gebhart/patrepeval huggingface dataset:
Requirement for exported proteins in secretion through the invasion-associated type III system of Salmonella typhimurium (1996)

The inv and spa loci of Salmonella typhimurium encode a type III protein secretion system which is essential for the ability of this microorganism to gain access to cultured epithelial cells. These loci are located at centisome 63 in the Salmonella chromosome. We have carried out a functional analysis of several genes of these loci and have found that two exported proteins encoded in this region, InvJ and SpaO, are required for secretion through the invasion-associated type III secretion system. These findings suggest the existence of a hierarchy in the export process, since mutations in other targets of this secretory system have no effect on protein secretion. We have also shown that the spaO, spaP, spaQ, and spaR genes are required for protein secretion and for the ability of S. typhimurium to gain access to cultured epithelial cells. In addition, we investigated the ability of an invJ S. typhimurium mutant strain to present the SipB protein to the bacterial surface and demonstrated that, in contrast to Spa32, its putative Shigella homolog, InvJ is not involved in the surface presentation of the Sip proteins.
Molecules in galaxies. III - The Virgo cluster (1986)

Using the 7 m Bell Laboratories antenna, observations of 47 spiral galaxies in the Virgo Cluster were made in the (C-12)O J = 1-0 line; CO emission from 25 of the galaxies was detected at greater than the 3 sigma level. Most of the galaxies were observed at the central position, as well as at four adjacent positions one beam-width away. A method is presented for estimating the total flux of the galaxy using this spatially undersampled map. The total CO emission is found to be correlated with radio continuum emission and 60 + 100 micron band far-infrared, reflecting direct relationships among molecular gas content, CO emission, and massive star formation in these galaxies. However, the total CO flux is only poorly correlated with visual blue luminosity.
Physical operation and device design of short-channel tunnel field-effect transistors with graded silicon-germanium heterojunctions (2013)

Using graded silicon-germanium heterojunctions, the green tunnel field-effect transistor (TFET) can be scaled down into sub-10 nm regimes without short-channel effects. This work elucidates numerically the physical operation and device design of extremely short-channel TFETs with graded silicon-germanium heterojunctions for future low-power and high-performance applications. Critical device factors, such as the drain profile and bandgap engineering, were examined to generate favorable characteristics in the on-current, on-off switching, and off-leakage of very short TFETs. A mildly doped drain with a pure Ge source is preferred in designing the graded TFETs to optimize a desirable green transistor for low-power integrated circuits.
Scorpion neurotoxins: structure/function relationships and application in agriculture (2000)

Continued use of non-specific chemical insecticides poses potential risks to the environment and to human health resulting from non-target toxicity and increased insect resistance to these agents. Scorpions produce anti-insect selective polypeptide toxins that bind to and modulate voltage-sensitive ion channels in excitable tissues, thus offering alternative, environmentally safer means for insect pest control. Despite this potential, little is known about their structural elements dictating anti-insect preference, which may be useful for the design of selective insecticides. We used a bacterial system for expression and genetic dissection of two pharmacologically distinct scorpion toxins: alpha and excitatory. By exploiting a multi-disciplinary approach consisting of mutagenesis, protein chemistry, electrophysiology, binding and toxicity assays, and structural studies, we elucidated the bioactive surface of two anti-insect toxins, LqhαIT and Bj-xtrIT. In both polypeptides the bioactive surface is composed of residues surrounding the C-terminal region. In addition, a direct, immediate approach in using the toxin genes was demonstrated by engineering baculoviruses with cDNAs encoding LqhIT2 (depressant toxin), and LqhIT1 (excitatory toxin) resulting in viral vectors with significantly improved insecticidal efficacy. © 2000 Society of Chemical Industry
Identification of the autophosphorylation sites and characterization of their effects in the protein kinase DYRK1A (2001)

Protein kinases of the DYRK ('dual-specificity tyrosine-regulated kinase') family are characterized by a conserved Tyr-Xaa-Tyr motif (Tyr-319-Tyr-321) in a position exactly corresponding to the activation motif of the mitogen-activated protein kinase (MAP kinase) family (Thr-Xaa-Tyr). In a molecular model of the catalytic domain of DYRK1A, the orientation of phosphorylated Tyr-321 is strikingly similar to that of Tyr-185 in the known structure of the activated MAP kinase, extracellular-signal-regulated kinase 2. Consistent with our model, substitution of Tyr-321 but not of Tyr-319 by phenylalanine markedly reduced the enzymic activity of recombinant DYRK1A expressed in either Escherichia coli or mammalian cells. Direct identification of phosphorylated residues by tandem MS confirmed that Tyr-321, but not Tyr-319, was phosphorylated. When expressed in COS-7 cells, DYRK1A was found to be fully phosphorylated on Tyr-321. A catalytically inactive mutant of DYRK1A contained no detectable phosphotyrosine, indicating that Tyr-321 is autophosphorylated by DYRK1A. MS identified Tyr-111 and Ser-97 as additional autophosphorylation sites in the non-catalytic N-terminal domain of bacterially expressed DYRK1A. Enzymic activity was not affected in the DYRK1A-Y111F mutant. The present experimental data and the molecular model indicate that the activity of DYRK1A is dependent on the autophosphorylation of a conserved tyrosine residue in the activation loop.
Stability, consistency, and heritability of electrodermal response lability in middle‐aged male twins (2004)

We examined individual differences in nonspecific electrodermal response (EDR) lability in terms of retest stability, cross-situational consistency, and heritability in a sample of 345 adult monozygotic and dizygotic twin pairs. We also examined the phenotypic and genetic relationships between EDR lability and speed of habituation of the specific EDR to a nonsignal stimulus. Individual variation in EDR lability showed substantial retest stability and cross-situational consistency and also predicted resistance to specific EDR habituation. Structural equation modeling showed that the covariation among EDR lability measures and resistance to specific EDR habituation operated through a single latent phenotype, which was influenced in approximately equal measure by genetic and unique environmental factors. We discuss these findings in terms of an information processing account of individual differences in phasic EDR activation.
Analyzing Disabled Vehicle Incident Durations and Crash Response to Identify Service Patrol Expansions and Reduce the Need for Law Enforcement Involvement (2022)

Florida’s Road Rangers (RRs) are the state’s safety service patrol. Over 60% of RR responses are for disabled vehicles. This paper investigates the impact RRs have on disabled vehicle events and identifies roads with potential for expansion of RR patrol hours by analyzing 2019 incident and crash data. Over 213,000 disabled vehicle incidents occurred on roadways with partial RR coverage, with 20% occurring during RR inactive periods. The average incident duration more than doubled during inactive periods from 49 min to 100 min. After analyzing several factors, such as incident duration differences and percentage of inactive events, I-10 in Florida’s panhandle was identified as the roadway which would most benefit from increased patrol hours. Ninety-five disabled vehicle crashes occurred on roadways with partial RR coverage, with 56% occurring during inactive patrol hours; these inactive period crashes resulted in 70% of the injuries and 67% of the fatalities. The Tampa area had many crashes (especially during inactive periods), so roadways in this area would benefit from increased patrol hours. A significant relationship between RR presence and response activity duration was found, with an average response activity duration of 106 min during inactive periods and 71 min during active periods. These results show the importance of increasing the periods of RR coverage and how RRs assist law enforcement by responding to disabled vehicle events and their associated crashes, allowing law enforcement to focus their efforts on more severe crashes or other traffic-impacting events.
Bacillus subtilis Strain Engineered for Treatment of Soil-Transmitted Helminth Diseases (2013)

Soil-transmitted helminths (hookworms, whipworms, and large roundworms) are agents of intestinal roundworm diseases of poverty that infect upwards of 2 billion people worldwide. A great challenge in treating these diseases is the development of anthelmintic therapeutics that are inexpensive, can be produced in great quantity, and are capable of delivery under varied and adverse environmental conditions. A potential solution to this challenge is the use of live bacteria that are acceptable for human consumption, e.g., Bacillus subtilis, and that can be engineered with therapeutic properties. In this study, we expressed the Bacillus thuringiensis anthelmintic protein Cry5B in a bacterial strain that has been used as a model for live bacterial therapy, Bacillus subtilis PY79. PY79 transformed with a Cry5B expression plasmid (PY79-Cry5B) is able to express Cry5B from the endogenous B. thuringiensis cry5B promoter. During sporulation of PY79-Cry5B, Cry5B is packaged as a crystal. Furthermore, Cry5B produced in PY79 is bioactive, with a 50% lethal concentration (LC50) of 4.3 μg/ml against the roundworm Caenorhabditis elegans. PY79-Cry5B was a significantly effective therapeutic in experimental Ancylostoma ceylanicum hookworm infections of hamsters. A single 10-mg/kg (0.071 μmol/kg of body weight) dose of Cry5B administered as a Cry5B-PY79 spore crystal lysate achieved a 93% reduction in hookworm burdens, which is superior on a molar level to reductions seen with clinically used anthelmintics. Given that a bacterial strain such as this one can be produced cheaply in massive quantities, our results demonstrate that the engineering and delivery of live bacterial strains have great potential to treat a significant contributor to poverty worldwide, namely, hookworm disease and other soil-transmitted helminthiasis.
Unified Three-Terminal Switch Model for Current Mode Controls (2012)

Current mode controls have been widely used in many power converters with various topologies. Small signal equivalent circuit model is an effective tool for controller design. However, no unified equivalent circuit model applicable to various converters is available. This paper proposes a unified three-terminal switch model for current mode controls with constant frequency and variable frequency modulations operating in continuous conduction mode, providing an accurate and simple equivalent circuit for various converters using current mode control schemes. By identifying the invariant three-terminal structure in current mode control pulsewidth modulation (PWM) converters, which consists of active switch, passive switch, inductor, and closed current loop, the terminal current and voltage relationships are studied and represented by a small signal equivalent circuit. A small signal model for a current mode control PWM converter can be obtained by point-by-point substitution of the PWM switch with its equivalent circuit. The proposed model is verified by simulation and experimental results of various converters, and compared with other models to demonstrate its accuracy. The proposed model is accurate up to half of switching frequency.
Differential VCO and frequency tripler using SiGe HBTs for the 24 GHz ISM band (2003)

A frequency source generator chip was designed and built in a commercial SiGe process for an integrated front-end transceiver operating in the 24 GHz ISM band. It consists of a negative resistance cross-coupled differential VCO, oscillating at 8 GHz with a 150 MHz tuning range, having an output power of 0 dBm and a phase noise of -90 dBc/Hz at 100 kHz offset. The VCO drives a differential amplifier used as a frequency tripler which results in an overall voltage control frequency source operating at a nominal frequency of 23.5 GHz with a 420 MHz tuning range. It has a -10 dBm output power and consumes 180 mW. Its phase noise is -80 dBc/Hz at 100 kHz. The total chip area measures 600 /spl times/ 300 /spl mu/m/sup 2/.
Macromolecular Dexamethasone Prodrug Ameliorates Neuroinflammation and Prevents Bone Loss Associated with Traumatic Brain Injury (S28.001) (2023)

We hypothesized that systemically administered N-(2-hydroxypropyl) methacrylamide (HPMA) copolymer-based dexamethasone (Dex) prodrugs (P-Dex) will target the brain trauma injury sites, substantially enhance the Glucocorticoid therapy efficacy, and improve its systemic safety.
Specific-Heat Anomalies at the Lower Critical Temperature in Reentrant Ferromagnetic Superconductors (1979)

A spike-shaped heat-capacity anomaly has been identified at the lower superconducting-to-normal transition temperature ${T}_{c2}$ of the magnetic superconducting system (${\mathrm{Er}}_{1\ensuremath{-}x}{\mathrm{Ho}}_{x}$)-${\mathrm{Rh}}_{4}$${\mathrm{B}}_{4}$. This anomaly can be distinguished from the feature due to long-range magnetic ordering and indicates that the transition at ${T}_{c2}$ is thermodynamically of first order.
Multivariate Base Rates of Low Scores and Reliable Decline on ImPACT in Healthy Collegiate Athletes Using CARE Consortium Norms (2019)

Clinical interpretation of low scores and reliable decline on ImPACT depends on the strictness of the low score cutoff, the reliable change criterion, and the number of scores exceeding these cutoffs. Race and ADHD influence the frequency of low scores at all cutoffs cross-sectionally.
Measurement of serum and peritoneal fluid LH concentrations as a diagnostic tool for human endometriosis (2001)

A rapid, sensitive enzymeimmunoassay for the measurement of LH concentrations in serum and peritoneal fluid samples of healthy women and women with endometriosis is reported. The ligand (LH) was captured by a readily available, widely used and well-characterized monoclonal antibody (mAb, 518B7) generated against the beta subunit of bovine LH. This mAb, although specific for LH, shows very little species specificity and detects LH by radioimmunoassay in humans. A polyclonal antiserum raised in rabbits against hCG was conjugated to horseradish peroxidase and was used as the second antibody signal. This anti-hCG antiserum crossreacts with LH. The enzymeimmunoassay uses the standard human LH (hLH) preparations (NIADDK-hLH-I-3, AFP-827OB) and results are based on the relative concentrations of LH in serum and peritoneal fluid. Total assay time was < 3 h. The range of the standard curve was 0.002-0.500 ng LH per well and the lowest concentration of hLH that could be distinguished from zero concentration was 0.15 +/- 0.02 ng ml(-1) serum and 0.058 +/- 0.021 ng ml(-1) peritoneal fluid. Clinical diagnostic parameters for the LH enzymeimmunoassay showed a sensitivity of 85.71%, specificity 92.50%, efficiency 88.54%, positive predictive value 94.11% and negative predictive value 82.22%. The study was retrospective. Serum LH concentrations of women with endometriosis were 13.67 +/- 7.21 ng ml(-1), whereas serum LH concentrations of women in the control group were 4.52 +/- 2.03 ng ml(-1). One-way ANOVA showed significant differences (P < 0.001) between women with endometriosis and control groups. Women in the control group had peritoneal fluid LH values of 5.65 +/- 2.43 ng ml(-1), whereas peritoneal fluid LH values of 64.06 +/- 16.44 ng ml(-1) were obtained in women with endometriosis (P < 0.001). A cycle-dependent pattern of serum and peritoneal fluid LH concentration was observed in women in the control group, which was not observed in the peritoneal fluid of the group with endometriosis. The application of this assay to serum or peritoneal fluid samples provides the attractive possibility that it could be included in the panel of markers used for diagnosis of endometriosis.
Important Lessons Derived from Animal Models of Celiac Disease (2011)

Several animal models have been recently developed to recapitulate various components of the complex process that is celiac disease. In addition to the increasing diversity of murine models there are now monkey models of celiac disease. Mouse strains and protocols have been developed that are now just beginning to address the complex interactions among the innate and adaptive immune responses to gluten, as well as gluten-dependent autoimmunity in celiac disease. The most important conclusion that these models have provided us with so far is that while all three components (innate gluten sensitivity, adaptive gluten sensitivity, and autoimmunity) are independent phenomena, all are necessary for celiac disease to develop.
Adversarial Geospatial Abduction Problems (2012)

Geospatial Abduction Problems (GAPs) involve the inference of a set of locations that “best explain” a given set of locations of observations. For example, the observations might include locations where a serial killer committed murders or where insurgents carried out Improvised Explosive Device (IED) attacks. In both these cases, we would like to infer a set of locations that explain the observations, for example, the set of locations where the serial killer lives/works, and the set of locations where insurgents locate weapons caches. However, unlike all past work on abduction, there is a strong adversarial component to this; an adversary actively attempts to prevent us from discovering such locations. We formalize such abduction problems as a two-player game where both players (an “agent” and an “adversary”) use a probabilistic model of their opponent (i.e., a mixed strategy). There is asymmetry as the adversary can choose both the locations of the observations and the locations of the explanation, while the agent (i.e., us) tries to discover these. In this article, we study the problem from the point of view of both players. We define reward functions axiomatically to capture the similarity between two sets of explanations (one corresponding to the locations chosen by the adversary, one guessed by the agent). Many different reward functions can satisfy our axioms. We then formalize the Optimal Adversary Strategy (OAS) problem and the Maximal Counter-Adversary strategy (MCA) and show that both are NP-hard, that their associated counting complexity problems are #P-hard, and that MCA has no fully polynomial approximation scheme unless P=NP. We show that approximation guarantees are possible for MCA when the reward function satisfies two simple properties (zero-starting and monotonicity) which many natural reward functions satisfy. We develop a mixed integer linear programming algorithm to solve OAS and two algorithms to (approximately) compute MCA; the algorithms yield different approximation guarantees and one algorithm assumes a monotonic reward function. Our experiments use real data about IED attacks over a 21-month period in Baghdad. We are able to show that both the MCA algorithms work well in practice; while MCA-GREEDY-MONO is both highly accurate and slightly faster than MCA-LS, MCA-LS (to our surprise) always completely and correctly maximized the expected benefit to the agent while running in an acceptable time period.
<title>DCATT dispersed fringe sensor: modeling and experimenting with the transmissive phase plates</title> (2000)

Control algorithms developed for coarse phasing the segmented mirrors of the Next Generation Space Telescope (NGST) are being tested in realistic modeling and on the NGST wavefront control testbed, also known as DCATT. A dispersed fringe sensor (DFS) is used to detect piston errors between mirror segments during the initial coarse phasing. Both experiments and modeling have shown that the DFS provides an accurate measurement of piston errors over a range from just under a millimeter to well under a micron.
Experimental comparison of RSSI-based localization algorithms for indoor wireless sensor networks (2008)

In this paper, we investigate the actual performance of some of the best known localization algorithms when deployed in real-world indoor environments. Among the plethora of possible localization schemes, we focus on those based on radio signal strength measurements only, since they do not require extra circuitry that would result in higher cost and energy consumption. For a fair comparison, we have first gathered thousands of radio signal strength measurements in two different indoor environments. To estimate the channel model parameters and to compare the different localization algorithms these data have been used.
Reversible optical data storage on poly(ethylene terephthalate) (1997)

Abstract A desirable feature of optical data storage processes is that they provide high contrast between the image and background. Thermal marking techniques are inherently advantageous in this regard, because of the nonlinearity of the response. A thermal method for lithography on polymer films has been developed based on selective exposure of the films to infrared laser radiation passing through a mask. Radiation induced crystallization, melting and ablation have been demonstrated with the processes prevailing at different levels of radiation intensity. These methods are capable of producing high resolution images with excellent edge acuity and minimal interference from diffraction. The absence of diffraction effects is due to the nonlinear response of the polymer film to the radiation. The best resolution obtained to date (submicron) is limited by the size of the smallest features present on the masks used to create the pattern. The ultimate resolution achievable by these methods is presently unknown.
Comparison of Scars from Total Hip Replacements Done with a Standard or a Mini-incision (2005)

Scar cosmesis is one of the proposed benefits of mini-incision total hip replacement as opposed to standard-incision procedures; however, there has been no scientific proof of this clinical outcome. The cosmetic appearances of healed incisions of 34 primary total hip replacement procedures done by one surgeon using either a mini-incision (20 procedures) or a standard-length incision (14 procedures) were compared at an average of 2 years postoperatively. Each scar’s appearance was graded independently by two plastic surgeons using a standardized rating system. Patients answered a questionnaire regarding their subjective assessment of their scar. The blinded observers found that more mini-scars (six of 20) were rated poor than standard scars (one of 14) and that more standard-incision patients had scars that were rated good. More mini-incision patients (two of 20 versus zero of 14) had wound-healing problems. All the patients thought that their hip scar was acceptable in appearance, but 30 of 31 patients rated the relief of pain and total hip replacement longevity as higher priorities than scar cosmesis. The cosmesis of mini-incision total hip replacement scars may be inferior to standard-incision scars because of skin and soft tissue damage produced by high retractor pressures needed for exposure using a limited skin incision. Level of Evidence: Therapeutic study, Level II-2 (prospective comparative study). See the Guidelines for Authors for a complete description of levels of evidence.