gebhart/patrepeval huggingface dataset:
Diagnosis and management of glutaric aciduria type I – revised recommendations (2011)

Glutaric aciduria type I (synonym, glutaric acidemia type I) is a rare organic aciduria. Untreated patients characteristically develop dystonia during infancy resulting in a high morbidity and mortality. The neuropathological correlate is striatal injury which results from encephalopathic crises precipitated by infectious diseases, immunizations and surgery during a finite period of brain development, or develops insidiously without clinically apparent crises. Glutaric aciduria type I is caused by inherited deficiency of glutaryl-CoA dehydrogenase which is involved in the catabolic pathways of L-lysine, L-hydroxylysine and L-tryptophan. This defect gives rise to elevated glutaric acid, 3-hydroxyglutaric acid, glutaconic acid, and glutarylcarnitine which can be detected by gas chromatography/mass spectrometry (organic acids) or tandem mass spectrometry (acylcarnitines). Glutaric aciduria type I is included in the panel of diseases that are identified by expanded newborn screening in some countries. It has been shown that in the majority of neonatally diagnosed patients striatal injury can be prevented by combined metabolic treatment. Metabolic treatment that includes a low lysine diet, carnitine supplementation and intensified emergency treatment during acute episodes of intercurrent illness should be introduced and monitored by an experienced interdisciplinary team. However, initiation of treatment after the onset of symptoms is generally not effective in preventing permanent damage. Secondary dystonia is often difficult to treat, and the efficacy of available drugs cannot be predicted precisely in individual patients. The major aim of this revision is to re-evaluate the previous diagnostic and therapeutic recommendations for patients with this disease and incorporate new research findings into the guideline.
The Effect That Mutations in the Conserved Capsular Polysaccharide Biosynthesis Genes<i>cpsA, cpsB,</i>and<i>cpsD</i>Have on Virulence of<i>Streptococcus pneumoniae</i> (2004)

Four genes, cpsA-cpsD, at the 5' end of the capsular polysaccharide (CPS) biosynthesis locus are conserved in nearly all of the 90 known serotypes of Streptococcus pneumoniae. In the present study, the impact that mutations in cpsA, cpsB, and cpsD have on CPS production and on virulence in mice infected via systemic and intranasal routes was investigated. Strains exhibiting rough colony morphologies (in which either the cpsB or cpsD gene had been deleted) were avirulent, but a smooth, partially encapsulated strain (in which the cpsA gene had been deleted) was as virulent as the wild-type strain. Interestingly, mucoid strains containing mutations affecting the [YGX](3)-repeat domain of CpsD were unable to cause bacteremia after intranasal challenge of CD1 mice, even though such strains were capable of killing BALB/c mice after intraperitoneal challenge. In our model, the ability of S. pneumoniae to regulate, via CpsD phosphorylation, CPS production was required for its transition from the lung to the bloodstream.
The effects of CGS 16949A, an aromatase inhibitor on adrenal mineralocorticoid biosynthesis. (1990)

The family of cytochrome P450 enzymes that mediates steroid hydroxylations are distinct but structurally related proteins. Inhibitors of these steroidogenic steps generally exhibit only relative and dose-related specificity. We evaluated an imidazole, cytochrome P450-related inhibitor, CGS 16949A, in postmenopausal patients with metastatic breast cancer. While a relatively specific aromatase inhibitor at daily dosages of 1-2 mg, CGS 16949A significantly blunted cortisol responses to ACTH at a dose of 16 mg daily. To further evaluate other inhibitory effects of this drug, we determined blood levels of aldosterone (ALDO) and 18-hydroxycorticosterone and their respective urinary metabolites, tetrahydroaldosterone and tetrahydro-18-hydroxy-11-dehydrocorticosterone in 16 postmenopausal women receiving CGS 16949A. At a dose of 16 mg/day, CGS 16949A produced significant (P less than 0.001) suppression of both basal and ACTH-stimulated ALDO production. This was accompanied by a significant rise in the blood 18-hydroxycorticosterone/ALDO ratio (11.4 +/- 0.19; normal, less than 2; P less than 0.001), consistent with a corticosterone methyloxidase type II inhibition. A similar significant elevation (7.5 +/- 1.2; normal, less than 5; P less than 0.001) in the urinary tetrahydro-18-hydroxy-11-dehydrocorticosterone/tetrahydroaldosterone ratio was also observed. These results suggest that CGS 16949A is a potent inhibitor of the corticosterone methyloxidase type II enzyme at a dose of 16 mg daily. At doses of 1-2 mg daily, CGS 16949A blocks aromatase without altering basal aldosterone production and, thus, exhibits dose-related specificity.
Approaches and principles of fall detection for elderly and patient (2008)

Fall detection for elderly and patient has been an active research topic due to that the healthcare industry has a big demand for products and technology of fall detection. This paper gives a survey of fall detection for elderly and patient, focusing on identifying approaches and principles of the existing fall detection methods. To properly build the classification tree of the methods of fall detection we first study the characteristics of fall. Then according to what sensors and how sensors are used we first divide the methods of fall detection into three approaches: wearable device, ambience device, and camera-based. Further we divide each approach into two to three classes according to the used principles. For each class of algorithm we analyze their merits and demerits. We also give comments on how we can improve some algorithms.
Computational Evidence for the Role of <i>Arabidopsis thaliana</i> UVR8 as UV–B Photoreceptor and Identification of Its Chromophore Amino Acids (2011)

A homology model of the Arabidopsis thaliana UV resistance locus 8 (UVR8) protein is presented herein, showing a seven-bladed β-propeller conformation similar to the globular structure of RCC1. The UVR8 amino acid sequence contains a very high amount of conserved tryptophans, and the homology model shows that seven of these tryptophans cluster at the 'top surface’ of the UVR8 protein where they are intermixed with positive residues (mainly arginines) and a couple of tyrosines. Quantum chemical calculations of excitation spectra of both a large cluster model involving all twelve above-mentioned residues and smaller fragments thereof reveal that absorption maxima appearing in the 280–300 nm range for the full cluster result from interactions between the central tryptophans and surrounding arginines. This observation coincides with the published experimentally measured action spectrum for the UVR8-dependent UV–B stimulation of HY5 transcription in mature A. thaliana leaf tissue. In total these findings suggest that UVR8 has in fact in itself the ability to be an ultraviolet-B photoreceptor in plants.
Role of the PKA‐Regulated Transcription Factor CREB in Development and Tumorigenesis of Endocrine Tissues (2002)

The cAMP pathway plays a major role in the development of endocrine tissues and various molecular defects of key components of this pathway (G protein, receptors, PKA, etc.) have been observed in endocrine tumors. The ubiquitous transcription factor CREB (cAMP-response element binding protein) binds to the cAMP response element (CRE) and stimulates transcription after phosphorylation on Ser(133) by PKA. The CREB family of transcription factors contains three members: CREB, CREM, and ATF-1. Targeted expression of dominant-negative mutants of CREB in transgenic mice leads to somatotrophs or thyroid hypoplasia. GH-secreting adenomas are benign secreting tumors expressing an activated mutant G alpha s protein (Gsp) in about 40% of cases. In GH-secreting adenomas CREB is always expressed and often highly phosphorylated. The CREM isoform ICER is stimulated by cAMP, and its expression is increased in Gsp-harboring tumors. After transfection in pituitary somatotroph cells, activating mutations of Gs protein (Gsp) and overexpression of wild-type G alpha S stimulate transcription of various CRE-containing promoters via CREB in a Ser(133)-specific-dependent manner. Activation of the cAMP pathway by ACTH is required for adrenal cortex (AdCx) maintenance and steroidogenesis. CREB is expressed in normal AdCx. Alterations of CRE binding proteins with loss of CREB expression and compensatory overexpression of CREMtau is observed in the human adrenocortical cancer cell line H295R. Similar alterations are found at the protein level in human malignant adrenocortical tumors. In conclusion, the CREB family of transcription factors plays an important role in the development, differentiation, and proliferation of endocrine tissues. Various alterations of the CREB family of transcription factors can be observed in endocrine tumors.
Glutamine supplementation (2011)

Intravenous glutamine supplementation is standard care when parenteral nutrition is given for critical illness. There are data of a reduced mortality when glutamine supplementation is given. In addition, standard commercial products for parenteral nutrition do not contain any glutamine due to glutamine instability in aqueous solutions. For the majority of critical ill patients who are fed enterally, the available evidence is insufficient to recommend glutamine supplementation. Standard formulation of enteral nutrition contains some glutamine: 2-4 g/L. However, this dose is insufficient to normalize glutamine plasma concentration.Plasma concentration of glutamine is low in many patients with critical illness and a low level is an independent risk factor for mortality. A low plasma glutamine concentration is the best indicator of glutamine depletion. Data are emerging about how the endogenous production of glutamine is regulated. We know that skeletal muscle is the major producer of glutamine and that a part of the profound depletion of skeletal muscle seen in critical illness is a reflection of the need to produce glutamine.Glutamine is utilized in rapidly dividing cells in the splanchnic area. Quantitatively most glutamine is oxidized, but the availability of glutamine in surplus is important for the de novo synthesis of nucleotides and necessary for cell division and protein synthesis. More knowledge about the regulation of the endogenous production of glutamine is needed to outline better guidelines for glutamine supplementation in the future.
Efficient Discovery of Loop Nests in Execution Traces (2010)

Execution and communication traces are central to performance modeling and analysis. Since the traces can be very long, meaningful compression and extraction of representative behavior is important. Commonly used compression procedures identify repeating patterns in sections of the input string and replace each instance with a representative symbol. This can prevent the identification of long repeating sequences corresponding to outer loops in a trace. This paper introduces and analyzes a framework for identifying the maximal loop nest from a trace. The discovery of loop nests makes construction of compressed representative traces straightforward. The paper also introduces a greedy algorithm for fast ``near optimal'' loop nest discovery with well defined bounds. Results of compressing MPI communication traces of NAS parallel benchmarks show that both algorithms identified the basic loop structures correctly. The greedy algorithm was also very efficient with an average processing time of 16.5 seconds for an average trace length of 71695 MPI events.
Picking winners using statistics (2000)

The Swinburne Sports Statistics web site www.swin.edu.au sport regularly has predictions for major sporting events, H4lich are also featured in the national media. In addition to our weekly computer tips for Australian rules football, predictions for tennis grand slam tournaments and the soccer and cricket world cups have been featured. We also provide estimates for the media on the chances of cet1ain sporting achievements, such as a golfer scoring less than 60 in a round. Some of the statistical methods used and results will be discussed.
Comparison of cobalt and titanium silicides for SALICIDE process and shallow junction formation (2003)

A comparison of TiSi/sub 2/ and CoSi/sub 2/ for the SALICIDE (self-aligned silicide) process is presented. Both TiSi/sub 2/ and CoSi/sub 2/ are formed by RTA in nitrogen. The comparison is based on the formation kinetics, film properties, process compatibilities, and electrical properties. The results are summarized in table form. Co silicide is found to be a better candidate for use in SALICIDE process for submicron devices because it has a less severe lateral gate-S/D encroachment problem, less sensitivity to oxygen, higher resistivity to dry/wet etch, less film stress, better sheet resistance control, less junction leakage, the capability to form low-resistance polycide, and shallow junctions. However, substrate cleaning must ensure no SiO/sub 2/ on Si surfaces that are to be converted to CoSi/sub 2/.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Middle Ear Overpressure Treatment of Endolymphatic Hydrops in Guinea Pigs (1997)

Guinea pigs placed outside or inside a pressure chamber and exposed to 49.2 cm H2O overpressure continuously for 24 h immediately after blockage of the endolymphatic duct showed no significant difference in the magnitude of endolymphatic hydrops when compared to controls, although there was a slight indication of a volume decrease in the outside-treatment group and an increase in the inside-treatment group. A pressure increase of 49.2 cm H2O in the external auditory canal for 1 h twice a day for 2 weeks outside the chamber significantly inhibited the development of hydrops. The latter result supports the merit of pressure application through the external auditory canal as a treatment for Meniere's disease.
Treatment of lower urinary tract infection caused by multidrug-resistant extended-spectrum- -lactamase-producing Escherichia coli with amoxicillin/clavulanate: case report and characterization of the isolate (2006)

47: 2385–92. 3. Poirel L,WeldhagenGF, Naas T et al. GES-2, a class A b-lactamase from Pseudomonas aeruginosa with increased hydrolysis of imipenem. Antimicrob Agents Chemother 2001; 45: 2598–603. 4. Castanheira M, Mendes RE, Walsh TR et al. Emergence of the extended-spectrum b-lactamase GES-1 in a Pseudomonas aeruginosa strain from Brazil: report from the SENTRY antimicrobial surveillance program. Antimicrob Agents Chemother 2004; 48: 2344–5. 5. Mavroidi A, Tzelepi E, Tsakris A et al. An integron-associated b-lactamase (IBC-2) from Pseudomonas aeruginosa is a variant of the extended-spectrum b-lactamase IBC-1. J Antimicrob Chemother 2001; 48: 627–30. 6. Poirel L, Brinas L, Fortineau N et al. Integron-encoded GES-type extended-spectrumb-lactamasewith increasedactivity towardaztreonam in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2005; 49: 3593–7.
Validation of 3-D curved objects: CAD model and fabricated workpiece (1994)

This paper proposes a new method to describe and identify a 3-D curved object for the purpose of validating a fabricated object to the design specification. Curved 3-D objects are, in general, difficult to represent and identify because they lack distinct properties such as edges, planes, or cylindrical surfaces which are the building blocks in representing objects. In this paper, the authors propose to use principal axes of a 3-D object to establish a reference for the representation. A method of obtaining an inertia matrix from a 3-D range image is developed. The unique set of principal axes is obtained from the inertia matrix of an object with an arbitrary 3-D position and orientation, and the object can be described uniquely on these principal axes. On the principal axes, an object is described by a set of features describing the shape of the object such as spine, section size, section orientation, and section contraction. The features are used for comparing two objects for the validation purpose. The authors also propose a direct measure of similarity between two objects as a mean-squared difference of radii. As an experiment, two 3-D object models are designed through a CAD package, and fabricated objects are compared with the designed models for validation purposes.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Phosphorylation-dependent binding of the chemotaxis signal molecule CheY to its phosphatase, CheZ (1994)

Bacterial chemotaxis is accomplished by regulating the direction of flagellar rotation. The primary target of the control appears to be CheY, a diffusible clockwise-signal molecule which interacts with the switch at the base of the flagellar motor and causes clockwise rotation. The regulatory mechanism appears to be phosphorylation/dephosphorylation of CheY. Here we demonstrate that CheZ, which accelerates the dephosphorylation of CheY, binds to CheY (immobilized on CNBr-activated Sepharose beads), that the binding to phosphorylated CheY is higher by over 2 orders of magnitude than the binding to nonphosphorylated CheY, and that the binding to both the phosphorylated and nonphosphorylated forms of CheY is significantly higher in the presence of Mg2+. We also show that the mutant proteins CheY13DK, CheY57DE, and CheY109KR bind CheZ to the same extent as wild-type CheY. The extent of the binding of these mutant proteins was not, however, increased in the presence of acetyl phosphate, the phosphorylating agent. The results indicate that neither a conformation which has a clockwise-causing activity in vivo nor phosphorylation is sufficient, alone, for maximal binding of CheZ to CheY and that Mg2+ is required for the binding of these proteins as well as for the phosphorylation and dephosphorylation of CheY.
A rapid, sensitive, reproducible and cost-effective method for mutation profiling of colon cancer and metastatic lymph nodes (2010)

An increasing number of studies show that genetic markers can aid in refining prognostic information and predicting the benefit from systemic therapy. Our goal was to develop a high throughput, cost-effective and simple methodology for the detection of clinically relevant hot spot mutations in colon cancer. The Maldi-Tof mass spectrometry platform and OncoCarta panel from Sequenom were used to profile 239 colon cancers and 39 metastatic lymph nodes from NSABP clinical trial C-07 utilizing routinely processed FFPET (formalin-fixed paraffin-embedded tissue). Among the 238 common hot-spot cancer mutations in 19 genes interrogated by the OncoCarta panel, mutations were detected in 7 different genes at 26 different nucleotide positions in our colon cancer samples. Twenty-four assays that detected mutations in more than 1% of the samples were reconfigured into a new multiplexed panel, termed here as ColoCarta. Mutation profiling was repeated on 32 mutant samples using ColoCarta and the results were identical to results with OncoCarta, demonstrating that this methodology was reproducible. Further evidence demonstrating the validity of the data was the fact that the mutation frequencies of the most common colon cancer mutations were similar to the COSMIC (Catalog of Somatic Mutations in Cancer) database. The frequencies were 43.5% for KRAS, 20.1% for PIK3CA, and 12.1% for BRAF. In addition, infrequent mutations in NRAS, AKT1, ABL1, and MET were detected. Mutation profiling of metastatic lymph nodes and their corresponding primary tumors showed that they were 89.7% concordant. All mutations found in the lymph nodes were also found in the corresponding primary tumors, but in 4 cases a mutation was present in the primary tumor only. This study describes a high throughput technology that can be used to interrogate DNAs isolated from routinely processed FFPET and identifies the specific mutations that are common to colon cancer. The development of this technology and the ColoCarta panel may provide a mechanism for rapid screening of mutations in clinically relevant genes like KRAS, PIK3CA, and BRAF. 
ClinicalTrials.gov: NSABP C-07: NC4931
Vehicle-Bus Interface with GMLAN for Data Collection. (2003)

Within a few years, nearly every vehicle that General Motors (GM) manufactures will have a microcontroller network known as GMLAN. A few GM vehicles already have the GMLAN network, and more vehicles with GMLAN will appear each year. GMLAN uses the Bosch-designed CAN (Controller Area Network) protocol, and it links all of a vehicle’s various processors or nodes to form an in-vehicle data network. CAN uses a Non-Return-to-Zero protocol, NRZ-5, with bit stuffing, and the network implements Carrier Sense Multiple Access with Collision Resolution (CSMA/CR). GMLAN actually includes two linked CAN buses: a high-speed dual-wire CAN for high-speed nodes and a lower-speed single-wire CAN for other nodes. The primary purpose of the GMLAN network is to improve reliability while simultaneously lowering cost by reducing the numbers of wires, connections, and special-purpose circuits in a vehicle. The GMLAN network also promotes synergism among the vehicle nodes to provide vehicle features that would simply not be feasible without the network. We have developed a Vehicle-Bus Interface (VBI) that allows us to collect test data directly from a vehicle’s nodes via the GMLAN network with a GM Standard Thermal Instrument (STI). The VBI facilitates vehicle testing by greatly reducing the need for external sensors and transducers. 1
HM74a Agonists: Will they be the New Generation of Nicotinic Acid? (2009)

The discovery of HM74a as a high affinity receptor for nicotinic acid has opened up new areas for investigation. Since its discovery, several new chemical entities have been reported as HM74a agonists. One of them, MK-0354, has been tested in phase II studies, but despite significant decreases in Free Fatty Acid levels with absence of flushing events in clinical studies, it failed to demonstrate effects on LDL-Cholesterol, Triglycerides and HDL-Cholesterol. These surprising results lead to questions about the reality of HM74a as the unique receptor responsible for the lipid modulating effects of nicotinic acid. This review summarizes these recent developments, and the novel HM74a antagonist structures recently published.
Controllable Atomic Scale Patterning of Freestanding Monolayer Graphene at Elevated Temperature (2013)

We show that by operating a scanning transmission electron microscope (STEM) with a 0.1 nm 300 kV electron beam, one can sculpt free-standing monolayer graphene with close-to-atomic precision at 600 °C. The same electron beam that is used for destructive sculpting can be used to image the sculpted monolayer graphene nondestructively. For imaging, a scanning dwell time is used that is about 1000 times shorter than for the sculpting. This approach allows for instantaneous switching between sculpting and imaging and thus fine-tuning the shape of the sculpted lattice. Furthermore, the sculpting process can be automated using a script. In this way, free-standing monolayer graphene can be controllably sculpted into patterns that are predefined in position, size, and orientation while maintaining defect-free crystallinity of the adjacent lattice. The sculpting and imaging processes can be fully computer-controlled to fabricate complex assemblies of ribbons or other shapes.