gebhart/patrepeval huggingface dataset:
Urinary ATP and visualization of intracellular bacteria: a superior diagnostic marker for recurrent UTI in renal transplant recipients? (2014)

Renal transplant recipients (RTR) are highly susceptible to urinary tract infections (UTIs) with over 50% of patients having at least one UTI within the first year. Yet it is generally acknowledged that there is considerable insensitivity and inaccuracy in routine urinalysis when screening for UTIs. Thus a large number of transplant patients with genuine urine infections may go undiagnosed and develop chronic recalcitrant infections, which can be associated with graft loss and morbidity. Given a recent study demonstrating ATP is released by urothelial cells in response to bacteria exposure, possibly acting at metabotropic P2Y receptors mediating a proinflammatory response, we have investigated alternative, and possibly more appropriate, urinalysis techniques in a cohort of RTRs. Mid-stream urine (MSU) samples were collected from 53 outpatient RTRs. Conventional leukocyte esterase and nitrite dipstick tests, and microscopic pyuria counts (in 1 μl), ATP concentration measurements, and identification of intracellular bacteria in shed urothelial cells, were performed on fresh unspun samples and compared to 'gold-standard' bacterial culture results. Of the 53 RTRs, 22% were deemed to have a UTI by 'gold-standard' conventional bacteria culture, whereas 87%, 8% and 4% showed evidence of UTIs according to leukocyte esterase dipstick, nitrite dipstick, and a combination of both dipsticks, respectively. Intracellular bacteria were visualized in shed urothelial cells of 44% of RTRs, however only 1 of the 23 RTRs (44%) was deemed to have a UTI by conventional bacteria culture. A significant association of the 'gold-standard' test with urinary ATP concentration combined with visualization of intracellular bacteria in shed urothelial cells was determined using the Fisher's exact test. It is apparent that standard bedside tests for UTIs give variable results and that seemingly quiescent bacteria in urothelial cells are very common in RTRs and may represent a focus of subclinical infection. Furthermore, our results suggest urinary ATP concentration combined with detection of intracellular bacteria in shed urinary epithelial cells may be a sensitive means by which to detect 'occult' infection in RTRs.
Ultralow-field magnetocaloric materials for compact magnetic refrigeration (2023)

Abstract Magnetic refrigeration around the liquid-helium temperature plays a critical role in many technological sectors. Even if gallium gadolinium garnet (GGG) has been regarded as the benchmark, its application is highly limited by the small magnetic entropy changes, the requirement of superconducting magnets, and the large device sizes. Here, we report that LiREF 4 (RE = rare earth) single crystals exhibit significantly superior magnetocaloric performance levels to commercial GGG. Under a small magnetic field of 5 kOe, which can be easily achieved by a permanent magnet, the magnetic entropy change reaches a record-high value of 16.7 J kg −1 K −1 in LiHoF 4 in contrast to the value of 1.0 J kg −1 K −1 in GGG. The combination of small driving fields, large entropy changes, and excellent thermal and/or magnetic reversibility enables this series to be employed as the ideal working material for compact magnetic refrigeration around the liquid-helium temperature.
Scalable synthesis and derivation of functional polyesters bearing ene and epoxide side chains (2013)

Functional polyester chemistry is well suited to improve delivery of biomacromolecular drugs because it enables tuning of degradation profiles and inclusion of key functional groups (e.g. cationic charges for nucleic acid binding). However, current approaches to introduce functionality suffer from inadequate scalability and modularity. We have developed a scalable library of functional polyesters based on the polymerization of trimethylolpropane allyl ether (TPAE) with diacid chlorides (poly(TPAE-co-AC)s). The reactive side chains can be easily modified with various functional thiols (e.g. alkyl-, amino-, and PEG-) and amines to generate a diverse set of materials, thereby tuning the chemistry for potential opportunities in drug delivery. The polymerization occurs readily under mild conditions at room temperature with Mw for poly(TPAE-co-suberoyl chloride) exceeding 42 000 g mol−1. In addition, poly(TPAE-co-adipoyl chloride) was polymerized on a 100+ gram scale in 71% final isolated yield. Due to the structural similarity to established non-functional polyesters such as PLGA, these new materials may find broad application as functional polyesters for gene delivery, tissue engineering, and other nanotechnology applications.
Thermal stability of chemical composition gratings in fluorine–germanium-doped silica fibers (2002)

A model based on diffusion of dopants in a periodic structure has been applied to describe thermal decay of chemical composition gratings in fluorine-germanium-doped silica fibers. The good agreement between previously reported values and the diffusion coefficients derived here from experiments and models in the 1000-1200 degrees C temperature range indicate that fluorine diffusion is the main mechanism of grating decay. Experimental results also indicate that the presence of phosphorous significantly increases the decay rate of chemical composition gratings.
Understanding Spin Structure in Metallacrown Single-Molecule Magnets using Magnetic Compton Scattering (2014)

The 3d-4f mixed metallacrowns frequently show single-molecule magnetic behavior. We have used magnetic Compton scattering to characterize the spin structure and orbital interactions in three isostructural metallacrowns: Gd2Mn4, Dy2Mn4, and Y2Mn4. These data allow the direct determination of the spin only contribution to the overall magnetic moment. We find that the lanthanide 4f spin in Gd2Mn4 and Dy2Mn4 is aligned parallel to the Mn 3d spin. For Y2Mn4 (manganese-only spin) we find evidence for spin delocalization into the O 2p orbitals. Comparing the magnetic Compton scattering data with SQUID studies that measure the total magnetic moment suggests that Gd2Mn4 and Y2Mn4 have only a small orbital contribution to the moment. In contrast, the total magnetic moment for Dy2Mn4 MCs is much larger than the spin-only moment, demonstrating a significant orbital contribution to the overall magnetic moment. Overall, these data provide direct insight into the correlation of molecular design with molecular magnetic properties.
Paper 09: Revision rate following primary hip arthroscopy in patients given prophylactic oral losartan for the prevention of post-surgical fibrosis versus no losartan (2023)

Objectives: To evaluate whether postoperative treatment with Losartan decreased the revision rate in patients undergoing primary hip arthroscopy. Methods: Patients underwent primary hip arthroscopy with labral repair and CAM osteoplasty and rim trimming between 2012 and 2017. Patients who underwent microfracture, labral debridement or reconstruction, core decompression, ligamentous teres repair or reconstruction, or capsular reconstruction were excluded. Losartan was added to all patients’ post-operative protocol in December 2015. Patients who underwent hip arthroscopy prior to November 2015 were included in the no-Losartan group (NOLOS) and patients who had arthroscopy between December 2015 and Dec 2017 were included in the losartan group (LOS). Results: Of the 964 cases, follow-up was obtained on 673 patients (70%). There were 405 patients in the NOLOS group and 268 in the LOS group. There was no difference in gender distribution (P=0.128) between groups. The LOS group was significantly older (36.6 ±13 years) compared to the NOLOS group (34.1±11)(p=0.012). Average follow-up in the NOLOS group was 5.8±2 years and was 4.1±1 years in the LOS group. Revision hip arthroscopy was required in 35 (8.6%) patients in the NOLOS group and 6 (2.2%) patients in the LOS group(p=0.001). There was no difference in age between those patients who required revision (32±11 years) and those who did not(35±12 years)(p=0.137). Conclusions: The prevalence of revision hip arthroscopy was significantly lower (2.2%) in patients who took Losartan as part of their post-operative protocol compared to those who did not (8.6%). Reduction in the need for revision hip arthroscopy can improve patient outcomes and reduce healthcare dollars spent.
Biocatalytic Asymmetric Hydrogen Transfer Employing <i>Rhodococcus ruber</i> DSM 44541 (2002)

Nonracemic sec-alcohols of opposite absolute configuration were obtained either by asymmetric reduction of the corresponding ketone using 2-propanol as hydrogen donor or by enantioselective oxidation through kinetic resolution of the rac-alcohol using acetone as hydrogen acceptor employing whole lyophilized cells of Rhodococcus ruber DSM 44541. The microbial oxidation/reduction system exhibits not only excellent stereo- and enantioselectivity but also a broad substrate spectrum. Due to the exceptional tolerance of the biocatalyst toward elevated concentrations of organic materials (solvents, substrates and cosubstrates), the process is highly efficient. The simple preparation of the biocatalyst and its ease of handling turns this system into a versatile tool for organic synthesis.
High performance ultra-low energy RRAM with good retention and endurance (2010)

High performance novel RRAM of 0.3 μW set power (0.1 μA at 3 V), 0.6 nW reset power (-0.3 nA at -1.8 V), fast 20 ns switching time, ultra-low 6 fJ switching energy, large 7×10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> resistance window for 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> sec retention at 125°C, and 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> cycling endurance were measured simultaneously. This is the first time that the switching energy of new non-volatile memory is close to existing Flash Memory.
Glucose supplementation stimulates peripheral branched-chain amino acid catabolism in lactating dairy cows during essential amino acid infusions (2015)

To determine how glucose modulates protein synthesis when essential AA are in abundant supply, 5 early-lactation, rumen-fistulated Holstein dairy cows were fed a diet containing 6.95 MJ/kg of net energy for lactation and 12.4% crude protein and abomasally infused for 5 d with saline, 844 or 1,126 g/d of a complete essential AA mix, with and without the inclusion of 1,000 g/d of glucose, in a 5×5 Latin square design. Infusion of essential AA increased milk yield by 4.1 kg/d, milk protein by 256 g/d, milk fat by 95 g/d, and milk urea nitrogen by 70% compared with saline, with no differences between the level of essential AA infusion. The addition of glucose to essential AA infusate did not stimulate milk protein yield or concentration, but reduced milk urea nitrogen by 17% and decreased milk fat yield. Arterial concentrations of total essential AA increased 3- to 4-fold, mammary clearance decreased 61%, and mammary uptake of essential AA increased 65% in response to essential AA infusion. Arterial branched-chain AA concentrations declined 29% in response to glucose and mammary clearance increased 48%, but mammary AA uptake was unchanged. Essential AA infusion increased plasma 3-methylhistidine by 50% and reduced muscle branched-chain α-keto acid dehydrogenase kinase abundance by 14%, indicating stimulation of muscle protein turnover and branched-chain AA catabolism, respectively. Glucose had no further effect on muscle branched-chain α-keto acid dehydrogenase kinase abundance but decreased mRNA expression of branched chain aminotransferase 1. Lack of further increases in plasma 3-methylhistidine or greater stimulation of muscle branched-chain AA catabolism indicates that muscle protein degradation was unchanged with glucose but that accretion may have been stimulated. The decrease in circulating branched-chain AA concentrations and nitrogen excretion in response to glucose suggests that surplus essential AA were redirected to peripheral, extra-mammary tissues.
Resistencia de Rhipicephalus (boophilus) microplus a ixodicidas en ranchos bovinos del municipio Evangelista, Veracruz, México (2013)

El objetivo del trabajo fue conocer la presencia de Rhipicephalus (Boophilus) microplus resistentes a Coumaphos, Deltametrina y Amitraz e identificar los factores de asociados a su presentación en unidades de producción bovinas (UPB) localizadas en el Municipio de San Juan Evangelista Veracruz. Se realizó un estudio epidemiológico de tipo transversal. Los municipios en donde se desarrollóo la investigación y el tamaño de muestra de las UPB, se determinaron a través de un esquema no probabilístico por conveniencia. Se muestrearon un total de 16 ranchos. Se aplicaron encuestas a los productores con las que se determinaron los posibles factores asociados a la aparición de resistencia y un muestreo al azar de los animales infestados con el ectoparásito, colectándose directamente de los animales de cada rancho 50 teleoginas (garrapatas adultas ingurgitadas), los resultados obtenidos en todas las UPB muestreadas en este Municipio se identificaron poblaciones de garrapatas con resistencia múltiple a OF, PS y AM; sin embargo, es importante mencionar que solo dos 2 de 16 no presentaron resistencia a organofosforados. Asimismo, La tasa (%) promedio de resistencia para las 16 UPB muestreadas fue del 16% para Coumaphos, 40% para Deltametrina y del 47% para el Amitraz. Se concluye que en las UPB muestreadas en el municipio de San Juan Evangelista Veracruz, México, existen cepas de garrapatas Rhipicephalus Boophilus microplus con resistencia múltiple a Coumaphos, Deltametrina y Amitraz propiciado por las malas prácticas de manejo durante el baño garrapaticida.
Distinct contracted conformations of the <i>Tcra/Tcrd</i> locus during <i>Tcra</i> and <i>Tcrd</i> recombination (2010)

Studies have suggested that antigen receptor loci adopt contracted conformations to promote long-distance interactions between gene segments during V(D)J recombination. The Tcra/Tcrd locus is unique because it undergoes highly divergent Tcrd and Tcra recombination programs in CD4(-)CD8(-) double negative (DN) and CD4(+)CD8(+) double positive (DP) thymocytes, respectively. Using three-dimensional fluorescence in situ hybridization, we asked whether these divergent recombination programs are supported by distinct conformational states of the Tcra/Tcrd locus. We found that the 3' portion of the locus is contracted in DN and DP thymocytes but not in B cells. Remarkably, the 5' portion of the locus is contracted in DN thymocytes but is decontracted in DP thymocytes. We propose that the fully contracted conformation in DN thymocytes allows Tcrd rearrangements involving V(delta) gene segments distributed over 1 Mb, whereas the unique 3'-contracted, 5'-decontracted conformation in DP thymocytes biases initial Tcra rearrangements to the most 3' of the available V(alpha) gene segments. This would maintain a large pool of distal 5' V(alpha) gene segments for subsequent rounds of recombination. Thus, distinct contracted conformations of the Tcra/Tcrd locus may facilitate a transition from a Tcrd to a Tcra mode of recombination during thymocyte development.
Soliton content with quadratic nonlinearities (2001)

We review our comprehensive investigations of the soliton content of multidimensional multicolor quadratic solitons as a function of the input light and material conditions. The first experimental demonstration of the concept is reported.
Demethylation of Specific Sites in the 5′-Flanking Region of the <i>CYP17</i> Genes When Bovine Adrenocortical Cells Are Placed in Culture (1992)

DNA methylation of CYP17 (steroid 17 alpha-hydroxylase) was studied in bovine adrenocortical cells, which lose the capacity to express this tissue-specific gene in culture by phenotypic switching. Restriction enzyme digestions, and sequencing of a lambda clone of a second CYP17 gene (CYP17A2), showed that there are at least three CYP17 genes in the bovine genome. Southern blotting of DNA digested with Msp I or Hpa II together with Eco RI was used to investigate the methylation status of Hpa II sites at -1.0 kb (H1), -1.8 kb (H2), and -2.3 kb (H4) in CYP17A1 and CYP17A2 and at -0.7 kb (H0) in CYP17A3. In cells and tissues other than white blood cells, H0 was nonmethylated whereas H1 was always methylated; H2 and H4 showed variation in methylation status among different cells and tissues. In particular, whereas H4 was methylated in the bovine adrenal cortex in vivo, there was a rapid and complete demethylation at H4 when adrenocortical cells were placed in culture. Sites downstream from H4 did not change methylation over the first six passages in culture; additionally, the coding region of CYP17 remained fully methylated under all conditions. In contrast to adrenocortical cells, DNA from fibroblasts was nonmethylated at H2, whereas all downstream sites were fully methylated. Digestion with another methylation-sensitive enzyme, Bsa HI, which has a site between H2 and H4, showed that this region is methylated in intact adrenal cortex but nonmethylated both in cultured adrenocortical cells and in fibroblasts. The specific changes in methylation at this site and at H4 in adrenocortical cells indicate a reproducible, environmentally determined change in methylation in adrenocortical cells when they are placed in culture.
Modelling Car Parking Choice using Microsimulation Traffic Model (2007)

Town center parking management policies involve a mix of controlling factors including parking charges, parking capacity, mobility of pedestrians and disabled motorists, parking durations, parking guidance information systems, and car park accessibility to restrict car dependency. Town center microsimulation models that include parking choice models based on above parameters can provide town planners with an effective tool to evaluate their parking management policies. This paper presents the methodology for developing a car parking choice model based on the above set of parameters, and including it in current microsimulation frameworks. The present work is based on postal questionnaire surveys conducted at car parks in two different areas in the UK. The objective of the surveys was to understand the factors that affect the car parking choice, such as catchments for various car parks, reason for choice of car park, choice for alternate car parking facility, and the impact of free parking space or business paid parking on parking choice.
Information extraction techniques for monitoring of stress symptoms in orchards (2003)

A hyperspectral data cube contains a huge amount of data. For most applications the relevant information is located within only a few bands. The selection of the relevant bands without loss of essential information is therefore a critical issue. In this project band selection and classification algorithms are developed and validated for precision farming applications, more precisely for the detection of stress symptoms in fruit trees. Experimental test plots are established in apple orchards. The apple trees are put under different types of stress (fungal infection, nutrient stress, aphids and virus). Three times throughout the growing season of 2002 leaves were sampled from both healthy and reference plots and their reflectance was determined. Nearly coincident in time reflectance measurements were performed above the trees. Finally CASI-2 (Compact Airborne Spectrographic Imager, Itres) and SASI (Shortwave Infrared Airborne Spectrographic Sensor, Itres) images were collected at the experimental test plots in September 2002. To detect under these increasing complex conditions (leaf, tree, airborne level) subtle reflectance differences between stressed and healthy trees, two different band reduction approaches are evaluated. In the first approach various spectral vegetation indices are calculated and tested as stress indicator at the leaf and tree level. The second approach evaluates the Discrete Wavelet Transform (DWT) as a tool for feature reduction and classification of the obtained reflectance data sets. Best results are obtained for the nutrient deficiency plots. Both methodologies are able to distinguish nutrient-deficient trees from their references at both leaf and tree level.
BRIEF COMMUNICATION Association of a Common Variant of the CASP8 Gene With Reduced Risk of Breast Cancer (2004)

Apoptosis, or programmed cell death, is perturbed in many cancers. We tested the hypothesis that coding poly-morphisms of the death receptor 4 (DR4), caspase-8 (CASP8), and caspase-10 (CASP10) genes might act as low-penetrance breast cancer genes. Single-nucleotide polymor-phisms (SNPs) of these genes were genotyped in a series of 999 breast cancer case patients and 996 control subjects from Sheffield, U.K., and in a second, independent U.K. population of 2192 case patients and 2262 control subjects from East Anglia. In the
Perspectives on outpatient administration of CAR-T cell therapy in aggressive B-cell lymphoma and acute lymphoblastic leukemia (2021)

Chimeric antigen receptor (CAR) T-cell therapies that specifically target the CD19 antigen have emerged as a highly effective treatment option in patients with refractory B-cell hematological malignancies. Safety and efficacy outcomes from the pivotal prospective clinical trials of axicabtagene ciloleucel, tisagenlecleucel and lisocabtagene maraleucel and the retrospective, postmarketing, real-world analyses have confirmed high response rates and durable remissions in patients who had failed multiple lines of therapy and had no meaningful treatment options. Although initially administered in the inpatient setting, there has been a growing interest in delivering CAR-T cell therapy in the outpatient setting; however, this has not been adopted as standard clinical practice for multiple reasons, including logistic and reimbursement issues. CAR-T cell therapy requires a multidisciplinary approach and coordination, particularly if given in an outpatient setting. The ability to monitor patients closely is necessary and proper protocols must be established to respond to clinical changes to ensure efficient, effective and rapid evaluation either in the clinic or emergency department for management decisions regarding fever, sepsis, cytokine release syndrome and neurological events, specifically immune effector cell-associated neurotoxicity syndrome. This review presents the authors' institutional experience with the preparation and delivery of outpatient CD19-directed CAR-T cell therapy.