using SOI CMOS have been commercially available since 1998. As the technology moves to the 0.13-µm generation, SOI is being used by more companies, and its application is spreading to lower-end microprocessors and SRAMs. In this paper, after giving a short history of SOI in IBM, we describe the reasons for performance improvement with SOI, and its scalability to the 0.1-µm generation and beyond. Some of the recent applications of SOI in high-end microprocessors and its upcoming uses in low-power, radio-frequency (rf) CMOS, embedded DRAM (EDRAM), and the integration of vertical SiGe bipolar devices on SOI are described. As we move to the 0.1-µm generation and beyond, SOI is expected to be the technology of choice for system-on-a-chip applications which require high-performance CMOS, low-power, embedded memory, and bipolar devices.
Stat3-Mediated Transformation of NIH-3T3 Cells by the Constitutively Active Q205L Gα o Protein (2000)

Expression of Q205L Galphao (Galphao*), an alpha subunit of heterotrimeric guanine nucleotide-binding proteins (G proteins) that lacks guanosine triphosphatase (GTPase) activity in NIH-3T3 cells, results in transformation. Expression of Galphao* in NIH-3T3 cells activated signal transducer and activator of transcription 3 (Stat3) but not mitogen-activated protein (MAP) kinases 1 or 2. Coexpression of dominant negative Stat3 inhibited Galphao*-induced transformation of NIH-3T3 cells and activation of endogenous Stat3. Furthermore, Galphao* expression increased activity of the tyrosine kinase c-Src, and the Galphao*-induced activation of Stat3 was blocked by expression of Csk (carboxyl-terminal Src kinase), which inactivates c-Src. The results indicate that Stat3 can function as a downstream effector for Galphao* and mediate its biological effects.
Ablation of post-surgical intra-atrial reentrant tachycardia. Predilection target sites and mapping approach (2002)

Knowledge of anatomical predilection sites and mapping the right (and/or left) atrium with a 'sweeping Halo technique' allow for effective ablation of most post-surgical atrial tachycardias. Severely damaged atria with multiple arrhythmias may require 'preventive' ablation of all recognizable channels.
Variability of gastrointestinal transit in healthy women and men. (1996)

Colonic transit was faster in men than in women. Although group means in the two studies were almost identical, single assessments of transit in subjects sometimes exhibited considerable variability, implying broad biological variations. Given this intrinsic variability, the influence of menstrual hormones on gastrointestinal transit must be small and of doubtful clinical significance.
An Improved, General ProceduretoS-Aryl Thiol Esters: A New Synthetic Applicationof Dry Arenediazoniumo-Benzenedisulfonimides (2003)

The reaction between dry arenediazonium o-benzenedi­sulfonimides (1) and sodium thioacetate or thiobenzoate in anhydrous acetonitrile at room temperature is an efficient and safe procedure, of general validity, for the preparation of S-aryl thiol esters. The products can be easily purified and the yields are always very high. Of the 28 considered examples, the average yield of the S-aryl thioacetates (7) was 86% and that of the S-aryl thiobenzoates (8) 88%. It was possible to recover, in good amount and from all the reactions, o-benzenedisulfonimide (9), reusable for the preparation of salts 1.
Remediation of soils contaminated with particulate depleted uranium by multi stage chemical extraction (2013)

Contamination of soils with depleted uranium (DU) from munitions firing occurs in conflict zones and at test firing sites. This study reports the development of a chemical extraction methodology for remediation of soils contaminated with particulate DU. Uranium phases in soils from two sites at a UK firing range, MOD Eskmeals, were characterised by electron microscopy and sequential extraction. Uranium rich particles with characteristic spherical morphologies were observed in soils, consistent with other instances of DU munitions contamination. Batch extraction efficiencies for aqueous ammonium bicarbonate (42-50% total DU extracted), citric acid (30-42% total DU) and sulphuric acid (13-19% total DU) were evaluated. Characterisation of residues from bicarbonate-treated soils by synchrotron microfocus X-ray diffraction and X-ray absorption spectroscopy revealed partially leached U(IV)-oxide particles and some secondary uranyl-carbonate phases. Based on these data, a multi-stage extraction scheme was developed utilising leaching in ammonium bicarbonate followed by citric acid to dissolve secondary carbonate species. Site specific U extraction was improved to 68-87% total U by the application of this methodology, potentially providing a route to efficient DU decontamination using low cost, environmentally compatible reagents.
Living Ring-Opening Polymerization of a Carbohydrate-Derived Lactone for the Synthesis of Protein-Resistant Biomaterials (2008)

An efficient living ring-opening polymerization (ROP) of a permethoxylated epsilon-caprolactone [(OMe)CL] catalyzed by yttrium(III) isopropoxide was developed for the synthesis of degradable protein-resistant polymers [P(OMe)CL]. The lactone monomer was efficiently prepared from a reduced sugar, D-dulcitol. Kinetic studies of the ROP revealed a linear dependence of ln[M]0/[M] on polymerization time as well as a linear correlation between the number-averaged molecular weight (M(n)) and monomer conversion; both support it is a living polymerization. A series of block copolymers of our permethoxylated lactone with epsilon-caprolactone [P(OMe)CL-b-PCL] were synthesized and fully characterized. In thermal analyses only single T(g)s were observed in all the block copolymers, suggesting that P(OMe)CL and PCL blocks are fully miscible. Finally, surface plasmon resonance (SPR) sensograms demonstrated that both P(OMe)CL and the P(OMe)CL-b-PCL block copolymers exhibit excellent resistance to fibrinogen and lysozyme.
Evaluation in combination of modified pericardial devascularization with splenorenal shunt for portal hypertension with upper digestive tract hemorrhage (2013)

Objective
To study the effect of modified pericardial devascularization (MPCDV) combined with splenorenal shunt (SRS) for portal hypertension with upper digestive tract hemorrage.


Methods
From September 2005 to May 2010, the clinical and follow-up data of 46 cases with portal hypertension with upper digestive tract hemorrage were collected. The survival analysis was conducted between MPCDV+SRS group (24 cases) and MPCDV group (22 cases) divided by treatment.


Results
There was no difference in baseline clinical data between the two groups. After treatment, the FPP in MPCDV+SRS group (37.1±9.7) cm H2O was higher than in MPCDV group (30.1±8.9) cm H2O (P<0.05). The positive rates of portal hypertensive gastropathy (PHG), upper digestive hemorrhage and portal embolism in MPCDV+SRS group were significantly lower than in MPCDV group after operation (P<0.05, respectively). But there was no difference in hepatic encephalopathy between the two groups.


Conclusion
The clinical effect of combination of MPCDV with SRS is better than only MPCDV.


Key words: 
Hypertension, Portal; Hemorrhage; Devascularization; Splenorenal shunt
Primer of Robotic and Telerobotic Surgery (2004)

Section I: Solutions to the Limitations of Laparoscopic Surgery Three Dimensional Video Imaging Systems Ergonomic Requirements for Laparoscopic Instruments Electronically and Computer Integrated Operating Rooms Virtual Operative Fields for Surgical Stimulation Section II: Introduction to Surgical Robots and Telerobots AESOP: A Voice-Controlled Camera Holder The EndoAssist Endoscopic Camera Holder New Robotic Surgical Assistants The Da Vinci Telerobotic Surgical System The Zues Telerobotic Surgical System The Next Generation of Surgical Robots Socrates: Telementoring for Telerobotics Cost Issues in Clinical Use of Telerobotics Section III: Surgical Experience with AESOP: A Voice-Controlled Robotic Camera Holder AESOP-Assisted Laparoscopic Foregut Surgery AESOP-Assisted Laparoscopic Colorectal Surgery AESOP-Assisted Laparoscopic Prostatectomy AESOP-Assisted Laparoscopic Urologic Surgery Section IV: Telerobotic-Assisted Cardiothoracic Surgery Telerobotic-Assisted Internal Mammary Artery Harvest and Coronary Artery Bypass Grafting Telerobotic-Assisted Cardiac Valve Surgery Section V: Telerobotic-Assisted Gastrointestinal Surgery Telerobotic-Assisted Antireflux Surgery Nissen Fundoplication Telerobotic-Assisted Gastric Surgery Telerobotic-Assisted Pancreatic Surgery Telerobotic-Assisted Bariatric Surgery Telerobotic-Assisted Colorectal Surgery Telerobotic-Assisted Pediatric Surgery Using Telerobots as Assistant Surgeons Section VI: Telerobotic-Assisted Urology Telerobotic-Assisted Nephrectomy Telerobotic-Assisted Prostatectomy Section VII: Telerobotics, Telemedicine, and Telementoring Credentialing and Privileging of Telerobotic Surgery The Virtual University: Telemedicine and Telementoring Telementoring Surgery in Third World Countries Virtual Systems for Simulated Surgical Resident Training