gebhart/patrepeval huggingface dataset:
Discriminative Robust transformation learning (2015)

This paper proposes a framework for learning features that are robust to data variation, which is particularly important when only a limited number of training samples are available. The framework makes it possible to tradeoff the discriminative value of learned features against the generalization error of the learning algorithm. Robustness is achieved by encouraging the transform that maps data to features to be a local isometry. This geometric property is shown to improve (K, ∊)-robustness, thereby providing theoretical justification for reductions in generalization error observed in experiments. The proposed optimization framework is used to train standard learning algorithms such as deep neural networks. Experimental results obtained on benchmark datasets, such as labeled faces in the wild, demonstrate the value of being able to balance discrimination and robustness.
Development of PLM-102, a novel dual inhibitor of FLT3 and RET as a new therapeutic option for acute myeloid leukemia. (2022)

e15103 Background: Mutations of the FMS-like tyrosine kinase 3 (FLT3) gene occur in approximately 30% of all acute myeloid leukemia (AML) cases, with the internal tandem duplication (ITD) representing the most common type of FLT3 mutation (FLT3-ITD; approximately 25% of all AML cases). Although several FLT3 inhibitors have been developed, occurrence of secondary TKD mutations of FLT3 such as FLT3/D835Y and FLT3/F691L causes the acquired resistance to the current FLT3 inhibitors and eventually become a key area of unmet medical needs. Here, we have revealed that PLM-102, a novel, orally active FLT3 and RET dual inhibitor, has a potential to overcome the acquired resistance to current FLT3 inhibitors. Methods: 1. Kinase assay- Biochemical assays for FLT3 (WT and D835Y) and RET (WT and Mutants) were performed according to ADP-Glo kinase assay protocol(Promega). 2. Cell proliferation and Apoptosis- Human leukemia cell line MV4-11 and MOLM-14 were purchased from ATCC and DSMZ. Cells were seeded at a density of 2 X 10 3 cells per well and treated with the indicated concentrations of inhibitors for 72 hours at 37°C. Cell viability was determined by an Alamar Blue assay (Bio-Rad). Caspase-3/7 activity was measured by using the Caspase-Glo 3/7 assay (Promega). 3. Western blot analysis- Immunoblotting using MOLM-14 cells was performed using anti-phospho-FLT3 (Cell Signaling Technology #3461) and anti-FLT3 antibody (Cell Signaling Technology #3462). 4. In vivo mouse models- The MV4-11 and MOLM-14 cells are implanted into the subcutaneous space of the left flank of the mice. Resulting tumors are monitored by calipering twice weekly. Treatment started after randomization when tumor volumes had reached a size of approximately 100-150 mm 3 . For statistical analysis, analysis of variance (ANOVA) was performed using Prism 9.0 to examine statistical differences. Results: In compared to FDA-approved Gilteritinib, PLM-102 showed stronger sub-nanomolar IC 50 values in FLT3 kinases regardless of wild-type, ITD, TKD and ITD/TKD mutants in both kinase- and cell-based assays. PLM-102 inhibited phosphorylation of FLT3 and its downstream signaling pathways, and induced apoptosis as evidenced by PARP-cleavage and caspase-3 activation. Moreover, PLM-102 showed an excellent anti-tumor activity in mouse xenograft models implanted with MV4-11 and MOLM-14 AML cells. Conclusions: Taken together, PLM-102 showing potent anti-cancer activity against various in vitro and in vivo AML models could be developed as a valuable agent overcoming the acquired resistance to the current FLT3 inhibitor.
Corrigendum to “Antidepressant Effect of Fraxinus rhynchophylla Hance Extract in a Mouse Model of Chronic Stress-Induced Depression” (2019)

[This corrects the article DOI: 10.1155/2018/8249563.].
Transcription Factors and Plants Response to Drought Stress: Current Understanding and Future Directions (2016)

Increasing vulnerability of plants to a variety of stresses such as drought, salt and extreme temperatures poses a global threat to sustained growth and productivity of major crops. Of these stresses, drought represents a considerable threat to plant growth and development. In view of this, developing staple food cultivars with improved drought tolerance emerges as the most sustainable solution toward improving crop productivity in a scenario of climate change. In parallel, unraveling the genetic architecture and the targeted identification of molecular networks using modern "OMICS" analyses, that can underpin drought tolerance mechanisms, is urgently required. Importantly, integrated studies intending to elucidate complex mechanisms can bridge the gap existing in our current knowledge about drought stress tolerance in plants. It is now well established that drought tolerance is regulated by several genes, including transcription factors (TFs) that enable plants to withstand unfavorable conditions, and these remain potential genomic candidates for their wide application in crop breeding. These TFs represent the key molecular switches orchestrating the regulation of plant developmental processes in response to a variety of stresses. The current review aims to offer a deeper understanding of TFs engaged in regulating plant's response under drought stress and to devise potential strategies to improve plant tolerance against drought.
Desulfurization–Oxygenation of Chiral 1,3-Thiazolidine-2-thiones and 1,3-Oxazolidine-2-thiones Using Propylene Oxide and Microwave Irradiation (2012)

An efficient method for the desulfurization–oxygenation of 1,3-thiazolidine-2-thiones and 1,3-oxazolidine-2-thiones using propylene oxide and employing microwave irradiation is described. This strategy of oxygenation of the thiocarbonyl group provides an attractive methodology to prepare chiral 1,3-thiazolidin-2-ones and 1,3-oxazolidin-2-ones from the corresponding precursors in good yields.
Site-Specific Rectocele Repair Compared With Standard Posterior Colporrhaphy (2005)

II-3.
Nonequilibrium Synthesis and Assembly of Hybrid Inorganic−Protein Nanostructures Using an Engineered DNA Binding Protein (2005)

We show that a protein with no intrinsic inorganic synthesis activity can be endowed with the ability to control the formation of inorganic nanostructures under thermodynamically unfavorable (nonequilibrium) conditions, reproducing a key feature of biological hard-tissue growth and assembly. The nonequilibrium synthesis of Cu(2)O nanoparticles is accomplished using an engineered derivative of the DNA-binding protein TraI in a room-temperature precursor electrolyte. The functional TraI derivative (TraIi1753::CN225) is engineered to possess a cysteine-constrained 12-residue Cu(2)O binding sequence, designated CN225, that is inserted into a permissive site in TraI. When TraIi1753::CN225 is included in the precursor electrolyte, stable Cu(2)O nanoparticles form, even though the concentrations of [Cu(+)] and [OH(-)] are at 5% of the solubility product (K(sp,Cu2O)). Negative control experiments verify that Cu(2)O formation is controlled by inclusion of the CN225 binding sequence. Transmission electron microscopy and electron diffraction reveal a core-shell structure for the nonequilibrium nanoparticles: a 2 nm Cu(2)O core is surrounded by an adsorbed protein shell. Quantitative protein adsorption studies show that the unexpected stability of Cu(2)O is imparted by the nanomolar surface binding affinity of TraIi1753::CN225 for Cu(2)O (K(d) = 1.2 x 10(-)(8) M), which provides favorable interfacial energetics (-45 kJ/mol) for the core-shell configuration. The protein shell retains the DNA-binding traits of TraI, as evidenced by the spontaneous organization of nanoparticles onto circular double-stranded DNA.
Implicit Bias of Gradient Descent on Linear Convolutional Networks (2018)

We show that gradient descent on full-width linear convolutional networks of depth $L$ converges to a linear predictor related to the $\ell_{2/L}$ bridge penalty in the frequency domain. This is in contrast to linearly fully connected networks, where gradient descent converges to the hard margin linear support vector machine solution, regardless of depth.
The Multifunctional Protein BAG3 (2018)

The B-cell lymphoma 2-associated anthanogene (BAG3) protein is expressed most prominently in the heart, the skeletal muscle, and in many forms of cancer. In the heart, it serves as a co-chaperone with heat shock proteins in facilitating autophagy; binds to B-cell lymphoma 2, resulting in inhibition of apoptosis; attaches actin to the Z disk, providing structural support for the sarcomere; and links the α-adrenergic receptor with the L-type Ca<sup>2+</sup> channel. When BAG3 is overexpressed in cancer cells, it facilitates prosurvival pathways that lead to insensitivity to chemotherapy, metastasis, cell migration, and invasiveness. In contrast, in the heart, mutations in BAG3 have been associated with a variety of phenotypes, including both hypertrophic/restrictive and dilated cardiomyopathy. In murine skeletal muscle and vasculature, a mutation in BAG3 leads to critical limb ischemia after femoral artery ligation. An understanding of the biology of BAG3 is relevant because it may provide a therapeutic target in patients with both cardiac and skeletal muscle disease.
Potential antitumor phenoxazines (1991)

From the various studies cited, spanning more than forty years, it is clear that some members of the phenoxazine and benzophenoxazine dye family selectively stain certain tumors and, when given in suitable concentrations in the feed, can prolong life and shrink tumors. In addition, some use has been made of these compounds as carriers for other antitumor agents based upon the idea of selective accumulation into tumor tissue. Although many analogs have been made and examined, the work has been done in a relatively unfocused manner and the field could benefit from a systematic study of the effect of structure on biological activity. None of the synthetic materials prepared and tested to date has the potency of the outstanding antitumor natural products bearing the ring system of the actinomycins. Advances in our understanding of the molecular mode of action of the actinomycins, based in large measure upon x-ray studies, suggest some avenues for future exploitation. To date, attempts to prepare simplified actinomycins or elaborate phenoxazines to accomplish this have been disappointing.
Health and offence histories of young offenders in Saskatoon, Canada (1994)

This paper examines the relationship between health and juvenile criminality in Saskatchewan, Canada. The data consist of anonymised demographic, health and juvenile offence information provided by Saskatchewan Social Service and Health agencies. They allow the examination of health and offence relationships among 315 offenders attaining the age of 17 years in 1987 or 1988. Two main research questions are explored: (1) the relationship between health and the criminal career patterns of the sample, and (2) the time course of the receipt of healthcare relative to times of offence to determine whether offending is associated with an increase of healthcare being sought. The findings indicate that there is little support for an association between any specific disease category and juvenile offending. Mental disorder is the health variable most consistently distinguishing offenders. Other variables suggest intriguing relationships that cannot be regarded as conclusive on the evidence presented here: for instance, perinatal disorders distinguish those whose offences are exclusively committed against the person. The data show clear differences between offenders and non‐offenders in the pattern of health contacts made according to age. A higher proportion of medical contacts made by non‐offenders are made before their eleventh birthday. The opposite is true of offenders. This could be interpreted as showing that parents and others respond to officially recorded offending by seeking medical accounts or mitigation of juvenile offending. However, much of the increase in health contacts by offenders occurs in the years before their official identification as offenders. This suggests that medical help is sought as children develop a pre‐delinquent lifestyle and also seek medical accounts of official delinquency once it has occurred. This is most true of those who start their official delinquency late.
Arthritis induced in cat by sodium urate: a possible animal model for tonic pain (1984)

An attempt has been made to determine whether cats rendered arthritic by the injection of monosodium urate (MSU) crystals (rod-shaped 40-130 micrometers length) into one knee joint capsule can be used as animal model of tonic (chronic) pain. A limp and a decrease in body weight supported by the injected hind leg's paw occurred approximately 1 h after the MSU (20 mg) injection, reached a maximum at 2-3 h, and lasted for more than 6 h before a gradual return to pre-injection levels. They were diminished by systemic administration and local (the dorsal part of the nucleus raphe dorsalis) application of morphine, this effect being blocked by naloxone. This suggests that the limping and the paw pressure decrease are the reflexion of pain. It is suggested that the animal model of the MSU-induced arthritis is useful for the study of tonic pain.
Immunogenicity of the Plasmodium vivax merozoite surface protein 1 paralog in the induction of naturally acquired antibody and memory B cell responses (2017)

The PvMSP1P-19 antigen has immunogenicity during the induction of the antibody response, in which both the levels and inhibitory activity are maintained after the patient recovered from P. vivax infection. The maintenance of the antibody response was associated with the response of PvMSP1P-19-specific memory B cells. Therefore, the PvMSP1P-19 antigen should also be considered as a reliable vaccine candidate to develop a blood-stage vaccine against P. vivax.
[Synthesis of bronchospasmolytically effective beta phenylethyl-aminoalkyl-xanthines]. (1977)

New theophylline and theobromine derivatives are synthetized from the beta-phenylethylaminoalkyl-xanthines, whose phenyl substituent is substitutent by one or two hydroxyl groups and partially also by other substituents. Different methods of synthesis are described, among them the production of the bronchospasmolytic 7-(3-[2-(3,5-dihydroxyphenyl)-2-hydroxy-ethylamino]-propyl)-theophylline (reproterol-HCl).
Study of blood glucose level in normal and low birth weight newborns and impact of early breast feeding in a tertiary care centre (2011)

Background and Objectives: Neonatal hypoglycemia, a common metabolic problem, often goes unnoticed owing to lack of specific symptoms. We designed this study to assess the incidence of hypoglycemia in healthy normal birth weight and low birth weight babies, including both preterm and small for gestational age (SGA) newborns, to evaluate the impact of early breastfeeding on hypoglycemia and to assess the impact of exclusive breast feeding on glucose values up to 48 h of age. Design and Settings: A hospital-based prospective longitudinal study. Materials and Methods: The study was conducted over six months involving one hundred fifty healthy (both term and preterm) appropriate for gestational age (AGA) or SGA babies with birth weight between 1.5 kg and 3.99 kg. Blood glucose values were measured at the age of 1 h, 6 h, 12 h, 24 h and 48 h after delivery which was independent of feeding time. Blood glucose value less than 40 mg/dl (2.2 mmol/l) was defined as hypoglycemia. Sick newborns, those less than 34 weeks of gestation or less than 1500 g, infant of diabetic mother, those with birth asphyxia, congenital malformations and endocrine deficiencies were excluded. Results: Overall incidence of hypoglycemia was 32%. Hypoglycemia was significantly greater in SGA and preterm as compared to AGA and term newborns respectively (P Conclusion: Low birth weight babies (both preterm and small-for-date) are prone to develop hypoglycemia especially in first 24 h of life with delayed introduction of breast feeding being an additional risk.
First Direct Dating of Alteration of Paleo-Oil Pools Using Rubidium-Strontium Pyrite Geochronology (2020)

Direct dating of petroleum systems by hydrocarbon or associated authigenic minerals is crucial for petroleum system analysis and hydrocarbon exploration. The precipitation of authigenic pyrite in petroliferous basins is commonly genetically associated with hydrocarbon generation, migration, accumulation, or destruction. Pyrite rubidium-strontium (Rb-Sr) isotope dilution thermal ionization mass spectrometry (ID-TIMS) is a well-developed technique, and its successful application for high-temperature ore systems suggests that this dating method has the potential to directly date key processes in the low-temperature petroleum systems. Rb-Sr data for pyrites in two Ordovician carbonate rock specimens collected from ~4952 m in the YD-2 well in the Yudong region, northern Tarim Basin (NW China), yield two identical isochron ages within analytical uncertainties: 206 ± 13 (2σ) and 224 ± 28 Ma (2σ). SEM investigations demonstrate that Rb and Sr atoms mainly reside in the crystal lattice of the pyrites due to the absence of fluid and mineral inclusions. The rigorous Rb-Sr isochron relations documented in the samples indicate that such residency can result in sufficient Rb/Sr fractionation and initial Sr isotopic homogenization for geochronology. In addition, the closure temperature (227–320 °C) for the Rb-Sr isotope system in pyrite is higher than the precipitation temperature for pyrite in petroleum-related environments (below 200 °C), suggesting that the Rb-Sr age of pyrite was not overprinted by post-precipitation alteration. Integrating the lead-strontium-sulfur isotopes of the pyrites with burial history analysis, the ages are interpreted as the timing of alteration of the paleo-oil pool by a hydrothermally-triggered thermochemical sulfate reduction process. This study, for the first time, demonstrates that Rb-Sr pyrite geochronology, combined with radiogenic and stable isotopic analyses, can be a useful tool to evaluate the temporal evolution of oil pools. This approach bears great potential for dating of petroleum systems anywhere else in the world.
Isolation and characterization of HeLa cell lines blocked at different steps in the poliovirus life cycle (1989)

Cotransfection of poliovirus RNA and R1, a poliovirus subgenomic RNA containing a deletion of nearly all of the capsid region, resulted in surviving cells, in contrast to the complete cell death observed after transfection with viral RNA. Cells that survived the cotransfection grew into colonies, produced infectious poliovirus, and underwent cycles of cell lysis (crisis periods) where less than 1% of the cells survived, followed by periods of growth. Poliovirus evolved during the persistent infection as judged by changes in plaque size. After passage for 6 months, a stable line called SOFIA emerged that no longer produced infectious virus and did not contain viral proteins or viral RNA. Cells frozen in liquid N2 while still in crisis and recultured 4 months later (named SOFIA N2) were also stabilized. After infection with poliovirus, SOFIA N2 cells showed a delay in the development of cytopathic effect, viral production, and cellular death when compared with HeLa cells. In contrast, SOFIA cells did not develop cytopathic effect and produced 10,000 times less virus than SOFIA N2 or HeLa cells. Viral production was delayed in SOFIA and SOFIA N2 cells transfected with poliovirus RNA when compared with HeLa cells, suggesting the presence of an intracellular block to poliovirus replication. Analysis of the cellular receptor for poliovirus by virus binding, an enzyme-linked immunosorbent assay, and in situ rosette assays with an antireceptor monoclonal antibody showed that receptors were expressed in SOFIA N2 cells but not in SOFIA cells. Echovirus 6, an enterovirus which uses a different cellular receptor, formed small plaques on SOFIA cells. Vesicular stomatitis virus formed plaques of similar size on SOFIA and HeLa cells, suggesting that the intracellular block was specific for enteroviruses. Cotransfection of the subgenomic replicon R1 with poliovirion RNA therefore resulted in the selection of HeLa cell variants containing blocks to poliovirus replication at the level of receptor and within the cell.
Regulation of p53 Activity by (+)-Epiloliolide Isolated from Ulva lactuca (2021)

<i>Ulva lactuca (U. lactuca)</i> is a green alga distributed worldwide and used as a food and cosmetic material. In our previous study, we determined the effects of <i>U. lactuca</i> methanol extracts on the UVB-induced DNA repair. In the present study, we fractionated <i>U. lactuca</i> methanol extracts to identify the effective compound for the DNA repair. MTT assay demonstrated that (+)-epiloliolide showed no cytotoxicity up to 100 μM in BJ-5ta human dermal fibroblast. Upon no treatment, exposure to UVB 400 J/m<sup>2</sup> decreased cell viability by 45%, whereas (+)-epiloliolide treatment for 24 h after UVB exposure significantly increased the cell viability. In GO and GESA analysis, a number of differentially expressed genes were uniquely expressed in (+)-epiloliolide treated cells, which were enriched in the p53 signaling pathway and excision repair. Immunofluorescence demonstrated that (+)-epiloliolide increased the nuclear localization of p53. Comet assay demonstrated that (+)-epiloliolide decreased tail moment increased by UVB. Western blot analysis demonstrated that (+)-epiloliolide decreased the levels of p-p53, p21, Bax, and Bim, but increased that of Bcl-2. Reverse transcription PCR (RT-PCR) demonstrated that (+)-epiloliolide decreased the levels of MMP 1, 9, and 13, but increased that of COL1A1. These results suggest that (+)-epiloliolide regulates p53 activity and has protective effects against UVB.
Multimodal dynamics modeling for off-road autonomous vehicles (2021)

Dynamics modeling in outdoor and unstructured environments is difficult because different elements in the environment interact with the robot in ways that can be hard to predict. Leveraging multiple sensors to perceive maximal information about the robot’s environment is thus crucial when building a model to perform predictions about the robot’s dynamics with the goal of doing motion planning. We design a model capable of long-horizon motion predictions, leveraging vision, lidar and proprioception, which is robust to arbitrarily missing modalities at test time. We demonstrate in simulation that our model is able to leverage vision to predict traction changes. We then test our model using a real-world challenging dataset of a robot navigating through a forest, performing predictions in trajectories unseen during training. We try different modality combinations at test time and show that, while our model performs best when all modalities are present, it is still able to perform better than the baseline even when receiving only raw vision input and no proprioception, as well as when only receiving proprioception. Overall, our study demonstrates the importance of leveraging multiple sensors when doing dynamics modeling in outdoor conditions.