gebhart/patrepeval huggingface dataset:
Helicobacter pylori Colonization Ameliorates Glucose Homeostasis in Mice through a PPAR γ-Dependent Mechanism (2012)

Gastric infection with some commensal strains of H. pylori ameliorates glucose homeostasis in mice through a PPAR γ-dependent mechanism and modulates macrophage and Treg cell infiltration into the abdominal white adipose tissue.
Abnormal B-cell response to T-cell-independent polyclonal B-cell activators in homosexuals presenting persistent generalized lymph node enlargement and HTLV-III antibodies. (1986)

B-cell functions were investigated in a well-defined high-risk group for the development of AIDS/AIDS-related complex (ARC). Stimulation of mononuclear cells (MNC) with T-cell-independent polyclonal B-cell activators failed to increase high spontaneous IgG levels observed in vivo and in vitro. The secretion of IgM following stimulation with Klebsiella M (Klebs M) or Salmonella (Salm) membrane preparation increased by a factor of 4 to 6 and thus ranged between the results of the control group and those of AIDS/ARC patients; the response to a T-cell-independent B-cell mitogen, Staphylococcus aureus Cowan I (SAC), showed profound abnormalities as well in this group. This indicates that functional B-cell abnormalities can be seen in addition to T-cell dysfunctions in patients at increased risk for the development of AIDS/ARC.
LVAD BRIDGE TO HEART TRANSPLANT THERAPY: EFFECTS ON OUTCOME, WAITING TIME, CENTER VOLUME, AND DONOR RESOURCE ALLOCATION (1998)

230 The availability of implantable LVAD's has increased their use while raising concerns of increasing donor shortage, waiting times, and shifting donor resource allocation. We compared transplant outcomes from a 12 month period (10/1/96-9/30/97) of LVAD (HeartMate, TCI, Inc., Woburn, MA) use to a 12 month period prior to acquisition of the LVAD (10/1/95-9/30/96). The HeartMate (IP-1000/VE models) were acquired at the UMich in 9/96. During the earlier period, 3 pts received circulatory support as a bridge to transplant (2 ECMO; 1 Abiomed). During the most recent period, 6 pts received circulatory support prior to transplant (6 HeartMate). All pts receiving LVAD's were in cardiogenic shock supported by 2 or more inotropes with 60% having IABP's (9 pts underwent HeartMate implantation-6 transplanted, 2 awaiting transplant, and 1 death). During the period of LVAD use there was a 65% increase in transplants performed (33 vs. 20). The number of pts transplanted as UNOS status I increased from 20% to 33% (4/20 vs 11/33). Median waiting time for status 1 pts increased from 0.25 to 1.6 months (mean 0.3±0.2 vs 1.9±1.5; p<0.05). Median waiting time for UNOS status II pts increased from 5.9 to 8.1 months (mean 9.8±9.3 vs 9.8±8.0; p=ns). There were no deaths in pts listed and awaiting transplant during the most recent period despite increased waiting time. The median total length of stay (LOS) from pre-transplant admission to post-transplant discharge increased from 21 to 25 days (mean 39±46 vs 44±45; p=ns). Median total LOS for pts transplanted as status I increased from 56 to 78 days (mean 84±83 vs 87±53; p=ns) as a result of increased pre-transplant LOS. Total LOS for pts transplanted as status II remained unchanged (median LOS 19 days; mean 28±25 vs 22±13; p=ns). Median post-transplant LOS for all pts increased from 15 to 17 days (mean 30±14 vs 23±18; p=ns). There was a significant decrease in median post-transplant LOS for pts transplanted as status I (45 vs 14 days; mean 70±84 vs 27±26; p<0.05). The median post-transplant LOS for pts transplanted as status II increased from 13 to 19 days (mean 20±13 vs 21±12 days). Actuarial 1 yr survival (KM) was 75% during the earlier period and 96% during the most recent period. Comparing the initial 6 months of each time period fewer hearts were sent out of our local organ procurement agency (11 vs 15) and more received from outside organ procurement agencies (3 vs 1) during the most recent period. Conclusions: Acquisition of an LVAD was associated with an increased transplant volume, a shift to performing more status I transplants, increased waiting time for both status I and II pts. a reduced post-transplant LOS for pts transplanted as status I, increased utilization of donor organs within our local organ procurement agencies, and increased overall survival. LVAD bridge to transplant therapy impacts favorably on heart transplant outcomes.
Combining Cost‐Efficient Cellulose and Short‐Chain Carboxylic Acid Production: The Polyoxometalate (POM)‐Ionosolv Concept (2020)

Full cost-effective exploitation of all wood components is key to growing a commercially successful biorefining industry. An innovative process is reported that combines fractionation of lignocellulosic biomass using a low-cost ionic liquid (Ionosolv) and production of bio-derived formic acid using polyoxometalates and molecular oxygen (OxFA process). We show that the hemicellulose and part of the lignin were selectively dissolved into the ionic liquid triethylammonium hydrogen sulfate and oxidised in situ to short-chain, distillable carboxylic acids by a Keggin-type polyoxometalate with high yields and selectivities. Characterization by several techniques, including ICP-OES, FTIR, GC, HPLC and NMR spectroscopy confirmed stability of the catalyst over three consecutive POM-Ionosolv recycles and stable formic acid yields.High formic acid yields of 26 % (pine chips), 23 % (beech chips), and 18 % (Miscanthus) were obtained with respect to the initial carbon content of the biomass, with unprecedented oxidation selectivities for formic acid of 54-62 % depending on vanadium substitution in the polyoxometalate, the processing temperature and the water content in the reaction mixture.. We also demonstrate that the cellulose rich pulp is a suitable source of glucose via enzymatic saccharification. We report cellulose yields of 37% for Miscanthus (from originally 48% glucan content), 33% for pine (from originally 49%) and 31% for beech (from originally 41%) were achieved, and a saccharification yield of up to 25% without optimisation. With further optimisation, this concept has the potential to generate two chemical products directly from lignocellulose in high yields and selectivities and hence a novel avenue for full utilisation of cellulose, hemicellulose and lignin.
Preorganized Metallomacrocycles:  Improved Binding and Selectivity of NH3 over Primary Amines (1998)

Three new metallohosts (2−4) were synthesized by the uranyl-templated macrocyclization of the appropriate dialdehydes 13a−c and 1,2-phenylenediamine in methanol. Cyclization of the dialdehyde 13b led to two isomers (3a, major, and 3b, minor), which only differed in the orientation of the isopropyl substituents on the outer phenolic rings of the terphenyl moiety. The binding constants in CDCl3 of ammonia and benzylamine were determined by 1H NMR spectroscopy. The binding of ammonia by these hosts follows 1 ≈ 2 ≈ 4 < 3b < 3a. The binding of benzylamine follows 1 ≈ 2 ≈ 4 ≈ 3b ≪ 3a. Monte Carlo free-energy perturbation calculations reproduced the binding of ammonia and n-propylamine quite well. The much larger binding of benzylamine by host 3a was rationalized by a much deeper positioning of the guest in the cavity of the host compared to 3b.
Fundamental CRISPR-Cas9 tools and current applications in microbial systems (2017)

Derived from the bacterial adaptive immune system, CRISPR technology has revolutionized conventional genetic engineering methods and unprecedentedly facilitated strain engineering. In this review, we outline the fundamental CRISPR tools that have been employed for strain optimization. These tools include CRISPR editing, CRISPR interference, CRISPR activation and protein imaging. To further characterize the CRISPR technology, we present current applications of these tools in microbial systems, including model- and non-model industrial microorganisms. Specially, we point out the major challenges of the CRISPR tools when utilized for multiplex genome editing and sophisticated expression regulation. To address these challenges, we came up with strategies that place emphasis on the amelioration of DNA repair efficiency through CRISPR-Cas9-assisted recombineering. Lastly, multiple promising research directions were proposed, mainly focusing on CRISPR-based construction of microbial ecosystems toward high production of desired chemicals.
Research data supporting "Scanning Kelvin Probe Microscopy Investigation of the Role of Minority Carriers on the Switching Characteristics of Organic Field-Effect Transistors" (2016)

Data underpinning the figures 1-4 in the manuscript
Reducing the impact of reticle CD-non-uniformity of multiple structures by dose corrections based on aerial image measurements (2010)

For many critical lithography applications the main contributor to wafer intra-field CD variation is the reticle CD variation. Current practice is that the input data needed to correct the effect of the reticle on the wafer CD is gathered using wafer exposures and SEM or scatterometry analysis. This approach consumes valuable scanner time and adds wafer costs. In this work we evaluate the potential for Intra-Field CD non-uniformity (CDU) correction based on aerial image reticle measurements for a complex 2D structure, including peripheral structures. The application selected is a 45nm rotated brick wall structure (active area DRAM). A total of 10 line / space structures (both horizontal and vertical) through pitch represent the periphery. Mask qualification has been performed using the newly developed Zeiss WLCD32 metrology tool, which measures wafer level CD on masks using aerial imaging technology. Excellent correlation is shown between intra-field wafer data and WLCD32 data. Furthermore, a comparison is made between the correction potential of ASML DoseMapper recipes based on wafer data and on WLCD32 mask data, indicating that the potential CDU improvement via both approaches is similar. Exposures with the resulting dose recipes have been used to confirm this predicted correction potential in a realistic setting.
Highly Durable and Selective Fe- and Mo-Based Atomically Dispersed Electrocatalysts for Nitrate Reduction to Ammonia via Distinct and Synergized NO2– Pathways (2022)

Aimed toward the pursuit of manufacturing ammonia in a carbon-neutral and decentralized manner, the electrocatalytic nitrate reduction reaction (NO3RR) not only promises an effective route for carbon-neutral ammonia synthesis but also offers potential advantages to wastewater remediation. Here, we describe the efficacy of bioinspired, atomically dispersed catalysts for the NO3RR in aqueous media via a catalytic cascade. Compared to nanoparticles with extended catalytic surfaces, atomically dispersed catalysts are largely underexplored in this field, despite their intrinsic selectivity toward mono-nitrogen species over their dinitrogen counterparts. Herein, we specifically report on a series of nitrogen-coordinated mono- and bimetallic, atomically dispersed, iron- and molybdenum-based electrocatalysts for ammonia synthesis via the NO3RR. The key role of the *NO2/NO2– intermediates was identified both computationally and experimentally, wherein the Fe–N4 sites and Mo–N4/*O–Mo–N4 sites carried distinct associative and dissociative adsorption of NO3– molecules, respectively. By integrating individual Fe and Mo sites on a single bimetallic catalyst, the unique reaction pathways were synergized, achieving a Faradaic efficiency of 94% toward ammonia. Furthermore, the robustness of the bimetallic FeMo–N–C catalyst was highlighted by five consecutive 12 h electrolysis cycles with the Faradaic efficiency being maintained above 90% over the entire 60 h. The utilization of catalytic cascades, synergizing distinct reaction pathways on heterogeneous single-atom sites, is largely unconstrained by linear scaling relations of reaction intermediates and sheds light on designing electrocatalysts for highly selective, efficient, and durable ammonia synthesis.
Pharmacokinetics of repinotan in healthy and brain injured animals (2005)

Repinotan hydrochloride (repinotan) is a highly potent and selective 5-HT(1A) full receptor agonist. The ability of repinotan to cross the blood-brain barrier (BBB) and penetrate into rat brain tissue was investigated, because rapid penetration into brain tissue is thought to be essential for neuroprotective efficacy. Intravenous (i.v.) repinotan was rapidly distributed into brain, and the distribution equilibrium between blood and brain was reached immediately after the start of infusion. Free concentrations of repinotan were identical in brain and plasma, indicating that repinotan crosses the BBB freely in both directions with diffusion as a driving force. The brain concentration of repinotan was determined by the free plasma concentration. Thus, the total plasma concentration of repinotan (sum of bound and unbound compound) is only indicative for the brain concentration as long as the unbound fraction remains constant. Metabolites of repinotan do not penetrate the BBB and are retained in the perfusing blood due to their increased polarity. The penetration of [14C] repinotan into ischemic areas of the brain was dependent on time. In studies using injured animals (pMCAO), high levels of [14C] repinotan could be detected in ischemic areas when the compound was administered up to 5 h post injury. [14C] repinotan radioactivity could no longer be detected in ischemic areas when administered 18 h after pMCA-O. After the end of infusion, repinotan was rapidly and completely eliminated from rat brains. Elimination occurred in parallel from plasma and brain with half-lives of about 1 h. In conclusion, repinotan rapidly and to a considerable extent penetrates into brain tissue of healthy and injured animals.
Gold Nanorod-Cored Biodegradable Micelles as a Robust and Remotely Controllable Doxorubicin Release System for Potent Inhibition of Drug-Sensitive and -Resistant Cancer Cells (2013)

Gold nanorod-cored biodegradable micelles were prepared by coating gold nanorods (AuNRs) with lipoylated poly(ethylene glycol)-b-poly(ε-caprolactone) (PEG-PCL-LA) block copolymer and investigated for remotely triggered release of doxorubicin (DOX) and effective inhibition of drug-sensitive and multidrug-resistant (MDR) cancer cells. The micelles had uniform sizes and excellent colloidal stability. The in vitro release studies showed that drug release from DOX-loaded AuNR-cored micelles (AuNR-M-DOX) was minimal under physiological conditions but markedly enhanced upon NIR irradiation at a low power density of 0.2 W/cm2, most likely due to photothermally induced phase transition of PCL regime. As revealed by confocal microscopy and flow cytometry, NIR could also trigger effective DOX release in drug-sensitive as well as drug-resistant MCF-7 cells. MTT assays showed that antitumor activity of AuNR-M-DOX to drug-sensitive MCF-7 cells was significantly boosted by mild NIR irradiation, reaching a comparable level to free DOX. Most remarkably, AuNR-M-DOX combined with NIR irradiation could also effectively kill drug-resistant MCF-7 cells, in which a cell viability of 38% was observed at a DOX dosage of 10 μg equiv/mL, whereas 100% cell viability was maintained for cells treated with free DOX under otherwise the same conditions. These AuNR-cored biodegradable micelles with high stability, photo-triggered drug release, and effective reversal of multidrug resistance in cancer cells have appeared as a novel platform for targeted cancer therapy.
Photoacoustic measurements of red blood cell oxygen saturation in blood bags in situ (2017)

Red blood cell (RBC) transfusion is a critical component of the health care services. RBCs are stored in blood bags in hypothermic temperatures for a maximum of 6 weeks post donation. During this in vitro storage period, RBCs have been documented to undergo changes in structure and function due to mechanical and biochemical stress. Currently, there are no assessment methods that monitor the quality of RBCs within blood bags stored for transfusion. Conventional assessment methods require the extraction of samples, consequently voiding the sterility of the blood bags and potentially rendering them unfit for transfusions. It is hypothesized that photoacoustic (PA) technology can provide a rapid and non-invasive indication of RBC quality. In this study, a novel PA setup was developed for the acquisition of oxygen saturation (SO<sub>2</sub>) of two blood bags in situ. These measurements were taken throughout the lifespan of the blood bags (42 days) and compared against the clinical gold standard method of the blood gas analyzer (BGA). SO<sub>2</sub> values of the blood bags increased monotonically throughout the storage period. A strong correlation between PA SO<sub>2</sub> and BGA SO<sub>2</sub> was found, however, PA values were on average 3.5% lower. Both techniques found the bags to increase by an SO<sub>2</sub> of approximately 20%, and measured very similar rates of SO<sub>2</sub> change. Future work will be focused on determining the cause of discrepancy between SO<sub>2</sub> values acquired from PA versus BGA, as well as establishing links between the measured SO<sub>2</sub> increase and other changes in RBC in situ.
Transformations and antioxidative activities of lignans and stilbenes at high temperatures (2022)

Thermal transformations of polyphenols from the lignan and stilbene families were investigated at temperatures ranging from 200 °C to 250 °C, in polyethylene glycol (PEG-400), dimethylformamide (DMF) and in sunflower oil (SO). The polyphenols showed varying degrees of thermal stabilities and in some cases intramolecular transformations were observed. The formed products were isolated and characterized. Oligomerization of the polyphenols at thermo-oxidative conditions was also investigated. Finally, the antioxidative activity of the polyphenols against thermo-oxidative degradation α-linoleic acid was investigated at 200 °C. The results suggested that the studied substrates retained their antioxidative properties at elevated temperatures, with stilbenes showing most efficient protection against thermo-oxidative degradation of polyunsaturated fatty acids.
Development of a Novel Vibration-Assisted Ultraprecision Cutting System for Fabricating Hierarchical Micro/Nanostructures (2022)

mechanical structure r= radius of the hinge n= the number of the level of the micro/nanostructure
Synthetic DNA‐Targeted Chemotherapeutic Agents And Related Tumor‐Activated Prodrugs (2021)

Abstract Synthetic drugs have always played an important role in cancer therapy. The first systemic anticancer drugs were synthetic DNA alkylating agents and DNA antimetabolites. The original antimetabolites such as cytosine arabinoside and 5‐fluorouracil have been augmented by more recent compounds such as gemcitabine, fludarabine, cladribine, and pentostatin, which inhibit DNA polymerase action during DNA synthesis. A new development is the related compounds deazacytidine and decitabine, which inhibit reactivate silenced genes by inhibition of cytosine methylation. Nitrogen mustards, platinum complexes, nitrosoureas, and triazene‐based DNA‐methylating agents are direct DNA‐modifying agents that still play an important role in clinical treatment. Methotrexate and more recent lipophilic analogs, together with older drugs such as 5‐fluorouracil, are used as inhibitors of different enzymes in the folate pathway necessary for the synthesis of pyrimidine nucleotides. The potent activity of natural products such as doxorubicin also led to the development of the synthetic topoisomerase inhibitors that are now another important group of drugs whose therapeutic effects are due to enzyme‐mediated DNA modification. Finally, an increasing understanding of tumor physiology and genetics has allowed the development of tumor‐activated prodrugs of DNA‐active agents. Using hypoxia, gene therapy or antibody targeting to activate such prodrugs specifically in tumor tissue has the potential to increase the therapeutic index of these agents by limiting the exposure of sensitive nontumor cell populations.
Implantable cardioverter defibrillators for prevention of sudden cardiac Death (2007)

Despite the multiple advances in the field of cardiovascular medicine, the incidence of sudden cardiac death (SCD) continues to rise. Of all SCDs, <25% occur in individuals deemed at high risk by current risk-stratification algorithms; hence, these risk-stratification algorithms are not satisfactory. Until better markers are identified to risk stratify patients, we will see an increasing use of implantable cardioverter defibrillators (ICDs). However, even with the increase in defibrillator use, the impact on overall incidence of SCD may only be modest, as many individuals experience SCD as the first manifestation of cardiovascular disease. Another important challenge is widespread availability of automated external defibrillators and effective utilization of public access defibrillation programs for timely and appropriate management of out-of-hospital victims with cardiac arrest. This review discusses the current understanding on SCD, risk stratification, and management aimed at reducing SCD, particularly with the use of ICDs.
TREATMENT OF PERIPROSTHETIC FEMORAL FRACTURES FOLLOWING TOTAL HIP ARTHROPLASTY WITH FEMORAL COMPONENT REVISION (2003)

Revision total hip arthroplasty for the treatment of a periprosthetic fracture around the stem of the femoral implant successfully restored function for most patients. The greatest long-term problems were prosthetic loosening and fracture nonunion. Better results were seen when an uncemented, extensively porous-coated stem was used.
Realization of Contact Surface Geometry by Dragging a Whisker-type Tactile Sensor Across Measuring Objects (2007)

Previously we reported a method for displaying the shape of an object by using an array of whisker sensors. The array of whiskers was pressed against the object to be measured and the deflection of each whisker was measured. The measurements were used as inputs to a neural network to recognize the shapes. However, the previous method needed a larger number of whiskers to recognize the wider surface, because the array of whiskers has to be in full contact with the entire surface. Therefore, this study presents a new method in which a much smaller number of whiskers are dragged across the surface of the measured object to distinguish the shapes. The method is performed in the following manner. Firstly, a smaller number of whiskers are dragged across an object and each whisker deflection direction is distinguished at discrete time intervals. Next, the neural network continuously monitors the output from the whiskers and produces a result that characterizes the surface at the current scan position. Lastly, by building up a map of the classification of the entire surface, the geometry of the measured object can be displayed. This study exhibits the hardware and software required for displaying shapes, and shows examples of the results obtained from the measurements of some objects.
Fluorescence Polarization Assay to Quantify Protein–Protein Interactions (2004)

A fluorescence polarization assay can be used to evaluate the strength of a protein-protein interaction. A green fluorescent protein variant is fused to one of the protein partners. The formation of a complex is then deduced from an increase in fluorescence polarization, and the equilibrium dissociation constant of the complex is determined in a homogeneous aqueous environment. The assay is demonstrated by using the interaction of the S-protein and S-peptide fragments of ribonuclease A as a case study.