gebhart/patrepeval huggingface dataset:
Distributed deep learning for robust multi-site segmentation of CT\n imaging after traumatic brain injury (2019)

Machine learning models are becoming commonplace in the domain of medical\nimaging, and with these methods comes an ever-increasing need for more data.\nHowever, to preserve patient anonymity it is frequently impractical or\nprohibited to transfer protected health information (PHI) between institutions.\nAdditionally, due to the nature of some studies, there may not be a large\npublic dataset available on which to train models. To address this conundrum,\nwe analyze the efficacy of transferring the model itself in lieu of data\nbetween different sites. By doing so we accomplish two goals: 1) the model\ngains access to training on a larger dataset that it could not normally obtain\nand 2) the model better generalizes, having trained on data from separate\nlocations. In this paper, we implement multi-site learning with disparate\ndatasets from the National Institutes of Health (NIH) and Vanderbilt University\nMedical Center (VUMC) without compromising PHI. Three neural networks are\ntrained to convergence on a computed tomography (CT) brain hematoma\nsegmentation task: one only with NIH data,one only with VUMC data, and one\nmulti-site model alternating between NIH and VUMC data. Resultant lesion masks\nwith the multi-site model attain an average Dice similarity coefficient of 0.64\nand the automatically segmented hematoma volumes correlate to those done\nmanually with a Pearson correlation coefficient of 0.87,corresponding to an 8%\nand 5% improvement, respectively, over the single-site model counterparts.\n
FEEDBACK-INSENSITIVE MUTANTS OF THE GENE FOR THE TYROSINE-INHIBITED DAHP SYNTHETASE IN YEAST (1974)

A yeast strain lacking the phenylalanine-sensitive DAHP synthetase exhibits a tyrosine-inhibited phenotype. Reversions from this phenotype were selected. They were the result of mutations affecting the tyrosine-sensitive DAHP synthetase which became insensitive to feedback inhibition, as shown by genetic and enzymatic studies. The feedback-insensitive mutations were located at five different sites scattered on the map of the aro4 gene.
Rounding pointers (2011)

Recent trends in secure operating systems indicate that an object-capability system is the security model with pre-eminent characteristics and practicality. Unlike traditional operating systems, which use a single global name space, object-capability systems name objects per protection domain. This allows a fine-grained isolation of the domains and follows the principle of least authority.
A linked data platform for mining software repositories (2012)

The mining of software repositories involves the extraction of both basic and value-added information from existing software repositories. The repositories will be mined to extract facts by different stakeholders (e.g. researchers, managers) and for various purposes. To avoid unnecessary pre-processing and analysis steps, sharing and integration of both basic and value-added facts are needed. In this research, we introduce SeCold, an open and collaborative platform for sharing software datasets. SeCold provides the first online software ecosystem Linked Data platform that supports data extraction and on-the-fly inter-dataset integration from major version control, issue tracking, and quality evaluation systems. In its first release, the dataset contains about two billion facts, such as source code statements, software licenses, and code clones from 18 000 software projects. In its second release the SeCold project will contain additional facts mined from issue trackers and versioning systems. Our approach is based on the same fundamental principle as Wikipedia: researchers and tool developers share analysis results obtained from their tools by publishing them as part of the SeCold portal and therefore make them an integrated part of the global knowledge domain. The SeCold project is an official member of the Linked Data dataset cloud and is currently the eighth largest online dataset available on the Web.
<p>Evaluating Refractive and Visual Outcomes After Bilateral Implantation of an Apodized Diffractive Multifocal Toric Intraocular Lens with a Moderate Add in the Dominant Eye and a Higher Add in the Fellow Eye</p> (2020)

This blended bifocal IOL modality appears to be well-tolerated by subjects with a good range of vision and minimal bother from visual disturbances.
Extraction of RNA from Mycobacteria (2003)

Genetic characterization of mycobacteria has advanced considerably in the last decade. The identificatlon of putative virulence genes and their products has prompted investlgation of how expression of these factors is controlled during infection. Regulation of virulence determinants at the level of gene transcription has been investigated for many gram-negative pathogens and sheds considerable light on the control of gene expression during pathogenesis. However, extraction of intact mRNA from mycobacteria is difficult owing to the physical strength of the cell wall and has hindered the characterization of mycobacterial-gene expression
Reuse through genericity in SUAVE (2002)

VHDL currently has a limited form of genericity in which component and entity declarations can be parameterized with formal generic constants. SUAVE extends the genericity mechanism by allowing formal generics types and by allowing generics to be specified in the interfaces of subprograms and packages. The approach is based on the features of Ada-95. It allows units to be re-used in a much wider variety of contexts without modifying the original code. We show that the genericity added by SUAVE enhances reuse across the spectrum of modeling, from high-level to gate level. In particular, the genericity extensions interact with the SUAVE extensions for object-oriented data modeling to significantly improve support for high-level behavioral modeling and for developing test-benches. We show that the genericity extensions integrate seamlessly with the existing language. Furthermore, the implementation burden is not large, and since generic instantiation is performed at elaboration time, there is no performance penalty in simulation or synthesis.
MEF2C and EBF1 Co-regulate B Cell-Specific Transcription (2016)

Hematopoietic stem cells are capable of self-renewal or differentiation along three main lineages: myeloid, erythroid, and lymphoid. One of the earliest lineage decisions for blood progenitor cells is whether to adopt the lymphoid or myeloid fate. Previous work had shown that myocyte enhancer factor 2C (MEF2C) is indispensable for the lymphoid fate decision, yet the specific mechanism of action remained unclear. Here, we have identified early B cell factor-1 (EBF1) as a co-regulator of gene expression with MEF2C. A genome-wide survey of MEF2C and EBF1 binding sites identified a subset of B cell-specific genes that they target. We also determined that the p38 MAPK pathway activates MEF2C to drive B cell differentiation. Mef2c knockout mice showed reduced B lymphoid-specific gene expression as well as increased myeloid gene expression, consistent with MEF2C's role as a lineage fate regulator. This is further supported by interaction between MEF2C and the histone deacetylase, HDAC7, revealing a likely mechanism to repress the myeloid transcription program. This study thus elucidates both activation and repression mechanisms, identifies regulatory partners, and downstream targets by which MEF2C regulates lymphoid-specific differentiation.
Differential Requirements for COPI Coats in Formation of Replication Complexes among Three Genera of Picornaviridae (2002)

Picornavirus RNA replication requires the formation of replication complexes (RCs) consisting of virus-induced vesicles associated with viral nonstructural proteins and RNA. Brefeldin A (BFA) has been shown to strongly inhibit RNA replication of poliovirus but not of encephalomyocarditis virus (EMCV). Here, we demonstrate that the replication of parechovirus 1 (ParV1) is partly resistant to BFA, whereas echovirus 11 (EV11) replication is strongly inhibited. Since BFA inhibits COPI-dependent steps in endoplasmic reticulum (ER)-Golgi transport, we tested a hypothesis that different picornaviruses may have differential requirements for COPI in the formation of their RCs. Using immunofluorescence and cryo-immunoelectron microscopy we examined the association of a COPI component, beta-COP, with the RCs of EMCV, ParV1, and EV11. EMCV RCs did not contain beta-COP. In contrast, beta-COP appeared to be specifically distributed to the RCs of EV11. In ParV1-infected cells beta-COP was largely dispersed throughout the cytoplasm, with some being present in the RCs. These results suggest that there are differences in the involvement of COPI in the formation of the RCs of various picornaviruses, corresponding to their differential sensitivity to BFA. EMCV RCs are likely to be formed immediately after vesicle budding from the ER, prior to COPI association with membranes. ParV1 RCs are formed from COPI-containing membranes but COPI is unlikely to be directly involved in their formation, whereas formation of EV11 RCs appears to be dependent on COPI association with membranes.
Nosocomial Candida glabrata Colonization: an Epidemiologic Study (1998)

Candida glabrata has emerged as an important nosocomial pathogen, yet little is known about its epidemiology. We prospectively followed 98 patients admitted to a medical intensive care unit and the bone marrow transplant unit of a university hospital. Samples from environmental surfaces and the hands of hospital personnel were also cultured. Patients with newly acquired C. glabrata strains were compared to controls who were culture negative for C. glabrata. C. glabrata was recovered from multiple sites from 24 patients and three environmental surfaces. Sixteen patients (17%) acquired C. glabrata after admission to the study units. Significant risk factors for the nosocomial acquisition of C. glabrata were prolonged duration of hospitalization in the unit and prior antimicrobial use. Strain delineation by restriction enzyme analysis revealed 28 different strains of C. glabrata; three strain types were common to nine patients. The environmental isolates were of the same strain type and common to five patients (four patients with newly acquired strains). These results suggest the possibility of exogenous nosocomial acquisition of C. glabrata, including the possible acquisition from the hospital environment. Transmission may be by indirect contact since identical strains of C. glabrata were recovered from patients who were geographically and temporally associated.
Structural and electrical analysis of the atomic layer deposition of HfO2/n-In0.53Ga0.47As capacitors with and without an Al2O3 interface control layer (2010)

High mobility III-V substrates with high-k oxides are required for device scaling without loss of channel mobility. Interest has focused on the self-cleaning effect on selected III-V substrates during atomic layer deposition of Al2O3. A thin (∼1 nm) Al2O3 interface control layer is deposited on In0.53Ga0.47As prior to HfO2 growth, providing the benefit of self-cleaning and improving the interface quality by reducing interface state defect densities by ∼50% while maintaining scaling trends. Significant reductions in leakage current density and increased breakdown voltage are found, indicative of a band structure improvement due to the reduction/removal of the In0.53Ga0.47As native oxides.
Distribution of Eigenvalues for 2x2 MIMO Channel Capacity Based on Indoor Measurements (2012)

Based on the non line-of-sight (NLOS) indoor measurements performed in the corridors on the third floor of the Electronics and Telecommunications Research Institute (ETRI) building in Daejeon city, Republic of Korea, we investigated the distribution of the eigenvalues of HH*, where H denotes a 2×2 multiple-input multiple-output (MIMO) channel matrix. Using the observation that the distribution of the measured eigenvalues matches well with the Gamma distribution, we propose a model of eigenvalues as Gamma distributed random variables that prominently feature both transmitting and receiving correlations. Using the model with positive integer k_i, i=1, 2, which is the shape parameter of a Gamma distribution, we derive the closed-form ergodic capacity of the 2×2 MIMO channel. Validation results show that the proposed model enables the evaluation of the outage and ergodic capacities of the correlated 2×2 MIMO channel in the NLOS indoor corridor environment.
Taichunins A–D, Norditerpenes from Aspergillus taichungensis (IBT 19404) (2019)

Four new norditerpenes, taichunins A-D (1-4), were isolated from the fungus Aspergillus taichungensis (IBT 19404). Compound 1 has a new carbon framework. The absolute configurations were determined by the calculated ECD spectral method. Compound 1 was cytotoxic against HeLa cells with an IC<sub>50</sub> value of 4.5 μM, whereas 2-4 were nontoxic at 50 μM.
Immunotargeting of glucose oxidase to endothelium in vivo causes oxidative vascular injury in the lungs (2000)

Vascular immunotargeting is a novel approach for site-selective drug delivery to endothelium. To validate the strategy, we conjugated glucose oxidase (GOX) via streptavidin with antibodies to the endothelial cell surface antigen platelet endothelial cell adhesion molecule (PECAM). Previous work documented that 1) anti-PECAM-streptavidin carrier accumulates in the lungs after intravenous injection in animals and 2) anti-PECAM-GOX binds to, enters, and kills endothelium via intracellular H(2)O(2) generation in cell culture. In the present work, we studied the targeting and effect of anti-PECAM-GOX in animals. Anti-PECAM-GOX, but not IgG-GOX, accumulated in the isolated rat lungs, produced H(2)O(2,) and caused endothelial injury manifested by a fourfold elevation of angiotensin-converting enzyme activity in the perfusate. In intact mice, anti-PECAM-GOX accumulated in the lungs (27 +/- 9 vs. 2.4 +/- 0.3% injected dose/g for IgG-GOX) and caused severe lung injury and 95% lethality within hours after intravenous injection. Endothelial disruption and blebbing, elevated lung wet-to-dry ratio, and interstitial and alveolar edema indicated that anti-PECAM-GOX damaged pulmonary endothelium. The vascular injury in the lungs was associated with positive immunostaining for iPF(2alpha)-III isoprostane, a marker for oxidative stress. In contrast, IgG-GOX caused a minor lung injury and little (5%) lethality. Anti-PECAM conjugated with inert proteins induced no death or lung injury. None of the conjugates caused major injury to other internal organs. These results indicate that an immunotargeting strategy can deliver an active enzyme to selected target cells in intact animals. Anti-PECAM-GOX provides a novel model of oxidative injury to the pulmonary endothelium in vivo.
The pyruvate, orthophosphate dikinase regulatory proteins of Arabidopsis possess a novel, unprecedented Ser/Thr protein kinase primary structure (2007)

Pyruvate, orthophosphate dikinase (PPDK) is a ubiquitous, low-abundance metabolic enzyme of undetermined function in C3 plants. Its activity in C3 chloroplasts is light-regulated via reversible phosphorylation of an active-site Thr residue by the PPDK regulatory protein (RP), a most unusual bifunctional protein kinase (PK)/protein phosphatase (PP). In this paper we document the molecular cloning and functional analysis of the two unique C3 RPs in Arabidopsis thaliana. The first of these, AtRP1, encodes a typical chloroplast-targeted, bifunctional C4-like RP. The second RP gene, AtRP2, encodes a monofunctional polypeptide that possesses in vitro RP-like PK activity but lacks PP activity, and is localized in the cytosol. Notably, the deduced primary structures of these two highly homologous polypeptides are devoid of any canonical subdomain structure that unifies all known eukaryotic and prokaryotic Ser/Thr PKs into one of three superfamilies, despite the direct demonstration that AtRP1 is functionally a member of this group. Instead, these C3 RPs and the related C4 plant homologues encode a conserved, centrally positioned, approximately 260-residue sequence currently described as the 'domain of unknown function 299' (DUF 299). We propose that vascular plant RPs form a unique protein kinase family now designated as the DUF 299 gene family.
Underwater acoustic ambient noise levels on the eastern Canadian continental shelf (1990)

This paper reports the analysis of shallow-water ambient noise levels collected by Defence Research Establishment Atlantic during 14 cruises over the period 1972 to 1985. A weighted average is formed to de-bias the samples, with the aim of answering the question: ‘‘If one were to pick a site randomly on the eastern Canadian continental shelf at a random time, and perform an ambient noise measurement, what would be the expected noise level?’’ The samples are also grouped according to whether they were taken on the Scotian Shelf, the Grand Banks, or the Flemish Cap, and according to season. The frequency range covered is 30 to 900 Hz. The weighted mean and standard deviation of the noise levels are presented, as well as the correlation coefficient between the noise levels and wind speed. The results show that the eastern Canadian continental shelf as a whole presents levels that are characteristic of areas with high shipping density and good acoustic propagation, with the Scotian Shelf showing generally higher ambient noise levels. Finally, a comparison with Piggott’s ambient noise measurements [C. L. Piggott, ‘‘Ambient sea noise at low frequency in shallow water of the Scotian Shelf,’’ J. Acoust. Soc. Am. 36, 2152–2163 (1964)] on the Scotian Shelf is made, and an explanation for the observed difference is suggested.
Dynamics Study of Lithium Ion Diffusion in Super Lithium Ion Conductors, Li10GeP2S12 (LGPS) (2016)

Fast ionic conduction in solid electrolytes plays a key role in feasibility of the all-solid-state battery system. Among the lithium ion conductors, the Li 10 GeP 2 S 12 (LGPS) system shows the conductivity comparable to organic liquid electrolytes [1]. The recent study focused on the synthesis of solid solutions of this material, which might introduce either lithium vacancy or interstitial lithium ions and might affect its ionic conductivity and electrochemical stability. The crystal structures of the solid solution were studied using neutron diffraction technique. Their conduction pathway was estimated using Maximum Entropy Method (MEM) based on the structure information. These results indicate the lithium conduction pathway in LGPS is one-dimensional pathway along c axis at room temperature, and three-dimensional one at higher temperature [2]. However, the results of MEM provided only the space area of possible lithium ion conduction. Then, the study of lithium diffusive behaviors is necessary to understand lithium ionic conductivity in more details. The dynamics of lithium ion diffusions can be obtained directly by using the Quasielastic Neutron Scattering (QENS) technique because the quasielastic scattering spectrum is a broadening of elastic peak caused by the diffusion of atoms or ions within a material. When ions cause diffusion motions on a fixed sublattice, the quasielastic scattering spectra can exhibit a Q -dependence, which provides information on the dynamical structure of the ions diffusion. In this study, the QENS measurements were performed using the high-resolution Si crystal analyzer TOF type near-backscattering spectrometer, DNA, at MLF/J-PARC, Tokai, Ibaraki, Japan, at the energy resolution of 3.6 µeV [3] . S ( Q , ω ) spectra from 150 to 640 K were collected. After the analyzed those using jump-diffuse model [4,5], self-diffusion constants, jump length and mean residence time of conduction lithium ions in LGPS system were determined. The jump length was 1.73 Å at 473K and 2.72 Å at 640 K respectively. The jump length at 473 K was consistent with conduction along c axis. The jump length at 640 K also corresponded to the three dimensional conduction model. In this presentation, the mechanism of lithium ion diffusion in LGPS system will be discussed. References [1] N. Kamaya, K. Homma, Y. Yamakawa, M. Hirayama, R. Kanno, M. Yonemura, T. Kamiyama, Y. Kato, S. Hama, K. Kawamoto and A. Mitsui, Nature Materials , 10, 5 (2011). [2] O. Kwon, M. Hirayama, K. Suzuki, Y. Kato, T. Saito, M. Yonemura, T. Kamiyama and R. Kanno, J. Mater. Chem. A , 3, 9 (2014). [3] K. Shibata, N. Takahashi, Y. Kawakita, M. Matsuura, T. Yamada, T. Tominaga, W. Kambara, M. Kobayashi, Y. Inamura, T. Nakatani, K. Nakajima, and M. Arai, JPS Conf. Proc. 8, 036022 (2015). [4] C.T. Chudley and R.J. Elliott, Proc. Phys. Soc. 77, 353 (1967) [5] P.A. Egelstaff, B.C. Haywood and F.J. Webb, Proc. Phys. Soc. 90, 681 (1967)
The Journal Impact Factor Should Not Be Discarded (2017)

The Journal Impact Factor (JIF) has been heavily criticized over decades. This opinion piece argues that the JIF should not be demonized. It still can be employed for research evaluation purposes by carefully considering the context and academic environment.
Natural Bioactive Products as Epigenetic Modulators for Treating Neurodegenerative Disorders (2023)

Neurodegenerative disorders (NDDs) are major health issues in Western countries. Despite significant efforts, no effective therapeutics for NDDs exist. Several drugs that target epigenetic mechanisms (epidrugs) have been recently developed for the treatment of NDDs, and several of these are currently being tested in clinical trials. Furthermore, various bioproducts have shown important biological effects for the potential prevention and treatment of these disorders. Here, we review the use of natural products as epidrugs to treat NDDs in order to explore the epigenetic effects and benefits of functional foods and natural bioproducts on neurodegeneration.
Botanically Templated Monolithic Macrostructured Zinc Oxide Materials for Photocatalysis (2018)

With an increased focus on light energy to facilitate catalytic processes, photocatalysts have been intensively studied for a wide range of energy and environmental applications. In this report, we describe the use of chemically dehydrated leaves as sacrificial foam-like templates for the growth of monolithic macrostructured semiconducting zinc oxide and nickel or cobalt doped zinc oxide materials. The composition and structure of these templated zinc oxides were characterized using X-ray powder diffraction, scanning electron microscopy, energy dispersive spectroscopy, and X-ray photoelectron spectroscopy. Optical properties were examined using solid-state UV–vis diffuse reflectance spectroscopy. The metal-doped ZnO materials have enhanced visible absorption and lower band gaps as compared to ZnO. The botanically templated ZnO materials retain the macroscopic cellular form of the leaf template with fused nanoparticle walls. Their UV photocatalytic oxidative abilities were investigated using methylene blue dye degradation in air. The leaf templated zinc oxides degrade ~85% of methylene blue dye with 30 min of UV illumination. Nickel and cobalt doped zinc oxides showed varying degrees of decreased UV and visible light photocatalytic activity, possibly due to metal-mediated charge recombination. The mild chemical dehydration process here allows complex soft botanical structures to be easily utilized for templating materials.
Covid-19 Rates by Time since Vaccination during Delta Variant Predominance (2021)

This article examines Covid-19 case and death rates among recipients of one of three FDA-approved vaccines. The data show that protection from infection attributable to the BNT162b2 and mRNA-1273 vaccine recipients and from death among older BNT162b2 recipients wanes over 6 months, whereas case and death rates among recipients of the Ad26.COV2.S vaccine are higher overall without a consistent pattern of waning immunity.