gebhart/patrepeval huggingface dataset:
Hybrid QM/MM vs Pure MM Molecular Dynamics for Evaluating Water Distribution within p21N-ras and the Resulting GTP Electronic Density (2019)

p21<sup>ras</sup> protein activity, regulated by GTP hydrolysis, constitutes an active field of research for the development of cancer targeted therapies that would concern ∼30% of human tumors to which specific mutations have been associated. Indeed, the catalyzing mechanisms provided by the protein environment during GTP hydrolysis and how they are impaired by specific mutations remain to be fully elucidated. In this article, we present results from molecular mechanics (MM) molecular dynamics (MD) simulations and density functional theory (DFT) calculations carried out for wild-type p21 <sup>N-ras</sup> and six Gln 61 mutants. In the first part, we present the water distribution within the active site of the wild-type protein according to MM MD. Significant differences are observed when comparing the results to the previous distribution assessed through quantum mechanics/molecular mechanics (QM/MM) MD. Such method-dependent results highlight the importance of accounting for the electrostatic coupling between the protein complex and the solvent molecules in identifying hydration sites. In the second part, we present the results from DFT calculations performed to determine the electronic distribution of the GTP ligand, considering the wild-type active site arrangement according to both classical and hybrid approaches. Only in the QM/MM-based configuration is the ligand electronic density similar to that of a GDP-like state observed experimentally. For this reason, in the last set of calculations carried out for p21 <sup>N-ras</sup> Gln 61 mutants, only the active site structural conformations obtained through hybrid MD are considered. Through the analysis of the GTP electronic density, we conclude that the wild-type active site arrangement according to QM/MM MD is closer to a catalytically efficient conformation of the protein than the arrangement according to MM MD. Hence, water distribution according to the hybrid approach must correspond to the optimal placement of solvent in the active site. Within all of the studied Gln 61 substituted proteins, p21<sup>ras</sup> major catalyzing effect, which consists of stabilizing a more GDP-like state, is lost.
Provably weak instances of Ring-LWE (2015)

The ring and polynomial learning with errors problems (Ring-LWE and Poly-LWE) have been proposed as hard problems to form the basis for cryptosystems, and various security reductions to hard lattice problems have been presented. So far these problems have been stated for general (number) rings but have only been closely examined for cyclotomic number rings. In this paper, we state and examine the Ring-LWE problem for general number rings and demonstrate provably weak instances of Ring-LWE. We construct an explicit family of number fields for which we have an efficient attack. We demonstrate the attack in both theory and practice, providing code and running times for the attack. The attack runs in time linear in q, where q is the modulus. Our attack is based on the attack on Poly-LWE which was presented in [Eisenträger-Hallgren-Lauter]. We extend the EHL-attack to apply to a larger class of number fields, and show how it applies to attack Ring-LWE for a heuristically large class of fields. Certain Ring-LWE instances can be transformed into Poly-LWE instances without distorting the error too much, and thus provide the first weak instances of the Ring-LWE problem. We also provide additional examples of fields which are vulnerable to our attacks on Poly-LWE, including power-of-$2$ cyclotomic fields, presented using the minimal polynomial of $ζ_{2^n} \pm 1$.
Platycodin d induces g2/m cell-cycle arrest, leading to endoreduplication, inhibition of proliferation and apoptosis in leukemia cells (2007)

B3 Platycodin D (PD), a major constituent of triterpene saponins in Platycodon grandiflorum, has also become an interesting candidate for cancer chemotherapy however, little is known about apoptotic mechanisms on cancer cells. We herein investigated the mechanisms that are related to PD-induced anti-proliferation and cell death in human leukemia cells (U937, THP-1 and K562 cells). Cell growth was assessed with proliferation assays, cell counting, flow cytometry, phase contrast microscopy and Western blot assay. Microtubule (MT) formation was measured with immunofluorescent staining and in vitro tubulin polymerization assay. Apoptotic effect was analyzed by assessing increase in annexin V-staining and caspase-3 activity. Treatment of synchronized leukemia cells with varying concentrations of PD resulted in significant G2/M cell cycle arrest and endoreduplication (END) via downregulation of Cdc2/cyclin B1 and upregulation of wee1 expression, and elevated the Cdk2 protein via downregulation of p21 within 48 h. We also researched PD’s induction of polyploidy through the MT polymerization. Immunofluorescent microscopy and Western blot analysis revealed that PD significantly caused MT polymerization in leukemia cells. We also found that very highconcentrations of PD (> 200 µM) were required to directly induce MT polymerization in vitro. Finally, PD exposure induced apoptosis and cell death significantly increased PARP and lamin A cleavage, and caspase-3 activity. We conclude that theprimary means by which PD induces END not only arrests cells in mitosis by suppressing spindle MT dynamics, but also promotes mitotic cell apoptosis in human leukemia cells.
Monoclonal antibody HMFG-2 retains activity in vivo and binds to high molecular weight components expressed by metastatic breast cancers. (1986)

The monoclonal antibody HMFG-2 was raised against components of the human milk fat globule and human milk epithelial cells. It recognizes an epitope on glycoproteins of varying molecular weight; it is tumour-associated and expressed heterogeneously by most breast cancers. An intravenous injection of 131I-labelled HMFG-2 has been given to patients with recurrent cutaneous metastasis from breast carcinomas. Clearance of radioactivity from the plasma was measured and the label was shown to be carried on intact circulating antibody that had the ability to bind in vitro to the specific determinant as expressed by both the patients own tumour and by cultured breast cancer cells. Antibody was found to be associated with biopsy material taken from skin metastases 24 hours after administration of labelled antibody. However, the amount of radioactivity was insufficient for the production of a positive isotopic scan.
Fate of a Bioactive Fluorescent Wortmannin Derivative in Cells (2007)

Here, we report on NBD-Wm, a fluorescent wortmannin (Wm) probe that maintains the bioactivity of Wm as an inhibitor of PI3 kinase and as an antiproliferative agent. The attachment of the NBD fluorochrome permits NBD-Wm in cells to be monitored by NBD fluorescence-based methods such as FACS or fluorescence microscopy or with an anti-NBD antibody. The fluorescence of NBD-Wm treated cells reached a peak at 1.5 h and then decreased because of the extrusion of a fluorescent compound into the culture media. Cells accumulated NBD-Wm to levels about 30-fold higher than those in the media. NBD-Wm modified five major proteins, with the modification of the catalytic subunit of PI3 kinase being a minor band. The bioactivity of NBD-Wm, coupled with a variety of techniques available for determining its disposition, suggest that NBD-Wm can be a useful tool in understanding the mechanism of action of viridins.
Controlling electron-ion rescattering in two-color circularly polarized femtosecond laser fields (2016)

Strong-field ionization in two-color circularly polarized fields is studied, where both experimental measurements and theoretical analyses suggest that the production of high-energy electrons from electron-ion rescattering is optimized in counterrotating fields, and when the ponderomotive energies of the two laser fields are equal.
Automated Detection of Real-World Falls: Modeled From People With Multiple Sclerosis (2020)

Falls are a major health problem with one in three people over the age of 65 falling each year, oftentimes causing hip fractures, disability, reduced mobility, hospitalization and death. A major limitation in fall detection algorithm development is an absence of real-world falls data. Fall detection algorithms are typically trained on simulated fall data that contain a well-balanced number of examples of falls and activities of daily living. However, real-world falls occur infrequently, making them difficult to capture and causing severe data imbalance. People with multiple sclerosis (MS) fall frequently, and their risk of falling increases with disease progression. Because of their high fall incidence, people with MS provide an ideal model for studying falls. This paper describes the development of a context-aware fall detection system based on inertial sensors and time of flight sensors that is robust to imbalance, which is trained and evaluated on real-world falls in people with MS. The algorithm uses an auto-encoder that detects fall candidates using reconstruction error of accelerometer signals followed by a hyper-ensemble of balanced random forests trained using both acceleration and movement features. On a clinical dataset obtained from 25 people with MS monitored over eight weeks during free-living conditions, 54 falls were observed and our system achieved a sensitivity of 92.14%, and false-positive rate of 0.65 false alarms per day.
A novel hardware approach to integrating active and passive rehabilitation in a single exoskeleton (2018)

The proposed exoskeleton is based on the elbow joint where patients can have active and passive rehabilitation in a single structure without changing its configuration. The structural formation of the exoskeleton has been designed in such a way that it offers two working regions namely; actuator based active rehabilitation in the first phase and passive rehabilitation in the second phase. The solution for integrating these two phases has been implemented using an innovative passive locking mechanism which uses a spring-based system for transformation. The stiffness of the spring is utilized to switch between active and passive rehabilitation regions. Besides this there are some other advantages this exoskeleton offers such as reduction of the actuation torque as well as ease of control. The paper is divided into three parts: the first part describes the existing designs, the second part gives an overview of the developed mechanism with structural description and the last part provides the solution with technical specification.
PL Signatures from Decoration of Dislocations in SiC Substrates and Epitaxial Wafers (2023)

Photoluminescence (PL) signatures of 4H-SiC bare and epitaxial wafers from a surface inspection tool have been studied. Large variations in PL black or white dot densities were confirmed for comparable crystal quality and growth process conditions. Comparison with KOH etching results confirms that both PL black and white dots are tied to discrete threading dislocations. PL spectra results suggest dislocation decoration by donor-acceptor pairs.
Dynamic hard Fractional Frequency Reuse for mobile WiMAX (2009)

Fractional frequency reuse (FFR) is gaining much attention in WiMAX standardization bodies to mitigate the inter-cell interference and reduce the throughput outage at the cell edges. A hard FFR pattern based on a time division of the available total bandwidth between inner and outer cell users is recommended in the IEEE 802.16e standard. The DL subframe is configured so that users close to the base station operate on the zone with all subchannels available, while for the edge users, each cell operates on the zone with a fraction of all subchannels available. In this paper, we propose a hard FFR scheme that dynamically adjusts the size of each zone according to the system load. Our approach is based on either a partial or a full coordination between the base stations. The effectiveness of our scheme is particularly proved when a non-uniform distribution of the users in the cell is considered.
Heparin Sequencing Using Enzymatic Digestion and ESI-MSn with HOST:  A Heparin/HS Oligosaccharide Sequencing Tool (2005)

Mass spectrometry, and specifically sequential stages of mass spectrometry (MSn), is an established tool for the analysis of carbohydrates, proteins, and more recently glycosaminoglycans. As this trend continues, the development of algorithms for the rapid and automatic interpretation of mass spectra to identify glycan structure is also expected to grow as an active field of research. The methodology described herein utilizes a combination of enzymatic digestion, ESI-MS, and MSn for the sequencing of small heparin oligosaccharides. The heparin oligosaccharide sequencing tool (HOST) is a basic software application that was developed to aid in the integration and analysis of the data generated from these experiments, facilitating the process involved in arriving at sequence information. The sequences of several heparin oligosaccharides were determined using this method to illustrate proof of principle. Tandem MS is a very rapid and efficient tool for oligosaccharide analysis when limited amounts of material are available. Having a means, such as HOST, for automating the interpretation of the MSn data generated from glycosaminoglycans, provides a practical methodology for the future analysis of heparin/HS oligosaccharides of unknown structure.
The yeast Sup35NM domain propagates as a prion in mammalian cells (2008)

Prions are infectious, self-propagating amyloid-like protein aggregates of mammals and fungi. We have studied aggregation propensities of a yeast prion domain in cell culture to gain insights into general mechanisms of prion replication in mammalian cells. Here, we report the artificial transmission of a yeast prion across a phylogenetic kingdom. HA epitope-tagged yeast Sup35p prion domain NM was stably expressed in murine neuroblastoma cells. Although cytosolically expressed NM-HA remained soluble, addition of fibrils of bacterially produced Sup35NM to the medium efficiently induced appearance of phenotypically and biochemically distinct NM-HA aggregates that were inherited by daughter cells. Importantly, NM-HA aggregates also were infectious to recipient mammalian cells expressing soluble NM-HA and, to a lesser extent, to yeast. The fact that the yeast Sup35NM domain can propagate as a prion in neuroblastoma cells strongly argues that cellular mechanisms support prion-like inheritance in the mammalian cytosol.
The majority of myeloid‐antigen‐positive (My+) childhood B‐cell precursor acute lymphoblastic leukaemias express TEL‐AML1 fusion transcripts (1997)

The t(12:21) translocation fuses the TEL and AML1 genes and has been found in up to 28% of paediatric B-cell precursor acute lymphoblastic leukaemias (BCP-ALL). The AML1 gene is a transcription factor which regulates expression of several myeloid differentiation associated genes. A molecular analysis of TEL-AML1, E2A-PBX1, MLL-AF4, BCR-ABL expression and an immunophenotypic study of CD13/CD33 myeloid antigen expression have been performed prospectively on tumour cells from 96 paediatric BCP-ALL patients. Percentages of CD13 or CD33 expressing leukaemic cells were found to be higher in TEL-AML1 positive cases (n = 22) than in TEL-AML1 negative (n = 74) cases (P<0.001). In 22/96 cases (23%) >10% of neoplastic cells were found to express at least one of the two markers. In 14 of these cases (63%), TEL-AML1 expression was detected, whereas t(4;11), t(11;19) and t(9;22) translocations were found by molecular methods in only three cases (14%). In four cases (18%) no molecular marker was found. These data show that TEL-AML1 expression is significantly associated with myeloid antigen expression by leukaemic cells and suggests that the prognostic significance of myeloid antigen expression in paediatric ALLs should be re-evaluated in the light of molecular cytogenetic markers.
Validation of an RNA cell cycle progression score for predicting death from prostate cancer in a conservatively managed needle biopsy cohort (2015)

The CCP score provides significant pretreatment prognostic information that cannot be provided by clinical variables and is useful for determining which patients can be safely managed conservatively, avoiding radical treatment.
Cardiac output is not a significant source of low frequency mean arterial pressure variability (2013)

Spontaneous mean arterial pressure (MAP) variability may be mainly due to fluctuations in cardiac output (CO) and total peripheral resistance (TPR). While high frequency (HF ∼ 0.25 Hz) oscillations in MAP are ultimately driven by respiration, the source of low frequency (LF ∼ 0.1 Hz) fluctuations has not been fully elucidated. It is known that CO buffers these oscillations, but there is no evidence on its potential role in also generating them. The main goal was to determine whether CO is a source of LF variability in MAP. Six dogs were chronically instrumented to obtain beat-to-beat measurements of CO and MAP while the dogs were fully awake and at rest. A causal dynamic model was identified to relate the fluctuations in CO to MAP. The model was then used to predict the MAP fluctuations from the CO fluctuations. The CO fluctuations were able to predict about 70% of the MAP oscillations in the HF band but showed no predictive value in the LF band. Hence, respiration induces CO fluctuations in the HF band that, in turn, cause MAP oscillations, while TPR fluctuations appear to be the dominant mediator of LF fluctuations of MAP. CO is not a significant source of these oscillations, and it may only be responsible for dampening them, likely through the baroreflex.
Room-temperature THz imaging based on antenna-coupled MOSFET bolometer (2013)

We report on the design, fabrication and measurements of a new THz sensor concept based on an antenna-coupled MOSFET bolometer for room-temperature passive THz imaging for security and medical-diagnostic applications. The device is fabricated in a 180-nm CMOS SOI technology followed by a post-CMOS MEMS process. In this sensor, the antenna absorbing the THz electromagnetic field is directly coupled to the bolometer for maximum energy collection, whereas its design aims at minimizing its thermal mass as is necessary for fast frame rates. DC measurements before and after the MEMS process as well as thermal time constant and THz antenna measurements are presented.
Factors Affecting Mouse-Based 3D Selection in Desktop VR Systems (2015)

We present two experiments on mouse-based point selection in a desktop virtual reality system using stereo display and head-tracking. To address potential issues of using a mouse cursor with stereo display, we also evaluate the impact of using a one-eyed (mono) cursor. While a one-eyed cursor visualization eliminates depth conflicts, recent work suggests it offers worse performance than stereo cursors, possibly due to eye discomfort. Our results indicate that presenting the cursor in stereo significantly reduces performance for targets at different depths. The one-eyed cursor eliminates this effect, offering better performance than both screen-plane and geometry-sliding cursors visualized in stereo. However, it also performed slightly worse than stereo cursors in situations without depth conflicts. Our study suggests that this difference is not due exclusively to the relative transparency of such a cursor, hence eye fatigue or similar may be responsible.
Nonlinear statistical mechanics drives intrinsic electrostriction and volumetric torque in polymer networks (2021)

Statistical mechanics is an important tool for understanding polymer electroelasticity because the elasticity of polymers is primarily due to entropy. However, a common approach for the statistical mechanics of polymer chains, the Gaussian chain approximation, misses key physics. By considering the nonlinearities of the problem, we show a strong coupling between the deformation of a polymer chain and its dielectric response, that is, its net dipole. When chains with this coupling are cross linked in an elastomer network and an electric field is applied, the field breaks the symmetry of the elastomer's elastic properties and, combined with electrostatic torque and incompressibility, leads to intrinsic electrostriction. Conversely, deformation can break the symmetry of the dielectric response, leading to volumetric torque and asymmetric actuation. Both phenomena have important implications for designing high-efficiency soft actuators and soft electroactive materials, and the presence of mechanisms for volumetric torque, in particular, can be used to develop higher degree of freedom actuators and to achieve bioinspired locomotion.
ICSI choreography: fate of sperm structures after monospermic rhesus ICSI and first cell cycle implications (2000)

We have dissected the initial stages of fertilization by intracytoplasmic sperm injection of single spermatozoa into prime oocytes from fertile rhesus monkeys (Macaca mulatta). DNA decondensation was delayed at the apical portion of the sperm head. It is possible that this asynchronous male DNA decondensation could be related to the persistence of the sperm acrosome and perinuclear theca after injection. However, incomplete male pronuclear formation did not prevent sperm aster formation, microtubule nucleation and pronuclear apposition. In contrast, DNA synthesis was delayed in both pronuclei until the sperm chromatin fully decondensed, indicating that male pronuclear formation constitutes an important checkpoint during the first embryonic cell cycle.