gebhart/patrepeval huggingface dataset:
Query-Dependent Banding (QDB) for Faster RNA Similarity Searches (2005)

When searching sequence databases for RNAs, it is desirable to score both primary sequence and RNA secondary structure similarity.Covariance models (CMs) are probabilistic models well-suited for RNA similarity search applications.However, the computational complexity of CM dynamic programming alignment algorithms has limited their practical application.Here we describe an acceleration method called query-dependent banding (QDB), which uses the probabilistic query CM to precalculate regions of the dynamic programming lattice that have negligible probability, independently of the target database.We have implemented QDB in the freely available Infernal software package.QDB reduces the average case time complexity of CM alignment from LN 2.4 to LN 1.3 for a query RNA of N residues and a target database of L residues, resulting in a 4-fold speedup for typical RNA queries.Combined with other improvements to Infernal, including informative mixture Dirichlet priors on model parameters, benchmarks also show increased sensitivity and specificity resulting from improved parameterization.
Genetic variation of seed dormancy in tetraploid wheat species (1997)

In western Canada, durum wheat cultiv vars (Triticum turgidum L. Var durum) have low to moderate levels of seed dormancy and are susceptible to pre-harvest sprouting .The objective of this study was to assess the level of seed dormancy and the length of afterripening in diverse tetraploid wheat species.The plants were grown under field conditions, spikes harvested at Zadok's Growth Stage 92 (ZGS92), dried for one week and stored in a freezer at -20 "C .In 1995 and 1996, length of afterripening was assessed in 17 durum cultivars and three common hexaploid wheats over a period of seven weeks .Most durum cultivars showed little or no dormancy at ZGS92 .Kyle was the only cultivar that exhibited some seed dormancy.On average, all cultivars but the hexaploid line RL4137 lost dormancy in a markedly similar pattern.Four species , Triticum turgidurn, T. turanicum, T. carthlicum an d T. polonicum obtained from the USDA wheat collection were screened for seed dormancy over a two year period .Averaged over years, accessions ranged from 2% to 100% in germination .The accessions in this experiment can be grouped into four classes: nondormant, slightly dormant, moderately dormant and highly dormant.With the exception o f T. turanicum, the tetraploid species contained highly dormant genotypes .The 10 most dormant wheat accessions were evaluated for length of afterripening.A number of accessions with higher levels of seed dormancy than the durum cultivar Kyle was identified.
Pattern discrimination software for uncertainty reduction in neonatal cardiovascular risk assessment (2002)

Genetic risk is a primary contributing factor to the predisposition of a newborn child to elevated blood pressure later in life. To determine if there is a correlation between potential genetic risk as established by family history and measured physiological variables in the neonate, the systolic and diastolic blood pressures and heart rates of 150 newborn babies were automatically monitored at about 30-minute intervals for 48 hours with a Nippon Colin device, starting early after birth. Based on questionnaires given to the parents, the neonates were assigned to a group of either a negative or positive family history of high blood pressure. Circadian characteristics and descriptive statistics for the 3 circulatory variables were used for classification by a "monotest", an all-subsets variable selection technique for biomedical discriminant analysis. For a particular combination of variables, the monotest performs as many separate analyses as the number of subjects, each subject's data being compared with those of all others. When the circadian amplitudes of systolic blood pressure and heart rate and the circadian range of heart rate were used as a combined classifier, the monotest yielded a 70% classification equivalent to prior criteria, the latter being based on the family history of high blood pressure. The combined use of time-specified sampling hardware with signal processing and discriminant analysis software allows one to recognize parameters of blood pressure circadian variability as a source of information for neonatal classification according to cardiovascular risk.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Coordinating collective locomotion in an amorphous modular robot (2010)

Modular robots can potentially assemble into a wide range of configurations to locomote in different environments. However, designing locomotion strategies for each configuration is often tedious and has generally relied on a priori known connection geometry. Here we present a framework for 2D modular robots made of square modules assembled with arbitrary geometry, which achieve collective and directed locomotion with no centralized controller. Individual modules communicate locally and provably achieve consensus in coordinating movement in a common travel direction. In experiments with simulations and hardware prototypes, we show that robots achieve effective locomotion, irrespective of the number of modules and their connectivity which can be highly asymmetric.
Electrically pumped Ge Laser at room temperature (2007)

The stimulated emission from (110) Ge was observed in the metal-insulator-semiconductor (MIS) laser diode with a simple Fabry-Perot cavity by current injection at room temperature. The lasing characteristics consist of (1) sudden increase of efficiency in the light-out current-in curve, (2) the transverse electrical mode polarization, (3) the strong directivity of the far field pattern, (4) the narrow line width in the emission spectra above the threshold, and (5) the population inversion confirmed by fitting the spontaneous emission spectrum near the threshold current. The lasing wavelength is suitable for Si photonics due to the emission energy lower the Si bandgap.
Th17 Cells in Type 1 Diabetes: Role in the Pathogenesis and Regulation by Gut Microbiome (2015)

Type 1 diabetes (T1D) is an autoimmune disease which is characterized by progressive destruction of insulin producing pancreatic islet β cells. The risk of developing T1D is determined by both genetic and environmental factors. A growing body of evidence supports an important role of T helper type 17 (Th17) cells along with impaired T regulatory (Treg) cells in the development of T1D in animal models and humans. Alteration of gut microbiota has been implicated to be responsible for the imbalance between Th17 and Treg cells. However, there is controversy concerning a pathogenic versus protective role of Th17 cells in murine models of diabetes in the context of influence of gut microbiota. In this review we will summarize current knowledge about Th17 cells and gut microbiota involved in T1D and propose Th17 targeted therapy in children with islet autoimmunity to prevent progression to overt diabetes.
N-Acetylglucosamine Induces White to Opaque Switching, a Mating Prerequisite in Candida albicans (2010)

To mate, the fungal pathogen Candida albicans must undergo homozygosis at the mating-type locus and then switch from the white to opaque phenotype. Paradoxically, opaque cells were found to be unstable at physiological temperature, suggesting that mating had little chance of occurring in the host, the main niche of C. albicans. Recently, however, it was demonstrated that high levels of CO 2 , equivalent to those found in the host gastrointestinal tract and select tissues, induced the white to opaque switch at physiological temperature, providing a possible resolution to the paradox. Here, we demonstrate that a second signal, N-acetylglucosamine (GlcNAc), a monosaccharide produced primarily by gastrointestinal tract bacteria, also serves as a potent inducer of white to opaque switching and functions primarily through the Ras1/cAMP pathway and phosphorylated Wor1, the gene product of the master switch locus. Our results therefore suggest that signals produced by bacterial co-members of the gastrointestinal tract microbiota regulate switching and therefore mating of C. albicans.
Synthesis of Amino- and Nitro-Substituted Heterocycles as Insensitive Energetic Materials (2001)

In this paper we will describe the synthesis of several amino- and nitro-substituted heterocycles, examples from a continuing research project targeted at the synthesis of new, insensitive energetic materials that possess at least 80% the power of HMX (28% more power than TATB). Recently we reported the synthesis and scale-up of the insensitive energetic material, 2,6-diamino-3,5-dinitropyrazine-1-oxide (LLM-105). The energy content (81% the power of HMX) and thermal stability of LLM-105 make it a viable candidate material for insensitive boosters and deep oil perforation. We will report on recent synthetic improvements and several performance and safety tests performed on LLM-105, including a 1 in. cylinder shot and plate dent. We will also report on the synthesis and characterization of 4-amino-3,5-dinitropyrazole (LLM-116), an interesting new insensitive energetic material with a measured crystal density of 1.90 g/cc, to our knowledge the highest density yet measured for a five-membered heterocycle containing amino- and nitro-substituents. LLM-116 was synthesized by reacting 3,5-dinitropyrazole with 1,1,1-trimethylhydrazinium iodide (TMHI) in DMSO in the presence of base. The synthesis and characterization of 4-amino-5-nitro-1,2,3-triazole (ANTZ) and 43-dinitro-1,2,3-triazole (DNTZ), first described by Baryshnikov and coworkers, will also be presented along with the synthesis of several new energetic materials derived from ANTZ and DNTZ.
Aging and the Mechanisms Underlying Head and Postural Control During Voluntary Motion (1997)

The quality of sensory information that is necessary for balance and postural stability will depend to a great extent on head stability as the body moves. How older persons coordinate head and body motion for balance during volitional activities is not known. The purposes of this article are to present a basis for understanding the influence of aging on head control during voluntary motion and to discuss some data that demonstrate how elderly people might control head movement to improve gaze and the quality of vestibular inputs. A "top-down" or "head-first" control scheme is proposed as the mechanism that elderly people without disabilities use to maintain head position during self-initiated motion. This type of control ensures that the angular position of the head in space remains relatively constant--through the use of a head-stabilization-in-space (HSS) strategy--regardless of the magnitude or direction of displacements in the body's center of force. The HSS strategy is thought to reduce potential ambiguities in the interpretation of sensory inputs for balance and is derived primarily from a geocentric (orientation to the vertical) frame of reference. Egocentric (orientation of the head with respect to the body) or exocentric (orientation to objects in the environment) frames of reference, however, refine the control of head stabilization. Preliminary research suggests that elderly people use the HSS strategy to control head pitch during difficult balance tasks. These findings, if supported by more definitive studies, may be useful in the treatment of patients with balance disorders. The treatment of patients with balance dysfunction is discussed within the conceptual framework of a "head-first" organization scheme.
Prevention of acquired transient defect in platelet plug formation by infused prostacyclin. (1981)

Cardiopulmonary bypass in baboons produced transient severe platelet dysfunction (bleeding times prolonged to 27.8 +/- 1.4 min compared with 3.9 +/- 0.7 baseline) that was associated with a parallel release of platelet alpha-granule proteins into plasma (platelet factor 4 and beta-thromboglobulin levels of 28.8 +/- 9.3 and 20.0 +/- 1.8 ng/ml, respectively) and their clearance into urine with a reciprocal depletion from circulating platelets. In contrast, platelet-dense granules did not undergo significant release. The bleeding times normalized rapidly following bypass (8.5 +/- 1.4 min at 1 hr). The infusion of prostacyclin (PGI2) into the bubble oxygenator during bypass (40--80 ng/kg/min) prevented the prolongation in bleeding time (p less than 0.01 compared with untreated control values) but did not block the release of alpha-granule proteins. Dosages outside this range were associated with prolonged bleeding times. These results show that transient platelet dysfunction occurring during cardiopulmonary bypass represents activation of platelets independent of alpha or dense granule release and is blocked by potent short-acting inhibition of platelet function using PGI2 infused into the oxygenator apparatus at optimal therapeutic doses.
Audiometric and histological differences between the effects of continuous and impulsive noise exposures (1993)

An experiment was designed to determine if, for equal SPL and power spectrum, the effects on hearing of high-kurtosis noise exposures and a Gaussian noise exposure are different and the extent to which any differences measured in terms of audiometric and histological variables are frequency specific. Three groups of chinchillas with 10 animals/group were exposed for 5 days at 90 dB SPL to one of three types of noise, each with the same power spectrum. The impulsiveness, defined by the kurtosis, and the region of the spectrum from which the impulsive components of the noise were created differed for two of the noises, while the third was a continuous Gaussian noise. The results show that the most impulsive noise produced up to 20 dB greater permanent threshold shift at the high frequencies than did the Gaussian noise exposure. However, these audiometric results were difficult to reconcile with the pattern of sensory cell losses that showed statistically significant larger losses of outer hair cells for the impulsive exposure in the 0.25-kHz region. When the impacts in a high-kurtosis noise were created from the energy in the 1- through 6-kHz region of the spectrum, the audiometric profile of hearing loss was similar to that produced by the Gaussian noise; however, inner hair cell losses were significantly greater in the 4-kHz octave band region of the cochlea.
Preemptive mechanical ventilation based on dynamic physiology in the alveolar microenvironment: Novel considerations of time-dependent properties of the respiratory system (2018)

The acute respiratory distress syndrome (ARDS) remains a serious clinical problem with the current treatment being supportive in the form of mechanical ventilation. However, mechanical ventilation can be a double-edged sword; if set properly, it can significantly reduce ARDS associated mortality but if set improperly it can have unintended consequences causing a secondary ventilator induced lung injury (VILI). The hallmark of ARDS pathology is a heterogeneous lung injury, which predisposes the lung to a secondary VILI. The current standard of care approach is to wait until ARDS is well established and then apply a low tidal volume (LVt) strategy to avoid over-distending the remaining normal lung. However, even with the use of LVt strategy, the mortality of ARDS remains unacceptably high at ~40%. In this review, we analyze the lung pathophysiology associated with ARDS that renders the lung highly vulnerable to a secondary VILI. The current standard of care LVt strategy is critiqued as well as new strategies used in combination with LVt to protect the lung. Using the current understanding of alveolar mechanics (i.e. the dynamic change in alveolar size and shape with tidal ventilation) we provide a rationale for why the current protective ventilation strategies have not further reduced ARDS mortality. New strategies of protective ventilation based on dynamic physiology in the micro-environment (i.e. alveoli and alveolar ducts) are discussed. Current evidence suggests that alveolar inflation and deflation is viscoelastic in nature, with a fast and slow phase in both alveolar recruitment and collapse. Using this knowledge, a ventilation strategy with a prolonged time at inspiration would recruit alveoli and a brief release time at expiration would prevent alveolar collapse, converting heterogeneous to homogeneous lung inflation significantly reducing ARDS incidence and mortality.
Role of the transcription factor HHEX in inner adrenal cortex homeostasis and response to progesterone signaling (2022)

Searchable abstracts of presentations at key conferences in endocrinology ISSN 1470-3947 (print) | ISSN 1479-6848 (online)
Fibre type-specific expression patterns of myosin heavy chain genes in adult torafugu Takifugu rubripes muscles (2009)

Comprehensive in silico studies, based on the total fugu genome database, which was the first to appear in fish, revealed that torafugu Takifugu rubripes contains 20 sarcomeric myosin heavy chain (MYH) genes (MYH genes) (Ikeda et al., 2007). The present study was undertaken to identify MYH genes that would be expressed in adult muscles. In total, seven MYH genes were found by screening cDNA clone libraries constructed from fast, slow and cardiac muscles. Three MYH genes, fast-type MYH(M86-1), slow-type MYH(M8248) and slow/cardiac-type MYH(M880), were cloned exclusively from fast, slow and cardiac muscles, respectively. Northern blot hybridization substantiated their specific expression, with the exception of MYH(M880). In contrast, transcripts of fast-type MYH(M2528-1) and MYH(M1034) were found in both fast and slow muscles as revealed by cDNA clone library and northern blot techniques. This result was supported by in situ hybridization analysis using specific RNA probes, where transcripts of fast-type MYH(M2528-1) were expressed in fast fibres with small diameters as well as in fibres of superficial slow muscle with large diameters adjacent to fast muscle. Transcripts of fast-type MYH(M86-1) were expressed in all fast fibres with different diameters, whereas transcripts of slow-type MYH(M8248) were restricted to fibres with small diameters located in a superficial part of slow muscle. Interestingly, histochemical analyses showed that fast fibres with small diameters and slow fibres with large diameters both contained acid-stable myofibrillar ATPase, suggesting that these fibres have similar functions, possibly in the generation of muscle fibres irrespective of their fibre types.
"Good Enough" to Release: A Probabilistic Assessment Methodology for Computer-Based Systems (2010)

A methodology for the probabilistic assessment of the good enough to quality of computer-based systems is presented in this dissertation. The 'Good Enough' to Release (GETR) Methodology is a process by which engineering judgment as to the acceptability and importance of disparate evidence is transformed into a system-level assessment as to the overall acceptability of a computer-based system for release to a user community. Formalizing what can be an intuitive, ad-hoc assessment brings several benefits, such as the abilities to document, reproduce, audit, and analyze an assessment. The process is also structured to provide identification and quantification of sources of uncertainty inherent in such an assessment. 
The methodology has three main components: a mathematical model of the assessment, methods for populating the model, and result analyses. The assessment is modeled using a Bayesian Belief Network (BBN); thus, the model presented in this dissertation is called GETR BBN. A novel means of populating the model, the Quantifying Judgment Method for Bayesian Belief Networks (QJ-BBN) is presented in this dissertation. QJ-BBN is a method by which expert opinion as to the contributions of various evidence are transformed into indices that can be calibrated into subjective conditional probabilities. Finally, GETR Methodology offers two types of Contribution Analyses (CA), providing information to direct future iterations of a given assessment: Contribution Importance Analysis (CIA) and Contribution Uncertainty Analysis (CUA). The importance measures are developed using the definition of the traditional sensitivity analysis measure, the partial derivative of system output with respect to a given input. CUA identifies sets of various evidence probabilities that result in certain overall GETR probabilities using Monte Carlo simulation. 
Finally, examples of how GETR Methodology can be used to support release assessments are given. The featured systems are in-house developed analytical tools. The choice to focus this research on this type of assessment was made primarily because of the challenges posed by the conditions under which the decisions are made and the perceived lack of support for release assessments for this class of unique computer-based systems among experts.
The structural role of the carrier protein – active controller or passive carrier (2012)

Common to all FASs, PKSs and NRPSs is a remarkable component, the acyl or peptidyl carrier protein (A/PCP). These take the form of small individual proteins in type II systems or discrete folded domains in the multi-domain type I systems and are characterized by a fold consisting of three major α-helices and between 60-100 amino acids. This protein is central to these biosynthetic systems and it must bind and transport a wide variety of functionalized ligands as well as mediate numerous protein-protein interactions, all of which contribute to efficient enzyme turnover. This review covers the structural and biochemical characterization of carrier proteins, as well as assessing their interactions with different ligands, and other synthase components. Finally, their role as an emerging tool in biotechnology is discussed.
Biosynthesis of membrane lipids in rat axons. (1991)

Compartmented cultures of sympathetic neurons from newborn rats were employed to test the hypothesis that the lipids required for maintenance and growth of axonal membranes must be synthesized in the cell body and transported to the axons. In compartmented cultures the distal axons grow into a compartment separate from that containing the cell bodies and proximal axons, in an environment free from other contaminating cells such as glial cells and fibroblasts. There is virtually no bulk flow of culture medium or small molecules between the cell body and axonal compartments. When [methyl-3H]choline was added to the cell body-containing compartment the biosynthesis of [3H]-labeled phosphatidylcholine and sphingomyelin occurred in that compartment, with a gradual transfer of lipids (less than 5% after 16 h) into the axonal compartment. Surprisingly, addition of [methyl-3H]choline to the compartment containing only the distal axons resulted in the rapid incorporation of label into phosphatidylcholine and sphingomyelin in that compartment. Little retrograde transport of labeled phosphatidylcholine and sphingomyelin (less than 15%) into the cell body compartment occurred. Moreover, there was minimal transport of the aqueous precursors of these phospholipids (e.g., choline, phosphocholine and CDP-choline) between cell compartments. Similarly, when [3H]ethanolamine was used as a phospholipid precursor, the biosynthesis of phosphatidylethanolamine occurred in the pure axons, and approximately 10% of the phosphatidylethanolamine was converted into phosphatidylcholine. Experiments with [35S]methionine demonstrated that proteins were made in the cell bodies, but not in the axons. We conclude that axons of rat sympathetic neurons have the capacity to synthesize membrane phospholipids. Thus, a significant fraction of the phospholipids supplied to the membrane during axonal growth may be synthesized locally within the growing axon.