gebhart/patrepeval huggingface dataset:
Genome-Wide Association Study Reveals Novel Genes Associated with Culm Cellulose Content in Bread Wheat (Triticum aestivum, L.) (2017)

Plant cell wall formation is a complex, coordinated and developmentally regulated process. Cellulose is the most dominant constituent of plant cell walls. Because of its paracrystalline structure, cellulose is the main determinant of mechanical strength of plant tissues. As the most abundant polysaccharide on earth, it is also the focus of cellulosic biofuel industry. To reduce culm lodging in wheat and for improved ethanol production, delineation of the variation for stem cellulose content could prove useful. We present results on the analysis of the stem cellulose content of 288 diverse wheat accessions and its genome-wide association study (GWAS). Cellulose concentration ranged from 35 to 52% (w/w). Cellulose content was normally distributed in the accessions around a mean and median of 45% (w/w). Genome-wide marker-trait association study using 21,073 SNPs helped identify nine SNPs that were associated (<i>p</i> < 1E-05) with cellulose content. Four strongly associated (<i>p</i> < 8.17E-05) SNP markers were linked to wheat unigenes, which included β<i>-tubulin, Auxin-induced protein 5NG4</i>, and a putative transmembrane protein of unknown function. These genes may be directly or indirectly involved in the formation of cellulose in wheat culms. GWAS results from this study have the potential for genetic manipulation of cellulose content in bread wheat and other small grain cereals to enhance culm strength and improve biofuel production.
Avoidance of Cyclosporine in Renal Transplantation (2000)

Cyclosporine (CsA) has been implicated in both acute and chronic graft dysfunction. The addition of humanized IL-2 receptor antibody daclizumab (DZB) to CsA-based immunosuppression decreases the rate of acute renal transplant rejection. Therefore, 45 patients were evaluated in an immunosuppressive protocol that included DZB, mycophenolate mofetil (MMF), and steroids without CsA. This was a prospective, nonrandomized, open-label trial of the efficacy and safety of the treatment. DZB was given intravenously at 2 mg/kg before transplantation and then at 1 mg/kg every 2 wk for four doses, MMF was given orally at 3 g/d, and methylprednisolone/prednisone was given at 7 mg/kg per day and tapered to 15 mg/d at 6 mo. CsA was added to the regimen when patients developed acute rejection episodes or adverse effects to steroids or MMF; 49% of patients were spared CsA maintenance. Patients without CsA had lower serum creatinine at 6 mo and needed fewer medications to control BP. Incidence of biopsyproven rejections was 31% and occurred early (median, 10 d). These rejection episodes occurred earlier in cadaver transplants (median, 7 d) and later in living donor transplants (median, 62 days). Acute rejections occurred at a higher frequency (46% versus 34%) and earlier (6.5 versus 15 d) in patients with delayed graft function compared with patients without delayed graft function. Most of the rejections were moderate and easily reversible. The actuarial 1-yr graft survival was 95% with 100% patient survival.
Fabrication of PDMS/SWCNT thin films as saturable absorbers (2011)

We present a novel technique to fabricate a saturable absorber thin film based on Polydimethylsiloxane doped with Single Wall Carbon Nanotubes. Using this film a passive mode-locked fiber laser in a standard ring cavity configuration was built by inserting the film between two angled connectors. Self-starting passively mode-locked laser operation was easily observed. The generated pulses have a width of 1.26 ps at a repetition rate of 22.7 MHz with an average power of 4.89 mW.
Multi-Band Compact Antenna for Smartphones Supporting LTE Carrier Aggregation (2015)

In this paper, we are proposing a dual feed compact antenna for a mobile phones that is capable of supporting the latest features of LTE, Carrier Aggregation (CA), which has been introduced to satisfy the ever increasing demand for data-rate. The antenna makes use of a dual resonator design to cover the low bands used in Long Term Evolution (LTE) from 699 to 960 MHz. The design of the RF Front End(FE) is simplified by the dual feed design which can have distributed components of the FE to relax its design and packaging requirements. The main antenna switch design can be relaxed and the high isolation between the two antennas removes the need for a diplexer. The antenna supporting the high bands (from 1710 to 2700 MHz) is fed through a matching network to increase the bandwidth while having a small volume. Inductive loading is used for the minimization of both elements. Even though the antenna occupies only an area of 30×10mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , many combinations of low and high band are available for CA. Despite the small volume it has a good efficiency which is close to -3 dB. The design principle has been evaluated through simulations and measurement with good agreement between them.
A prospective validation of a deep learning-based automated workflow for the interpretation of the echocardiogram (2022)

Abstract Funding Acknowledgements Type of funding sources: Private company. Main funding source(s): Us2.ai Background. Deep learning can automate the interpretation of medical imaging tests. This study aimed to prospectively assess the interchangeability of deep learning algorithms with expert human measurements for interpreting echocardiographic studies, the primary method for assessing cardiac structure and function. Methods. We compared a deep learning interpretation of 23 echocardiographic parameters—including cardiac volumes, ejection fraction, and Doppler measurements—with three repeated measurements by core lab human experts in a prospective study for submission to the United States Food and Drug Administration (FDA). The primary outcome metric was the individual equivalence coefficient (IEC), which compares the disagreement between deep learning and human readers relative to the disagreement among human readers. The pre-determined non-inferiority criterion was 0.25 for the upper bound of the 95% confidence interval (CI). Secondary outcomes included measures of agreement, including the mean absolute deviation. Results. We included 602 studies from 600 participants (421 with heart failure, 179 controls, 69% women) with a mean age of 57 ± 16 years. The point estimates of IEC were all &amp;lt;0, indicating that the disagreement between the deep learning and human measures were lower than the disagreement among three core lab readers, and the upper bound of the 95% CI of IECs fell below the prespecified success criterion of 0.25. Secondary endpoints showed good agreement of automated with human expert measurements (Figure), with comparable or lower mean absolute deviations between automated and human experts relative to the mean absolute deviation among human experts. Conclusion. This prospective validation study demonstrated excellent agreement between deep learning and expert human interpretation for a wide range of echocardiographic measurements. These results highlight the potential of deep learning algorithms to improve efficiency and reduce costs of echocardiography. Abstract Figure.
Blood-based host biomarker diagnostics in active case finding for pulmonary tuberculosis: a diagnostic case-control study (2021)

Abstract Background There is a need to identify scalable tuberculosis screening strategies among high burden populations. The WHO has identified a non-sputum-based triage test as a development priority. Methods We performed a diagnostic case-control study of point-of-care C-reactive protein (CRP) and Xpert-MTB-Host-Response (Xpert-MTB-HR) assays in the context of a mass screening program for tuberculosis in two prisons in Brazil. All incarcerated individuals irrespective of symptoms were screened by sputum Xpert-MTB/RIF and sputum culture. Among consecutive, Xpert-MTB/RIF or culture-confirmed cases and Xpert-MTB/RIF and culture-negative controls, CRP was quantified in serum by a point-of-care assay (iChroma-II) and a 3-gene expression score was quantified from whole blood using the Xpert-MTB-HR cartridge. We evaluated receiver operating characteristic area under the curve (AUC) and assessed specificity at 90% sensitivity and sensitivity at 70% specificity, consistent with WHO target product profile (TPP) benchmarks. Findings Two hundred controls and 100 culture- or Xpert-positive tuberculosis cases were included. Half of tuberculosis cases and 11% of controls reported any tuberculosis symptoms. AUC for CRP was 0·79 (95% CI: 0·73-0·84) and for Xpert-MTB-HR was 0·84 (95% CI: 0·79-0·89). At 90% sensitivity, Xpert-MTB-HR had significantly higher specificity (53·0%, 95% CI: 45·0-69·0%) than CRP (28·1%, 95% CI: 20·2-41·8%) (p=0·003), both well below the TPP benchmark of 70%. Among individuals with medium or high sputum Xpert semi-quantitative load, sensitivity (at 70% specificity) of CRP (90·3%, 95% CI: 74·2-98·0) and Xpert-MTB-HR (96·8%, 95% CI: 83·3-99·9%) was higher. Interpretation For active case finding in this high tuberculosis-burden setting, CRP and Xpert-MTB-HR did not meet TPP benchmarks for a triage test. However, Xpert-MTB-HR was highly sensitive in detecting individuals with medium or high sputum bacillary burden. Funding National Institutes of Health (R01 AI130058 and R01 AI149620) and Brazilian National Council for Scientific and Technological Development (CNPq-404182/2019-4).
Impact of Bony Stress Injuries on Professional Basketball Performance (2017)

Objectives: Players in the National Basketball Association (NBA) subject their lower extremities to significant repetitive loading during the season as well as during off-season training. Little is known about the incidence and impact of lower extremity bony stress injuries in these athletes. Methods: Using the player injury database maintained by the NBA Players’ Association, all bony stress injuries from 1992 to May 2016 were identified. Those not involving the lower extremity were excluded from the study. Stress fractures and stress reactions were grouped together. Number of games missed due to the injury as well as player statistics including points per game (ppg), assists per game (apg), steals per game (spg), and blocks per game (bpg) were collected from two years prior to the injury to two years after the injury. Results: 76 lower extremity bony stress injuries were identified involving 75 different NBA players with an average player age of 25.4 ± 4.1 years. 55.3% (42/76) involved the foot, 21.1% (16/76) involved the ankle or fibula, 17.1% (13/76) involved the tibia, and 6.6% (5/76) involved either the knee or patella. The majority of injuries occurred in season 82.9% (63/76) with half of the injuries occurring within the first 6 weeks of the season. 38.2% (29/76) of these injuries were managed surgically. An average of 25.1 ± 21.3 games were missed. 19.7% (15/76) of patients who sustained a stress fracture also had a subsequent injury. 29.2% (21/76) of players were not able to return to professional basketball after the season in which the injury was sustained; however, those who were able to return to the same level of play did not see a significant change in performance as measured by ppg, apg, spg, or bpg when comparing the season prior to the injury and either one or two years after the injury. Stress injuries to the foot carried the worst prognosis, 57.1% (12/21) of those unable to return to professional basketball sustained such an injury. Conclusion: While not extremely common in NBA players, lower extremity bony stress injuries may be career-ending. However, if they are able to return to the NBA following this injury, then their level of play should return to their pre-injury level.
Single‐sensor maximum power point tracking algorithms (2013)

Single‐sensor maximum power point tracking algorithms for photovoltaic systems are presented. The algorithms have the features, characteristics and advantages of the widely used incremental conductance (INC) algorithm. However; unlike the INC algorithm which requires two sensors (the voltage sensor and the current sensor), the single‐sensor algorithms are more desirable because they require only one sensor: the voltage sensor. The algorithms operate by maximising power at the DC–DC converter output, instead of the input.
Image-guided phased array system for ultrasound thermotherapy (2002)

An image-guided ultrasonic phased array system for non-invasive tissue ablation is described. Image guidance is provided by processing beamformed RF-data from a commercially available scanner. Two dimensional estimates of tissue temperature are obtained in real-time by implementing a high-speed displacement tracking algorithm. Experimental results validate our approach for image guidance in which the therapy array is initially driven at low (non-destructive) intensity sufficient to cause a small change in temperature at the focus. Two-dimensional non-invasive temperature data is then used to localize and assess the quality of the focus. If the extent and location of the focal spot are consistent with expected values, a high-intensity pulse capable of causing tissue ablation is delivered. Preliminary in-vitro beef muscle experiments are reported, showing successful visualization of the location and quality of the HIFU focus followed by an ablative pulse. Dissection revealed lesion formation (/spl sim/2 mm dia., 12 mm long, 30 mm deep within the tissue) at the expected location.
Improved Low Temperature Performance of Graphite/Li Cells Using Isoxazole as a Novel Cosolvent in Electrolytes (2021)

An investigation of novel electrolyte formulations to improve low temperature performance of Li/graphite half cells has been conducted. A novel electrolyte co-solvent, isoxazole (IZ), has been investigated in electrolyte systems composed of lithium difluoro(oxalato)borate (LiDFOB) in fluoroethylene carbonate (FEC) and LiDFOB in ethylene carbonate (EC). Cells containing 1 M LiDFOB FEC: IZ electrolyte have a significant improvement in capacity retention and reversible capacity at −10 °C. Ex-situ surface analysis of the cycled electrodes suggests that reduction of LiDFOB results in an oxalate rich solid electrolyte interphase (SEI). Addition of FEC, results in improved stability of the anode SEI preventing further decomposition of isoxazole solvent and improving cycling performance.
Pathogenesis of Diabetic Nephropathy: Biochemical and Functional Alterations of Glomerular Basement Membrane and Mesangium (2001)

In patients with diabetic nephropathy (DN), the composition of the mesangium and glomerular basement membrane is changed. Accumulation of extracellular matrix proteins such as collagens, laminin, fibronectin and decreased expression of heparan sulphate proteoglycens (HSPG) are amongst other prominent characteristics that can be observed in DN. These changes are likely to be a result of a complex interplay of different factors like hyperglycaemia, the local production of angiotensin II and transforming growth factor-β. HSPG expression may directly contribute to mesangial expansion. In this chapter biochemical and functional alteration of the glomerular basement membrane and mesangium are discussed with emphasis on HSPG.
Acoustic Tweezing Cytometry Induces Rapid Initiation of Human Embryonic Stem Cell Differentiation (2018)

Mechanical forces play critical roles in influencing human embryonic stem cell (hESC) fate. However, it remains largely uncharacterized how local mechanical forces influence hESC behavior in vitro. Here, we used an ultrasound (US) technique, acoustic tweezing cytometry (ATC), to apply targeted cyclic subcellular forces to hESCs via integrin-bound microbubbles (MBs). We found that ATC-mediated cyclic forces applied for 30 min to hESCs near the edge of a colony induced immediate global responses throughout the colony, suggesting the importance of cell-cell connection in the mechanoresponsiveness of hESCs to ATC-applied forces. ATC application generated increased contractile force, enhanced calcium activity, as well as decreased expression of pluripotency transcription factors Oct4 and Nanog, leading to rapid initiation of hESC differentiation and characteristic epithelial-mesenchymal transition (EMT) events that depend on focal adhesion kinase (FAK) activation and cytoskeleton (CSK) tension. These results reveal a unique, rapid mechanoresponsiveness and community behavior of hESCs to integrin-targeted cyclic forces.
Dual-Pumped Degenerate Optical Parametric Oscillator in a Silicon Nitride Microresonator (2016)

We demonstrate frequency-degenerate optical parametric oscillation via four-wave mixing using dual pumps in a silicon-nitride microresonator. The system offers potential for realization of coherent optical computing and all-optical quantum random number generation.
A Survey on Bounding Volume Hierarchies for Ray Tracing (2021)

Abstract Ray tracing is an inherent part of photorealistic image synthesis algorithms. The problem of ray tracing is to find the nearest intersection with a given ray and scene. Although this geometric operation is relatively simple, in practice, we have to evaluate billions of such operations as the scene consists of millions of primitives, and the image synthesis algorithms require a high number of samples to provide a plausible result. Thus, scene primitives are commonly arranged in spatial data structures to accelerate the search. In the last two decades, the bounding volume hierarchy (BVH) has become the de facto standard acceleration data structure for ray tracing‐based rendering algorithms in offline and recently also in real‐time applications. In this report, we review the basic principles of bounding volume hierarchies as well as advanced state of the art methods with a focus on the construction and traversal. Furthermore, we discuss industrial frameworks, specialized hardware architectures, other applications of bounding volume hierarchies, best practices, and related open problems.
The Mechanism and Substrate Specificity of the NADPH:Flavin Oxidoreductase from Escherichia coli (1995)

The NAD(P)H:flavin oxidoreductase from Escherichia coli, Fre, is a monomer of 26.2 kDa that catalyzes the reduction of free flavins by NADPh or NADH. Overexpression in E. coli now allows the preparation of large amounts of pure protein. Structural requirements for recognition of flavins as substrates and not as cofactors were studied by steady-state kinetics with a variety of flavin analogs. The entire isoalloxazine ring was found to be the essential part of the flavin molecule for interaction with the polypeptide chain. Methyl groups at C-7 and C-8 of the isoalloxazine ring and the N-3 of riboflavin also play an important role in that interaction, whereas the ribityl chain of the riboflavin is not required for binding to the protein. On the other hand, the presence of the 2'-OH of the ribityl chain stimulates the NADPH-dependent reaction significantly. Moreover, a study of competitive inhibitors for both substrates demonstrated that Fre follows a sequential ordered mechanism in which NADPH binds first followed by riboflavin. Lumichrome, a very good inhibitor of Fre, may be used to inhibit flavin reductase in E. coli growing cells. As a consequence, it can enhance the antiproliferative effect of hydroxyurea, a cell-specific ribonucleotide reductase inactivator.
III-Nitride Materials and Devices for Power Electronics (2013)

Group III-Nitride based devices are expected to compete and possibly outperform state of the art silicon carbide based devices for power electronic applications. GaN, AlGaN, AlInGaN and other III-Nitride compound materials offer a very high breakdown field. Devices based on III-Nitride compounds have very high electron density and mobility in the device channel, leading to record low device on-resistance, high temperature stability and low gate capacitance enabling high switching speed and low switching loss. In order to enable III-Nitride based devices for power applications continuous efforts are underway in the area of material growth, novel power device concepts, designs, modeling and simulations.
Nucleotide sequence of the metL gene of Escherichia coli. Its product, the bifunctional aspartokinase ii-homoserine dehydrogenase II, and the bifunctional product of the thrA gene, aspartokinase I-homoserine dehydrogenase I, derive from a common ancestor. (1983)

The total nucleotide sequence (2427 nucleotides) of the metL gene ofEscherichia coli coding for the dimeric aspartokinase Il-homoserine dehydrogenase II (809 amino acid residues, M, = 88,726jchain) is presented.Comparison of the translated sequence with that of aspartokinase I-homoserine dehydrogenase I, the product of the thrA gene of the same organism, shows that the two proteins are highly homologous and that they derive from a common ancestor.
Contribution of altered signal transduction associated to glutamate receptors in brain to the neurological alterations of hepatic encephalopathy (2006)

Patients with liver disease may present hepatic encephalopathy (HE), a complex neuropsychiatric syndrome covering a wide range of neurological alterations, including cognitive and motor disturbances. HE reduces the quality of life of the patients and is associated with poor prognosis. In the worse cases HE may lead to coma or death. The mechanisms leading to HE which are not well known are being studied using animal models. The neurological alterations in HE are a consequence of impaired cerebral function mainly due to alterations in neurotransmission. We review here some studies indicating that alterations in neurotransmission associated to different types of glutamate receptors are responsible for some of the cognitive and motor alterations present in HE. These studies show that the function of the signal transduction pathway glutamate-nitric oxide-cGMP associated to the NMDA type of glutamate receptors is impaired in brain in vivo in HE animal models as well as in brain of patients died of HE. Activation of NMDA receptors in brain activates this pathway and increases cGMP. In animal models of HE this increase in cGMP induced by activation of NMDA receptors is reduced, which is responsible for the impairment in learning ability in these animal models. Increasing cGMP by pharmacological means restores learning ability in rats with HE and may be a new therapeutic approach to improve cognitive function in patients with HE. However, it is necessary to previously assess the possible secondary effects. Patients with HE may present psychomotor slowing, hypokinesia and bradykinesia. Animal models of HE also show hypolocomotion. It has been shown in rats with HE that hypolocomotion is due to excessive activation of metabotropic glutamate receptors (mGluRs) in substantia nigra pars reticulata. Blocking mGluR1 in this brain area normalizes motor activity in the rats, suggesting that a similar treatment for patients with HE could be useful to treat psychomotor slowing and hypokinesia. However, the possible secondary effects of mGluR1 antagonists should be previously evaluated. These studies are setting the basis for designing therapeutic procedures to specifically treat the individual neurological alterations in patients with HE.