gebhart/patrepeval huggingface dataset:
Characterization of HIV Type 1 Clades in the Caribbean Using pol Gene Sequences (2003)

To date, 11 HIV-1 M group clades, A to K, have been characterized, displaying different distributions, prevalences, and biological properties. Approximately 90% of new HIV-1 infections occur in developing countries, including the Caribbean. However, information on HIV-1 subtypes from this region is limited. We report subtype characterization of viruses from 71 individuals, obtained during the period 2000-2002. RNA from the pol region was sequenced, generating data on subtype and drug resistance associated mutations for 71 specimens from 9 countries. Sixty-seven (94.4%) sequences were classified as clade B, three (4.2%) as D/B, and one (1.4%) as clade C. Numerous polymorphisms were observed, including some associated with drug resistance, but not signifying exposure to chemotherapy. This study adds to our knowledge of HIV-1 clades in the Caribbean, and indicates possibilities for monitoring HIV-1 chemotherapy.
A RANDOMIZED DOUBLE-BLIND PLACEBO CONTROLLED EFFICACY STUDY OF INTRADISCAL ELECTROTHERMAL THERAPY FOR THE TREATMENT OF CHRONIC DISCOGENIC LOW BACK PAIN (2006)

Introduction: Intra-Discal Electrothermal Therapy (IDET) has been proposed as a treatment for chronic discogenic low back pain. Reports from prospective outcome studies demonstrate statistically significant improvements, but there are no published randomized controlled trials assessing efficacy against a placebo group. Methods: Ethical committee approval was obtained prior to the study. Patients with chronic low back pain who failed conservative treatment were considered for the study. Inclusion criteria included one or two level symptomatic internal disc disruption as determined by provocative CT/discography. Patients were excluded if there was > 50% loss of disc height or had had previous back surgery. Fifty-seven patients were randomized with a 2:1 (IDET: Placebo) ratio, 38 to the active IDET arm and 19 to the sham (placebo). The IDET catheter was positioned under sedation to cover at least 75% of the annular tear as defined by the CT/discogram. An independent technician connected the catheter to the generator and either delivered electrothermal energy (active group) or did not (sham group). Surgeon, patient and independent outcome assessor were all blinded. All patients followed a standard rehabilitation programme. Outcome Measures: Low Back Outcome Score (LBOS), Oswestry Disability Index (ODI), SF-36 questionnaire, Zung Depression Index (ZDI) and Modified Somatic Perceptions Questionnaire (MSPQ) were measured at baseline and 6 months. Successful outcome was defined as: No neurological deficit resulting from the procedure, improvement > 7 points in LBOS, improvements > 7 points in SF-36 subsets (pain / disability, physical functioning and bodily pain) Results: Two subjects withdrew from the study (both IDET). Baseline demographic data, employment and worker’s compensation status, sitting tolerance, initial LBOS, ODI, SF-36, ZDI and MSPQ were similar for both groups. No neurological deficits occurred as a result of either procedure. No subject in either treatment arm showed improvement of > 7 points in LBOS or the specified domains of the SF-36. Mean ODI was 41.4 at baseline and 39.7 at 6 months for the IDET group compared to 40.7 at baseline and 41.5 at six months for the Placebo group. There was no significant change in ZDI or MSPQ scores for either group. Discussion: No subject in either treatment arm met criteria for successful outcome. There was no significant change in outcome measures in either group at six months. This study demonstrates no significant benefit from IDET over placebo.
Active and Recyclable Gold Metal Nanoparticles Catalyst Supported on Nitrogen‐Doped Mesoporous Carbon for Chemoselective Hydrogenation of Cinnamaldehyde to Cinnamyl Alcohol (2021)

Several supported gold metal catalysts with different Au nanoparticles sizes were prepared and evaluated for the chemoselective hydrogenation of cinnamaldehyde (CA) to cinnamyl alcohol (CAL). To investigate the structure-activity relationship, stability of catalyst, heterogeneity and recyclability, the structural characteristics of materials and Au catalysts (fresh and spent catalysts) were studied by employing variety of physico-chemical techniques. The interrelationship among Au nanoparticles size (nm) with turnover frequency (h<sup>-1</sup> ) of Au catalysts has also been explored. Among the various Au catalysts tested, nitrogen-doped mesoporous carbon (NMC) supported Au catalyst having homogeneously dispersed (78.8%) Au nanoparticles (1.6 nm) synthesized by sol-immobilization method (Au-NMC-SI) demonstrated improved catalytic activity affording 78% CAL selectivity and 94.2% CA conversion without using any promoter. Moreover, Au-NMC-SI catalyst exhibited good recyclability and stability. The catalyst synthesis approach described in this investigation opens up a novel strategy for the design of highly efficient metal nano-catalysts supported on NMC materials.
Jet pump oscillating-flow behavior at different Womersley numbers (2016)

Few numerical works simulate the laminar-flow behavior within the diverging passages of typical thermoacoustic jet pumps. The associated boundary-layer separation is mostly delayed by maintaining a slowly increasing flow passage and thereby the corresponding pressure drop and consumed acoustic energy are noticeably reduced. Of equal importance is the effect of the transition to turbulence on the boundary-layer separation and the resulting flow-pattern. To our knowledge, no simulation has been developed that numerically predict and capture the conditionally turbulent flow regime within typical jet pumps. Here, a new finite-volume model is reported that employs the non-linear CFD solver of ANSYS FLUENT. The k-kl-ω transition model is considered and its parameters are particularly adjusted for present application. A sinusoidal pressure oscillation is enforced at one end, while the far-field approximation is considered at the other end to model the non-reflecting boundary condition. An axisymmetric model along with careful meshing are applied. The transient simulation run proceeds till stationary flow behavior is obtained. Both the flow streamlines and vorticity field are plotted for three different acoustic frequencies, Womersley numbers of which correspond to 5, 15, and 30. The numerical results capture the onset of flow transition into turbulence and characterize the flow patterns at different frequencies. The results also illustrate the influence of the developed turbulent flow-patterns on the boundary-layer separation.
Medical applications of stable isotopes: mass spectroscopy and nuclear magnetic resonance (1982)

https://www.clinicaltrials.gov. Unique identifiers: NCT01920711 (PARAGON-HF), NCT01035255 (PARADIGM-HF).
Expression of HIF1a and HIF2a in bone metastatic clear cell renal cell cancer and use as prognostic markers. (2013)

e15523 Background: Bone metastasis is a frequent complication of ccRCC and predictors of this type of progression are scanty. The aim of this study was to analyse HIF and HIF regulated gene expressions in bone metastatic ccRCC. Methods: A pre-target therapy era cohort of 125 ccRCC patients with &lt;100 month follow-up period have been collected with paraffin embedded primary tumors. 65 patients developed bone metastasis where 45 metastases were available for analysis. RNA was isolated from FFPE tissues and gene expression of HIF1A, HIF2A as well as HIF-regulated genes GLUT1, LDH5, GAPDH, CAIX, VEGF, VEGFR2 and EPOR were measured by RT-PCR using B2M as control. Protein product of these genes was measured on TMA arrays using standardized immunohistochemistry and an image analysis program (Mirax Viewer, 3DHistech). Results: Expression of HIF1A and HIF2A was significantly increased in bone metastatic primary ccRCC tumor tissues both at mRNA and protein levels. Significant upregulation of 3 out of 7 HIF-regulated genes (VEGFR2, EPOR and LDH5) in the primary tumor tissues of bone metastatic ccRCC was proved at mRNA levels and confirmed at protein level for VEGFR2 as well. In bone metastatic tissues a significant overexpression of HIF2A and VEGF mRNA was also detected compared to the primary site. Prognostic power of the protein expression in primary tumor was found for HIF1A (p= .001), HIF2A (p = .041), and VEGFR2 (p = .001) (confirmed at mRNA levels as well) for overall survival at time of surgical removal of primary renal tumor using Kaplan-Meier method and log-rank statistics. To further test the power of HIF1A and HIF2A as prognostic factors we have performed multivariate analysis considering available clinicopathological variables (gender, Fuhrman grade, stage) and found that HIF2A protein level outperformed all other factors in the model. Conclusions: These data indicate that HIF genes are overexpressed in bone metastatic ccRCC among which HIF2A expression at mRNA and protein levels can be used as a strong independent prognostic marker.
A minimalistic wind estimation method for small unmanned aircraft (2016)

This paper presents a computationally efficient wind estimation method which can be run onboard a miniature Unmanned Aerial Vehicle. Estimated wind can be used to calculate parachute deploy position during automated parachute landing phase. The method involves flying in an orbit at drop zone for one round. We formulate wind estimation problem into a linear least square minimization problem. Structure of the problem allows all calculations to be done onboard a microcontroller. Simulation and flight test results are also discussed.
Real Time Viterbi Optimization of Hidden Markov Models for Multi Target Tracking (2007)

In this paper the problem of tracking multiple objects in im- age sequences is studied. A Hidden Markov Model describ- ing the movements of multiple objects is presented. Previ- ously similar models have been used, but in real time sys- tem the standard dynamic programming Viterbi algorithm is typically not used to find the global optimum state se- quence, as it requires that all past and future observations are available. In this paper we present an extension to the Viterbi algorithm that allows it to operate on infinite time sequences and produce the optimum with only a finite de- lay. This makes it possible to use the Viterbi algorithm in real time applications. Also, to handle the large state spaces of these models another extension is proposed. The global optimum is found by iteratively running an approximative algorithm with higher and higher precision. The algorithm can determine when the global optimum is found by main- taining an upper bound on all state sequences not evalu- ated. For real time performance some approximations are needed and two such approximations are suggested. The theory has been tested on three real data experiments, all with promising results.
Role of Immunoglobulin M and A Antibodies in the Neutralization of Severe Acute Respiratory Syndrome Coronavirus 2 (2020)

IgG, IgM, and IgA are critical components of convalescent plasma used for treatment of coronavirus disease 2019 (COVID-19).
Pulmonary imaging after stereotactic radiotherapy—does RECIST still apply? (2016)

The use of stereotactic ablative radiotherapy (SABR) for the treatment of primary lung cancer and metastatic disease is rapidly increasing. However, the presence of benign fibrotic changes on CT imaging makes response assessment following SABR a challenge, as these changes develop with an appearance similar to tumour recurrence. Misclassification of benign fibrosis as local recurrence has resulted in unnecessary interventions, including biopsy and surgical resection. Response evaluation criteria in solid tumours (RECIST) are widely used as a universal set of guidelines to assess tumour response following treatment. However, in the context of non-spherical and irregular post-SABR fibrotic changes, the RECIST criteria can have several limitations. Positron emission tomography can also play a role in response assessment following SABR; however, false-positive results in regions of inflammatory lung post-SABR can be a major clinical issue and optimal standardized uptake values to distinguish fibrosis and recurrence have not been determined. Although validated CT high-risk features show a high sensitivity and specificity for predicting recurrence, most recurrences are not detected until more than 1-year post-treatment. Advanced quantitative radiomic analysis on CT imaging has demonstrated promise in distinguishing benign fibrotic changes from local recurrence at earlier time points, and more accurately, than physician assessment. Overall, the use of RECIST alone may prove inferior to novel metrics of assessing response.
Spinmotive force due to motion of magnetic bubble arrays driven by magnetic field gradient (2014)

Interaction between local magnetization and conduction electrons is responsible for a variety of phenomena in magnetic materials. It has been recently shown that spin current and associated electric voltage can be induced by magnetization that depends on both time and space. This effect, called spinmotive force, provides for a powerful tool for exploring the dynamics and the nature of magnetic textures, as well as a new source for electromotive force. Here we theoretically demonstrate the generation of electric voltages in magnetic bubble array systems subjected to a magnetic field gradient. It is shown by deriving expressions for the electric voltages that the present system offers a direct measure of phenomenological parameter β that describes non-adiabaticity in the current induced magnetization dynamics. This spinmotive force opens a door for new types of spintronic devices that exploit the field-gradient.
A trust scheme based DRM model for P2P system (2006)

With the maturation of P2P technology, there are more and more challenges to the protection of digital rights. DRM for traditional Client/Server model can not satisfy the requirement of digital right protection of P2P network. With practical application of P2P network technology and new generational DRM technology, the article proposes a DRM model for P2P system based on trust degree. The proposed model shares the secret key to the trusty peers and affords necessary security ensure for digital content delivery based on P2P technology. Mathematic analyses and simulations show that, compared to the current DRM model, the proposed model is more robust toleration of transmit and security.
Periodic pattern formation in an achiral bent core nematic (2018)

We investigated a periodic flexoelectric domain pattern, which appeared as regular parallel stripes in an achiral bent core nematic liquid crystal when dc electric field was applied. We found that such a pattern was first formed at the substrate surface and took place in sandwich cells with a gap larger than 2μm. The field-induced periodic pattern was preserved in the field-off state by a polymer network formed in the cell and was found to exhibit a polar as well as a linear electro-optic response due to in-plane switching of the sample optic axis. A comparison between this response and the one obtained in short cholesteric liquid crystals, aligned in ULH (uniform lying helix) texture, and short pitch ferroelectric liquid crystals, respectively, suggested that a heliconical molecular order is most probably formed in the field-induced periodic stripe pattern, with the helix axis orthogonal to the stripes. To our knowledge, this is the first experimental evidence of field-induced chiral-symmetry breaking in the flexoelectric periodic stripe pattern in achiral bent core nematic, resulting in heliconical molecular order, resembling the one of twist-bend (TB) nematic phase in this kind of nematics.
Inclusion Complexation of Propofol with 2-Hydroxypropyl-β- cyclodextrin. Physicochemical, Nuclear Magnetic Resonance Spectroscopic Studies, and Anesthetic Properties in Rat (1998)

An aqueous formulations of propofol 1 can be prepared by solubilizing it in the presence of 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD). This is potentially useful for parenteral administration of the drug. The aqueous solubility of 1 linearly increased as a function of HP-beta-CD concentration and showed features of an AL type diagram. Thermodynamic parameters were obtained by using the temperature dependence of the stability constant at temperatures of between 25 and 37 degrees C. The results indicate that complex formation is enthalpically, rather than entropically, driven and that it may involve van der Waals (dispersive) forces, rather than hydrophobic interactions. The structure of the inclusion complex propofol/HP-beta-CD was investigated in D2O, using 1H and 13C NMR spectroscopy. These studies revealed that the whole aromatic ring, as well as part of the isopropyl groups of the guest molecule, is located inside the HP-beta-CD cavity, while the hydroxy group is located at the rim of the wider cavity end. The geometrical features of the inclusion complex 1-HP-beta-CD are confirmed by 1D NOE difference spectra and molecular modeling experiments. The anesthetic activity in rat was investigated, and it was found that there are significant differences in induction time and sleeping time between 1 solubilized in the presence of HP-beta-CD and the formulation currently used (Diprivan), which is a 1% w/v oil/water emulsion.
Direct N-Acylation of Lactams, Oxazolidinones, and Imidazolidinones with Aldehydes by Shvo’s Catalyst (2012)

Direct N-acylation of lactams, oxazolidinones, and imidazolidinones was achieved with aldehydes by Shvo's catalyst without using any other stoichiometric reagent. The N-acylations with α,β-unsaturated aldehydes were achieved with excellent yields.
Epidemiology of Cancer Risk and Vitamin D (1999)

Even though great differences exist in incidence and mortality rates of colon cancer (1) and breast cancer (2,3) according to latitude of residence, the etiologies of these cancers remain largely unexplained. Two other cancers, ovarian (4) and prostate (5–7), are also inversely related to latitude. Profound changes in incidence and mortality rates from colon and breast cancer also occur in immigrants from low-risk to high-risk areas. The rise in incidence rates occurs in the immigrants themselves for colon cancer (8), but mainly in their daughters for breast cancer (9).
ChemInform Abstract: MACROCYCLIC STEREOCONTROL. TOTAL SYNTHESIS OF (.+‐.)‐3‐DEOXYROSARANOLIDE (1984)

Abstract Die Synthese der Titelverbindung (IX) wird beschrieben.
Limb, joint and pelvic kinematic control in the quail coping with step perturbations (2022)

Abstract Small cursorial birds display remarkable walking skills and can negotiate complex and unstructured terrains with ease. The neuromechanical control strategies necessary to adapt to these challenging terrains are still not well understood. Here, we analyzed the 2D- and 3D pelvic and leg kinematic strategies employed by the common quail to negotiate visible step-up and step-down perturbations of 1 cm, 2.5 cm, and 5 cm. We used biplanar fluoroscopy to accurately describe joint positions in three dimensions and performed semi-automatic landmark localization using deep learning. Quails negotiated vertical perturbations without major problems and rapidly regained steady-state locomotion. When coping with step-up perturbations, the quail mostly adapted the trailing limb to permit the leading leg to step on the elevated substrate in a similar way as it did during level locomotion. When the quail negotiated step-down perturbations, both legs showed significant adaptations. For small and moderate perturbations (not inducing aerial running) the quail kept the function of the distal joints (i.e., their kinematic pattern) largely unchanged during uneven locomotion, and most changes occurred in proximal joints. The hip regulated leg length, while the distal joints maintained the spring-damped limb patterns. However, to negotiate the largest visible step perturbations, more dramatic kinematic alterations were observed. For these large perturbations, all joints contributed to leg lengthening/ shortening in the trailing leg and both the trailing and leading legs stepped more vertically and less abducted. This indicates a shift from a dynamic walking program to strategies that are focused on maximizing safety.
Direct Measurement of High-Gain and Complementary Charge-Steering Amplifiers (2017)

This brief presents direct measurement of two novel dynamic amplifiers utilizing the “charge-steering” topology. Employing a delayed clocking scheme, a four-stage charge-steering amplifier achieves the highest gain of any reported charge-steering topology. A complementary charge-steering amplifier exploits both charging and discharging cycles to double the throughput while reducing power consumption by 22%. Fabricated in 180-nm technology, this brief presents, for the first time, direct measurement results of charge-steering amplifiers, including gain, noise, linearity, common-mode response, and power supply rejection ratio.
Treatment of Displaced Intra-Articular Fractures of the Distal End of the Radius with Plates* (1997)

Thirty-four displaced intra-articular fractures of the distal aspect of the radius in thirty-four patients were treated with open reduction and internal fixation with plates and screws. Although there was a high rate of complications (nine [26 per cent] of thirty-four fractures), twenty-eight patients (82 per cent) had a good or excellent result according to the system of Gartland and Werley and twenty patients (59 per cent) had a good or excellent result according to the modified system of Green and O'Brien at the most recent evaluation. Immediately postoperatively, the articular surface of the distal aspect of the radius was restored to a mean of 2 degrees of volar tilt and 20 degrees of radial angulation and radial length was improved by a mean of ten millimeters compared with the preoperative length. The articular surface was restored to congruity or to at most one millimeter of step-off in twenty-six patients (76 per cent). By the time of the most recent evaluation, the initial postoperative alignment had changed markedly in three patients (9 per cent) and degenerative osteoarthrosis (grade II or III) had developed in six patients (18 per cent). We considered that the initial postoperative alignment had changed markedly when the articular surface was displaced by two millimeters or more, when the extra-articular alignment had changed by more than 10 degrees of radial tilt, or when there was more than five millimeters of radial shortening. The potential for restoration of normal alignment and the stability of the fixation are the main advantages of internal fixation with plates. Restoration of congruity to the joint was the major difficulty in this group of patients.
Masked Imitation Learning: Discovering Environment-Invariant Modalities in Multimodal Demonstrations (2022)

Multimodal demonstrations provide robots with an abundance of information to make sense of the world. However, such abundance may not always lead to good performance when it comes to learning sensorimotor control policies from human demonstrations. Extraneous data modalities can lead to state over-specification, where the state contains modalities that are not only useless for decision-making but also can change data distribution across environments. State over-specification leads to issues such as the learned policy not generalizing outside of the training data distribution. In this work, we propose Masked Imitation Learning (MIL) to address state over-specification by selectively using informative modalities. Specifically, we design a masked policy network with a binary mask to block certain modalities. We develop a bi-level optimization algorithm that learns this mask to accurately filter over-specified modalities. We demonstrate empirically that MIL outperforms baseline algorithms in simulated domains including MuJoCo and a robot arm environment using the Robomimic dataset, and effectively recovers the environment-invariant modalities on a multimodal dataset collected on a real robot. Our project website presents supplemental details and videos of our results at: https://tinyurl.com/masked-il