gebhart/patrepeval huggingface dataset:
Targeting energy metabolism via the mitochondrial pyruvate carrier as a novel approach to attenuate neurodegeneration (2018)

Several molecular pathways are currently being targeted in attempts to develop disease-modifying therapies to slow down neurodegeneration in Parkinson's disease. Failure of cellular energy metabolism has long been implicated in sporadic Parkinson's disease and recent research on rare inherited forms of Parkinson's disease have added further weight to the importance of energy metabolism in the disease pathogenesis. There exists a new class of anti-diabetic insulin sensitizers in development that inhibit the mitochondrial pyruvate carrier (MPC), a protein which mediates the import of pyruvate across the inner membrane of mitochondria. Pharmacological inhibition of the MPC was recently found to be strongly neuroprotective in multiple neurotoxin-based and genetic models of neurodegeneration which are relevant to Parkinson's disease. In this review, we summarize the neuroprotective effects of MPC inhibition and discuss the potential putative underlying mechanisms. These mechanisms involve augmentation of autophagy via attenuation of the activity of the mammalian target of rapamycin (mTOR) in neurons, as well as the inhibition of neuroinflammation, which is at least partly mediated by direct inhibition of MPC in glia cells. We conclude that MPC is a novel and potentially powerful therapeutic target that warrants further study in attempts to slow Parkinson's disease progression.
Magnetometer Sensor Feasibility for Railroad and Highway Equipment Detection (2006)

This Innovations Deserving Exploratory Analysis (IDEA) study investigated the feasibility of using Anisotropic Magneto-Resistive (AMR) magnetometers to detect train or vehicle presence and to determine train speed for the activation of grade crossing warning systems. Laboratory, parking lot, and railroad field tests were performed using 3-axis digital AMR magnetometers for train and vehicle detection as well as speed measurement. It was determined that the sensors drift with changes in the ambient temperature. However, by periodic bias removals (auto-calibrations), the impact of these bias drifts can be eliminated. It was also determined that the detection distance for vehicles depends on the amount of magnetic material (iron, nickel, or cobalt) and varies as the inverse cubed (3rd) power of the distance from the sensor. Changes in the ambient electro-magnetic field, such as caused by variable current power lines, are also detected with an inverse (1st power) distance relationship. Hence, electromagnetic interference may travel a longer distance than a magnetic signature, depending on the magnitudes of these two signals. Overall, it was found that the 3-axis measurement capability of the AMR magnetometers permits the unique identification of different vehicles. It also permits the separation of vehicle signatures from noise signatures. Hence, these magnetometers provide an alternative, more flexible, approach for activating crossing warning systems than the current use of track circuits.
Optimal and suboptimal error spectrum shaping for cascade-form digital filters (1984)

Error spectrum shaping (ESS) can significantly reduce finite-wordlength error in recursive fixed-point digital filters. Most past work on ESS has focused on second-order filters. In this paper, expressions for the ESS coefficients minimizing the roundoff error are derived for high-order filters composed of cascaded second-order sections. A comparison of the noise gains is made between optimal and suboptimal ESS structures and the section-optimal structure; the ESS structures perform well in comparison. A heuristic section-ordering strategy, based on ideas underlying ESS, is proposed and deemed useful, particularly for elliptic filters.
Virions and antigens of herpes virus type 2 in cervical carcinoma. (1973)

Summary Herpesvirus type 2 (HSV-2) has been associated with squamous cancer of the human cervix on the basis of seroepidemiological data. Findings providing information on the basis of the association of the HSV-2 genome with cervical cancer cells are presented. A herpesvirus isolated from degenerated cervical tumor cells grown in vitro is identified as a type 2 on the basis of biological and immunological properties. Surface antigens, HSV-2-specific, are observed in a small proportion of cells from a second culture of cervical tumor cells. Exfoliated but not biopsied tumor cells from patients with cervical carcinoma contain HSV-2 antigens, but virus particles are not observed. Finally, 90% of patients with cervical carcinoma have antibody to a HSV-2-induced antigen different from neutralizing antigens. This antibody, present only in 10% of a matched control group, appears to be of prognostic significance. The results are discussed in terms of the virus-host cell interaction. The data suggest that cervical tumor cells harbor the viral genome in a partially repressed state characterized by the expression of only some viral functions. Under conditions of stress, such as high pH, complete expression of the viral genome may occur resulting in the formation of viral components and/or infectious virus.
Wide-range, high-accuracy, white light piston sensor for segmented optics (1995)

Optical systems with segmented mirrors require precision coalignment of their segments to attain the desired performance. A novel sensor for measuring piston over a ± 10 wave range by analyzing the image of a white light point source is described. The sensor combines a Young's two-slit aperture pair for coarse sensing with another set of apertures, which include a phase retardation portion for fine sensing. The course sensor has an accuracy of ± 0.25 wave over the full range. The fine sensor works within ± 0.5 wave of zero with ± 0.005 wave accuracy, and a repeatability of the order of ± 0.001 wave. Theoretical derivation and experimental results are provided.
Switching rates of selection diversity and switch-and-stay diversity on mixed high-speed train channels (2015)

Due to tunnels, mountains, corridors and other geographical features as well as their high mobility, high speed train users may experience different channel fadings on two or more antennas mounted on the top of the train, varying in time and location. The switching rates of dual selection combining diversity and dual switch-and-stay diversity for the mixed Nakagami-m and Rician fading are investigated. New closed-form expressions are derived for the case of independent but not identically distributed fading links, that is, unbalanced channels.
Design of an Optical Fiber Supporting 16 OAM Modes (2014)

We present the design and fabrication of an optical fiber to support 16 OAM modes. The effective indices of each vector mode are designed for maximal separation facilitating the use of OAM modes for space-division multiplexing.
Pressure-Driven Hardware Managed Thread Concurrency for Irregular Applications (2017)

Given the increasing importance of efficient data intensive computing, we find that modern processor designs are not well suited to the irregular memory access patterns found in these algorithms. This research focuses on mapping the compiler's instruction cost scheduling logic to hardware managed concurrency controls in order to minimize pipeline stalls. In this manner, the hardware modules managing the low-latency thread concurrency can be directly understood by modern compilers. We introduce a thread context switching method that is managed directly via a set of hardware-based mechanisms that are coupled to the compiler instruction scheduler. As individual instructions from a thread execute, their respective cost is accumulated into a control register. Once the register reaches a pre-determined saturation point, the thread is forced to context switch. We evaluate the performance benefits of our approach using a series of 24 benchmarks that exhibit performance acceleration of up to 14.6X.
The Role of Goldschmidt’s Tolerance Factor in the Formation of A2BX6 Double Halide Perovskites and its Optimal Range (2019)

Abstract Vacancy‐ordered double perovskites is a new branch of lead‐free halide perovskites with properties promising for photovoltaic application. In this study, data about the crystal structure of 170 known A 2 BX 6 ( X = I, Br, Cl, F) are collected and analyzed to solve a question of applicability of the Goldschmidt’s tolerance factor and octahedral factor to double perovskites. It is found that Goldschmidt’s tolerance factor is applicable for double perovskites in analog with ABX 3 perovskites. Suggested optimal ranges of Goldschmidt’s factor expand the geometrical approach from ABX 3 perovskites to A 2 BX 6 double perovskites. The result is useful for up to 796 new full inorganic compounds having double‐perovskite structure and designing new hybrid organic–inorganic double perovskites.
Anterior or Posterior Sacrospinous Vaginal Vault Suspension (2001)

In Brief OBJECTIVE To compare vaginal anatomy and sexual function after the conventional posterior and anterior sacrospinous vault suspension. METHODS A retrospective repeated measures cohort study included all 168 consecutive sacrospinous vault suspension procedures between July 1990 and February 1997. The posterior suspension (n = 92) used a posterior vaginal incision and pararectal dissection. Anterior suspension (n = 76) involved an anterior rather than posterior vaginal incision, retropubic perforation, and dissection of a paravaginal-paravesical rather than pararectal space to accommodate the vaginal vault. Two polytetrafluoroethylene (00) sutures anchored the anterior vaginal cuff (for the anterior sacrospinous suspension) or the posterior vaginal cuff (for the posterior sacrospinous suspension) to the ligament. Postoperative evaluation included an examination using the pelvic organ prolapse quantitative system, assessment of vaginal width and axis, and symptom questionnaire. RESULTS Total vaginal length and apical suspension were slightly greater after the anterior suspension, and recurrent anterior vaginal relaxation was less likely. No differences were found in maximal dilator size or apical narrowing between the two groups. New onset dyspareunia was reported by two subjects in the anterior vault suspension group, and two in the posterior vault suspension group. Three of these four cases of de novo dyspareunia were attributable to either severe atrophy or recurrent prolapse, and none to vaginal narrowing or shortening. CONCLUSION After anterior sacrospinous vault suspension, vaginal length and apical suspension were slightly increased, and recurrent anterior vaginal prolapse decreased compared with the posterior sacrospinous suspension technique. Upper vaginal caliber and sexual function appear well preserved using either technique. Anterior sacrospinous vaginal vault suspension results in anatomic and functional outcomes similar to the conventional posterior approach, and may reduce the risk of recurrent anterior compartment prolapse.
Autoimmune hemolytic anemias, Evans' syndromes, and pure red cell aplasia in non-Hodgkin lymphomas (2007)

We analyzed 108 cases of non-CLL non-Hodgkin lymphoma (NHL) associated with autoimmune hemolytic anemia (AIHA) (+/- pure red cell aplasia (PRCA)) or Evans' syndrome. The analysis was based on cases reported in the literature, which were retrieved by means of Pubmed and Medline searches and of an original series of 121 patients with NHL as well as reference lists of papers in the field. The number of cases in various NHL subtypes was small (n = 6-25). Nevertheless, interesting and sometimes unexpected differences in sex prevalence, temporal relationship between onset of lymphoma and AIHA, stage of lymphoma, relative frequency of warm antibody-AIHA (WA-AIHA) and cold antibody (CA-AIHA), association with PRCA and response of AIHA to treatments were noted for various lymphoma entities. WA-AIHA was more frequent in B-cell lymphomas, while CA-AIHA and PRCA predominantly occurred in T-cell lymphomas. Anti-lymphoma treatment seemed to be more effective against AIHA than conventional therapy with steroids or immunoglobulin. Although generated by a literature survey, this compilation of data indicates a complex relation of lymphoma and AIHA and warrants more attention and specific studies.
Fatal encephalopathy with wild‐type JC virus and ruxolitinib therapy (2019)

This expands the spectrum of identified JCV diseases associated with broad-spectrum immunosuppression, including JAK-STAT inhibitors, and sheds light on an additional neurotropic virus strain of the archetype variety. ANN NEUROL 2019;86:878-884.
Microbubble enhanced mass transfer efficiency of CO2 capture utilizing aqueous triethanolamine for enzymatic resorcinol carboxylation (2021)

The present study focuses on the aeration of aqueous triethanolamine acting as reaction medium for biocatalytic carboxylations. For enhancing mass transfer in a bubble column reactor, microbubble aeration is applied and compared to conventional macrobubble aeration. Application of a 0.5 μm porous sparger enables microbubble CO<sub>2</sub> aeration with bubble size distributions below 150 μm in Sauter mean diameter, correlating with the highest measured mass transfer rates. During CO<sub>2</sub> saturation of the aqueous triethanolamine, bubble size distributions changed according to the level of CO<sub>2</sub> saturation. For microbubbles, less foaming was observed compared to macrobubble aeration by a 10 μm porous sparger. This microbubble effect is attributed to their accelerated dissolution assisted by the Laplace pressure lowering the amount of bubbles reaching the surface of the liquid. The experiments reveal that the rate of interfacial area generation, which is calculated based on measured bubble size distributions, influences the biocatalyst activity.
Cysteine Redox Sensor in PKGIa Enables Oxidant-Induced Activation (2007)

Changes in the concentration of oxidants in cells can regulate biochemical signaling mechanisms that control cell function. We have found that guanosine 3',5'-monophosphate (cGMP)-dependent protein kinase (PKG) functions directly as a redox sensor. The Ialpha isoform, PKGIalpha, formed an interprotein disulfide linking its two subunits in cells exposed to exogenous hydrogen peroxide. This oxidation directly activated the kinase in vitro, and in rat cells and tissues. The affinity of the kinase for substrates it phosphorylates was enhanced by disulfide formation. This oxidation-induced activation represents an alternate mechanism for regulation along with the classical activation involving nitric oxide and cGMP. This mechanism underlies cGMP-independent vasorelaxation in response to oxidants in the cardiovascular system and provides a molecular explantion for how hydrogen peroxide can operate as an endothelium-derived hyperpolarizing factor.
On the Lombard Effect Induced by Vehicle Interior Driving Noises, Regarding Sound Pressure Level and Long-Term Average Speech Spectrum (2012)

In this paper, the inﬂuence of typically appearing interior driving noises on the production of speech inside vehicles is described. The automatic reﬂex of raising one’s voice in noisy environments, known as the Lombard Eﬀect [1], is quantiﬁed both in the sound pressure level and in the long-term spectral distribution of read speech. For this purpose, a laboratory experiment with 30 participants was performed. In addition to a noise-free reference condition, driving noises at various sound pressure levels as well as noises with white and speech-like spectra were presented to the test attendees while reading out loud a written text. The eﬀects of these diﬀerent noises on the speech’s sound pressure level and spectral distribution were quantiﬁed. In conclusion, there is no signiﬁcant impact of the noise shape on the spectral content of the respective speech, while the noise-aﬀected speech is signiﬁcantly diﬀerent to speech under the quiet condition. In regard to the speech’s sound pressure level, an octave-band analysis of the background noises with a band weighting commonly used for speech intelligibility measurements is proposed to predict speech levels in the tested noise environments.
Discovery of Taniborbactam (VNRX-5133): A Broad-Spectrum Serine- and Metallo-β-lactamase Inhibitor for Carbapenem-Resistant Bacterial Infections (2019)

A major resistance mechanism in Gram-negative bacteria is the production of β-lactamase enzymes. Originally recognized for their ability to hydrolyze penicillins, emergent β-lactamases can now confer resistance to other β-lactam drugs, including both cephalosporins and carbapenems. The emergence and global spread of β-lactamase-producing multi-drug-resistant "superbugs" has caused increased alarm within the medical community due to the high mortality rate associated with these difficult-to-treat bacterial infections. To address this unmet medical need, we initiated an iterative program combining medicinal chemistry, structural biology, biochemical testing, and microbiological profiling to identify broad-spectrum inhibitors of both serine- and metallo-β-lactamase enzymes. Lead optimization, beginning with narrower-spectrum, weakly active compounds, provided <b>20</b> (VNRX-5133, taniborbactam), a boronic-acid-containing pan-spectrum β-lactamase inhibitor. In vitro and in vivo studies demonstrated that <b>20</b> restored the activity of β-lactam antibiotics against carbapenem-resistant <i>Pseudomonas aeruginosa</i> and carbapenem-resistant Enterobacteriaceae. Taniborbactam is the first pan-spectrum β-lactamase inhibitor to enter clinical development.
Emergency Medical Services Utilization during an Outbreak of Severe Acute Respiratory Syndrome (SARS) and the Incidence of SARS‐associated Coronavirus Infection among Emergency Medical Technicians (2004)

During the outbreak of SARS, the overall EMS volume did not change significantly, but the non-SARS EMS activities decreased. Compared with the general population, EMS providers are at higher risk of contracting the SARS virus regardless of different perceived levels of risk. Standard protections and procedures for infection control should be strictly followed during transport and within the hospital environment.
Low complexity motion estimation algorithm by multiresolution search for long-term memory motion compensation (2003)

We propose a new low complexity motion estimation (ME) algorithm using multiresolution motion search for long term memory motion compensation (LTMC). While multiresolution motion search has been used for standard single-frame motion compensation, here we introduce several novel techniques to exploit it efficiently in the context of LTMC. The proposed algorithm compute a coarse motion vector from a lower resolution sequence to locate motion search windows (MSW). Because the coarse motion vectors are good approximations to the actual vectors, small MSW whose sizes are chosen based on the error surface smoothness information can be used without significant loss in quality, leading to significant reduction in complexity. Our approach also incorporates temporal reduction of the motion search range to reduce the complexity further. The proposed algorithm provides particularly significant gains for video sequences which contain large motions, where directed search also results in promising gains in PSNR over non-directed search.
Computational methods in optimization (1971)

By incorporating a distance function into the finite element simulation, we investigate the flow-driven competition between two soft capsules passing through a narrow pore, employing the arbitrary Lagrangian-Eulerian formulation to satisfy the boundary conditions for fluid flow and capsule deformation. In our simulations, the motion and deformation of the capsules can be described in an intuitive manner, and the order in which capsules of different sizes pass through a pore can be clearly determined. Meanwhile, when the capsules are near the narrow pore, the change of the flow field is also very interesting and can be expressed intuitively. It is shown that, driven by the Poiseuille flow, the larger capsule has a stronger tendency to pass through the pore than the small one, which can be attributed to the greater resistance and the volume advantage of the larger capsule. In addition, we demonstrate that this tendency can be reversed by changing the inlet velocity and setting the initial position of the smaller capsule closer to the axis of the pore. And as long as the large one passes through first, the small one will offset the axis to the same orientation as the initial, while the large one always moves along the axis.
Intrusion of Herbal Antilipidemics – Cardiac Protective Through Electromagnetic Thermal Device Patches (2017)

Objective: Development of an innovated, economic and simple herbal formulation as cardiac protective through designed electromagnetic thermal device patches which induced the drugs directly to coronary arteries. This opens the blocked vessels even between 50-80% without Coronary artery bypass grafting (CABG). Material & Methods: The electromagnetic thermal device is designed with polysiloxane adhesive tape, centrally mounted with PVC membrane and over that consists of drug reservoir and in top embedded with electromagnetic vibrator. Drug use to be injected with micro-syringe and patch is operated with remote control. So, the generated heat and vibration penetrates the drug (Allicin & Arjuna) directly, vertically to coronary arteries (CA) under pericardium membrane, stored in pericardium fluid. Finally a high concentration of drugs opens the lipid choked in CA. Result & Discussion: Before and after cardiac patch drug delivery therapy ECG report, TMT, Doppler test, Angiogram analysis with the help of graphics and images, has been carried-out to evaluate the % of blockage opened. The comparative study of opening of vascular blockage through this new mechanics against other conventional drugs and CABG which proves its superior valuation. Due to herbal nature of drug contents and without any mechanical invasion, it has no adverse effects and drug interaction. Conclusion: The new innovated designed cardiac patches open the coronary artery blockage in very simply, economically, without medication error, without side effects due to herbal origin and treatment without surgery. This concludes globally emergence of the first time innovated cardiac patches convenience to patient world in medical science.
PROTEIN-PROTEIN DOCKING REFINEMENT USING RESTRAINT MOLECULAR DYNAMICS SIMULATIONS (2016)

A realistic prediction of the structure of protein-protein complexes is of major importance to obtain three-dimensional models for the interaction of proteins to form complexes and assemblies. In addition to the systematic search for putative binding sites on the surface of two binding partners, the second step of a docking effort, the refinement of docked complexes, is a major bottleneck to obtain realistic interaction geometries. Typically, the first initial systematic search employs rigid partner structures or few flexible degrees of freedom, whereas the refinement step involves fully flexible partner structures. The possibility to refine docked complexes using restraint MD simulations combined with an implicit solvent (Generalized Born) model was explored on three example test complexes starting from unbound partner structures. Significant improvement, both in scoring and agreement with the native complex structure after refinement was observed for two test cases. No improvement was found for a test case of a complex with lower binding affinity. The method can be easily applied to any docked protein-protein complex, however, more general applicability requires further improvements in the scoring function.