gebhart/patrepeval huggingface dataset:
MP48-09 SAFE AND EFFECTIVE PARTIAL NEPHRECTOMY IS FEASIBLE IN APPROPRIATELY SELECTED PATIENTS WITH COMPLEX (RENAL NEPHROMETRY SCORE 10-12) RENAL TUMORS: A MULTI-INSTITUTIONAL ANALYSIS (2018)

metastatic disease was collected from the medical record. All patients with known histology prior to partial nephrectomy were excluded from the study, as were patients with mixed histology or patients who underwent laparoscopic/robotic procedures.
Residual Votes Attributable to Technology: An Assessment of the Reliability of Existing Voting Equipment (2001)

American elections are conducted using a hodge-podge of different voting technologies: paper ballots, lever machines, punch cards, optically scanned ballots, and electronic machines. And the technologies we use change frequently. Over the last two decades, counties have moved away from paper ballots and lever machines and toward optically scanned ballots and electronic machines. The changes have not occurred from a concerted initiative, but from local experimentation. Some local governments have even opted to go back to the older methods of paper and levers.
Human neural stem cells ameliorate autoimmune encephalomyelitis in non‐human primates (2009)

Herein, we provide the first evidence that human CNS stem cells ameliorate EAE in nonhuman primates without overt side effects. Immune regulation (rather than neural differentiation) is suggested as the major putative mechanism by which NPCs ameliorate EAE in vivo. Our findings represent a critical step toward the clinical use of human NPCs in MS.
Pet fur color and texture classification (2007)

Object segmentation is important in image analysis for imaging tasks such as image rendering and image retrieval. Pet owners have been known to be quite vocal about how important it is to render their pets perfectly. We present here an algorithm for pet (mammal) fur color classification and an algorithm for pet (animal) fur texture classification. Per fur color classification can be applied as a necessary condition for identifying the regions in an image that may contain pets much like the skin tone classification for human flesh detection. As a result of the evolution, fur coloration of all mammals is caused by a natural organic pigment called Melanin and Melanin has only very limited color ranges. We have conducted a statistical analysis and concluded that mammal fur colors can be only in levels of gray or in two colors after the proper color quantization. This pet fur color classification algorithm has been applied for peteye detection. We also present here an algorithm for animal fur texture classification using the recently developed multi-resolution directional sub-band Contourlet transform. The experimental results are very promising as these transforms can identify regions of an image that may contain fur of mammals, scale of reptiles and feather of birds, etc. Combining the color and texture classification, one can have a set of strong classifiers for identifying possible animals in an image.
Flux balance analysis of the ammonia-oxidizing bacterium Nitrosomonas europaea ATCC19718 unravels specific metabolic activities while degrading toxic compounds (2022)

The ammonia-oxidizing bacterium Nitrosomonas europaea has been widely recognized as an important player in the nitrogen cycle as well as one of the most abundant members in microbial communities for the treatment of industrial or sewage wastewater. Its natural metabolic versatility and extraordinary ability to degrade environmental pollutants (e.g., aromatic hydrocarbons such as benzene and toluene) enable it to thrive under various harsh environmental conditions. Constraint-based metabolic models constructed from genome sequences enable quantitative insight into the central and specialized metabolism within a target organism. These genome-scale models have been utilized to understand, optimize, and design new strategies for improved bioprocesses. Reduced modeling approaches have been used to elucidate Nitrosomonas europaea metabolism at a pathway level. However, genome-scale knowledge about the simultaneous oxidation of ammonia and pollutant metabolism of N. europaea remains limited. Here, we describe the reconstruction, manual curation, and validation of the genome-scale metabolic model for N. europaea, iGC535. This reconstruction is the most accurate metabolic model for a nitrifying organism to date, reaching an average prediction accuracy of over 90% under several growth conditions. The manually curated model can predict phenotypes under chemolithotrophic and chemolithoorganotrophic conditions while oxidating methane and wastewater pollutants. Calculated flux distributions under different trophic conditions show that several key pathways are affected by the type of carbon source available, including central carbon metabolism and energy production.
Condensed bridgehead nitrogen heterocyclic systems: Microwave assisted synthesis and bioactivity of s -triazolo[3,4- ][1,3,4]thiadiazoles, s -triazolo[3,4- ][1,3,4]thiadiazines and s -triazolo [3' ,4' :2,3]-thiadiazino[5,6- ]quinoxaline (2006)

[3-(4-Amino-5-mercapto-4 -[1,2,3]triazol-3-yl)-4,5,6,7-tetrahydrobenzo[ ] thiophen-2-yl]acetamide on condensation with chloroacetic acid, -haloketone and benzoin furnishes [1,2,4]triazolo[3,4][1,3,4]thiadiazine derivatives , and respectively, while condensation with 2,3-dichloroquinoxaline, carbon disulphide, aromatic carboxylic ac id and aromatic carboxaldehydes yield the cyclic products, [1,2,4] triazolo[3,4][1,3,4]thiadiazo le derivatives , , , respectively. The compounds have been characterized on the basis of elemental analysis and spectral data. The antibacterial, antifungal and antitubercular activities of the compounds have also been evaluated.
Direct Synthesis of Tungsten Carbide Nanoparticles by Mechanically Assisted Carbothermic Reduction of Natural Wolframite (2005)

Carbothermic reduction of natural wolframite (FeWO 4 ) to nano‐sized tungsten carbide (WC) particles was achieved by calcining mechanically activated mixtures of FeWO 4 and active carbon at 1100°C under flowing Ar gas. The average particle size ranged between 20 and 25 nm. Intermediates, Fe 6 W 6 C and Fe 3 W 3 C, were observed between 900° and 1100°C, which decomposed to give the final product, WC. Homogeneity increase and associated decrease in the diffusion path by milling are mainly responsible for the successful production of WC. The process paves the way to rational utilization of natural FeWO 4 directly to fine advanced materials.
Crystallization and preliminary X-ray diffraction analysis of the catalytic domain of recombinant human phosphodiesterase 3B (2003)

The catalytic domain of human phosphodiesterase 3B has been cloned, expressed in Escherichia coli and purified in the presence of the PDE3 inhibitors IBMX (3-isobutylmethylxanthine) or MERCK1 by affinity chromatography. Initial screening of crystallization conditions for these complexes in the hanging-drop vapor-diffusion mode resulted in three different crystal forms, all characterized by quite large unit-cell parameters, elevated solvent content and poor diffraction quality. Subsequent optimization of these conditions led to crystals that diffract to 2.4 A and belong to space group C2, with unit-cell parameters a = 146.7, b = 121.5, c = 126.3 A, beta = 100.6 degrees. Rotation-function analysis indicates that the asymmetric unit contains four copies of the monomeric enzyme, corresponding to a solvent content of 64%. To solve the structure of the PDE3B catalytic domain, molecular replacement as well as multiple isomorphous replacement methods are currently being utilized.
Automated Vulnerability Testing Identifies Patients With Inadequate Defibrillation Safety Margin (2012)

An automated system identified all patients who failed conventional safety margin testing, while inducing only 19% of patients. Although limited by sample size, this study suggests the feasibility of automated implant testing that substantially reduces the need for VF induction in patients receiving implantable cardioverter-defibrillators.
Influence of Artificial Diet on Southern Corn Rootworm Life History and Susceptibility to Insecticidal Compounds (2021)

Because of their economic importance, corn rootworms (Diabrotica spp.) are currently reared extensively in laboratories throughout the United States. Most industrial labs use Diabrotica in insecticide discovery screening operations. Insects of high quality, genetic heterozygosity, and uniformity are critical to the success of the screening operation. In Monsanto's Insect Control Discovery Program, corn rootworms reared on their natural diet (corn) (Marrone et al. 1985) proved to be of acceptable quality. However, the rearing methods were time consuming and labor intensive, so we developed an artificial diet procedure that was more efficient than rearing on corn (Marrone et al. 1985). We reared southern corn rootworms (SCR) for over 25 generations on the artificial diet. To determine if the diet colony was as vigorous as the corn colony, we compared several life history parameters, such as adult and larval survival, fecundity, and susceptibility to insecticidal compounds.
Diketopiperazine Formation in Fungi Requires Dedicated Cyclization and Thiolation Domains (2019)

Cyclization of linear dipeptidyl precursors derived from nonribosomal peptide synthetases (NRPSs) into 2,5-diketopiperazines (DKPs) is a crucial step in the biosynthesis of a large number of bioactive natural products. However, the mechanism of DKP formation in fungi has remained unclear, despite extensive studies of their biosyntheses. Here we show that DKP formation en route to the fungal virulence factor gliotoxin requires a seemingly extraneous couplet of condensation (C) and thiolation (T) domains in the NRPS GliP. In vivo truncation of GliP to remove the CT couplet or just the T domain abrogated production of gliotoxin and all other gli pathway metabolites. Point mutation of conserved active sites in the C and T domains diminished cyclization activity of GliP in vitro and abolished gliotoxin biosynthesis in vivo. Verified NRPSs of other fungal DKPs terminate with similar CT domain couplets, suggesting a conserved strategy for DKP biosynthesis by fungal NRPSs.
Probe Vehicle Runs or Loop Detectors? (2007)

Freeway congestion monitoring can be based either on sampling-based methods, such as probe vehicle runs, or on continuous data from loop detector infrastructure. Sample size, in terms of the number of days sampled, affects the accuracy of sampling-based methods; detector spacing or detector density affects the accuracy of the detector-based method. This paper presents an empirical model of the effect of the two parameters—sample size and detector spacing—on the accuracy of both methods in estimating the annual average of three congestion parameters: total delay, average duration of congestion, and average spatial extent of congestion. The model is developed with data from four urban freeway corridors in California. Among other conclusions, the model predicts that to measure the congestion parameters with 10% error, 4 to 6 days’ worth of good probe vehicle data or loop detector data with half-mile spacing is needed. The proposed model facilitates comparison of the two alternatives in regard to the cost for achieving the same target accuracy. The result can also be used as a guide to determine the sample size or detector spacing in planning new congestion monitoring.
Nonenzymatic bilin addition to the alpha subunit of an apophycoerythrin. (1994)

C-Phycoerythrin is a light-harvesting protein whose alpha and beta subunits carry thioether-linked phycoerythrobilin (PEB) at cysteine residues alpha-82, alpha-139, beta-48,59 (doubly-linked), beta-80, and beta-165. The two subunits of Calothrix sp. PCC 7601 C-phycoerythrin, overexpressed together as apopolypeptides in Escherichia coli, formed inclusion bodies. Purified apo-alpha was soluble in the absence of urea, whereas the apo-beta subunit was only soluble at high urea concentrations. Products of nonenzymatic addition of PEB and phycocyanobilin (PCB) to apo-alpha were characterized by isolation of bilin peptides and spectroscopy. Reaction of PEB with the apo-alpha subunit led primarily to 15,16-dihydrobiliverdin (Cys-82) or urobilin (Cys-139) adducts, and small amounts of the natural PEB adducts at both Cys-82 and Cys-139. PCB reacted primarily with Cys-82 to form phycocyanobilin and mesobiliverdin adducts. Both PEB and PCB also formed relatively small amounts of adducts with Cys-59, which is not a bilin attachment residue in natural phycoerythrin. Sodium azide was found to promote the addition of PEB to simple thiols but not to apo-alpha phycoerythrin.
Defining “Co-Primary Spectrum Sharing”— A new Business Opportunity for MNOs? (2014)

This paper seeks to identify and discuss mobile network operators’ (MNOs) business opportunities in spectrum sharing where the several MNOs would share the same spectrum band. This sharing model, here called co-primary spectrum sharing (CoPSS), aims to increase the efficiency of spectrum use by intr
Ubiquitinated PCNA Drives USP1 Synthetic Lethality in Cancer (2022)

CRISPR Cas9-based screening is a powerful approach for identifying and characterizing novel drug targets. Here, we elucidate the synthetic lethal mechanism of deubiquitinating enzyme USP1 in cancers with underlying DNA damage vulnerabilities, specifically BRCA1/2 mutant tumors and a subset of BRCA1/2 wild-type (WT) tumors. In sensitive cells, pharmacologic inhibition of USP1 leads to decreased DNA synthesis concomitant with S-phase-specific DNA damage. Genome-wide CRISPR-Cas9 screens identify RAD18 and UBE2K, which promote PCNA mono- and polyubiquitination respectively, as mediators of USP1 dependency. The accumulation of mono- and polyubiquitinated PCNA following USP1 inhibition is associated with reduced PCNA protein levels. Ectopic expression of WT or ubiquitin-dead K164R PCNA reverses USP1 inhibitor sensitivity. Our results show, for the first time, that USP1 dependency hinges on the aberrant processing of mono- and polyubiquitinated PCNA. Moreover, this mechanism of USP1 dependency extends beyond BRCA1/2 mutant tumors to selected BRCA1/2 WT cancer cell lines enriched in ovarian and lung lineages. We further show PARP and USP1 inhibition are strongly synergistic in BRCA1/2 mutant tumors. We postulate USP1 dependency unveils a previously uncharacterized vulnerability linked to posttranslational modifications of PCNA. Taken together, USP1 inhibition may represent a novel therapeutic strategy for BRCA1/2 mutant tumors and a subset of BRCA1/2 WT tumors.
Joint Training of a Convolutional Network and a Graphical Model for\n Human Pose Estimation (2014)

This paper proposes a new hybrid architecture that consists of a deep\nConvolutional Network and a Markov Random Field. We show how this architecture\nis successfully applied to the challenging problem of articulated human pose\nestimation in monocular images. The architecture can exploit structural domain\nconstraints such as geometric relationships between body joint locations. We\nshow that joint training of these two model paradigms improves performance and\nallows us to significantly outperform existing state-of-the-art techniques.\n
Down-regulation of the ATP-binding Cassette Transporter 2 (Abca2) Reduces Amyloid-β Production by Altering Nicastrin Maturation and Intracellular Localization (2011)

Clinical, pharmacological, biochemical, and genetic evidence support the notion that alteration of cholesterol homeostasis strongly predisposes to Alzheimer disease (AD). The ATP-binding cassette transporter-2 (Abca2), which plays a role in intracellular sterol trafficking, has been genetically linked to AD. It is unclear how these two processes are related. Here we demonstrate that down-regulation of Abca2 in mammalian cells leads to decreased amyloid-β (Aβ) generation. In vitro studies revealed altered γ-secretase complex formation in Abca2 knock-out cells due to the altered levels, post-translational modification, and subcellular localization of Nicastrin. Reduced Abca2 levels in mammalian cells in vitro, in Drosophila melanogaster and in mice resulted in altered γ-secretase processing of APP, and thus Aβ generation, without affecting Notch cleavage.
COVID-19: Review of a 21st Century Pandemic from Etiology to Neuro-psychiatric Implications (2020)

COVID-19 is a severe infectious disease that has claimed >150,000 lives and infected millions in the United States thus far, especially the elderly population. Emerging evidence has shown the virus to cause hemorrhagic and immunologic responses, which impact all organs, including lungs, kidneys, and the brain, as well as extremities. SARS-CoV-2 also affects patients', families', and society's mental health at large. There is growing evidence of re-infection in some patients. The goal of this paper is to provide a comprehensive review of SARS-CoV-2-induced disease, its mechanism of infection, diagnostics, therapeutics, and treatment strategies, while also focusing on less attended aspects by previous studies, including nutritional support, psychological, and rehabilitation of the pandemic and its management. We performed a systematic review of >1,000 articles and included 425 references from online databases, including, PubMed, Google Scholar, and California Baptist University's library. COVID-19 patients go through acute respiratory distress syndrome, cytokine storm, acute hypercoagulable state, and autonomic dysfunction, which must be managed by a multidisciplinary team including nursing, nutrition, and rehabilitation. The elderly population and those who are suffering from Alzheimer's disease and dementia related illnesses seem to be at the higher risk. There are 28 vaccines under development, and new treatment strategies/protocols are being investigated. The future management for COVID-19 should include B-cell and T-cell immunotherapy in combination with emerging prophylaxis. The mental health and illness aspect of COVID-19 are among the most important side effects of this pandemic which requires a national plan for prevention, diagnosis and treatment.
Dorsal genital nerve stimulation for the treatment of overactive bladder symptoms (2007)

Electrodes to stimulate the DGN can be placed percutaneously and a home testing period showed a reduction in overactive bladder symptoms with DGN stimulation.
Achievable bit rates of DMT and FMT systems in the presence of phase noise and multipath (2002)

We examine a modulation technique related to orthogonal frequency division multiplexing (OFDM), called filtered multitone (FMT) modulation, which exhibits significantly lower spectral overlapping between adjacent subchannels than other OFDM schemes like discrete multitone (DMT). In particular, we compare FMT and DMT systems in the presence of phase noise due to the frequency down-conversion circuit, as well as multipath fading of the radio channel. As a measure of system performance we consider the achievable bit rate, which is given by the sum of the bit rates each subchannel is eligible to deliver with a certain bit error probability.
Interleukin 1-dependent paracrine granulopoiesis in chronic granulocytic leukemia of the juvenile type. (1988)

Marrow and peripheral blood cells from nine children with juvenile chronic granulocytic leukemia (JCGL) demonstrated intense (94 +/- 16% maximum) spontaneous granulocyte/macrophage colony growth but cells from five children with the adult variety of CGL did not. This unusual pattern of colony growth depended upon a stimulatory protein(s) produced by mononuclear phagocytes. No GM-CSA activity was found in any chromatofocused fraction of JCGL monocyte-conditioned media but an activity that induced GM-CSA in umbilical vein endothelial cells was detected at pI 6.9-7.2. Moreover, the CSA-inducing monokine was neutralized by an anti-IL-1 antibody in vitro and, in the one case so tested, the same antibody also inhibited "spontaneous" colony growth. Therefore granulocyte/macrophage colony growth in JCGL is characteristically abnormal and distinguishes JCGL from the adult form of the disease. This abnormality depends upon the production, by mononuclear phagocytes, of IL-1 which, in turn, stimulates the release of high levels of colony stimulating activity by other cells. The high proliferative activity of CFU-GM we found in JCGL patients, and the high levels of GM-CSA found in their serum are compatible with the view that the in vitro abnormality reflects a similar abnormality in vivo.
A comparative study of Jungian psychology and Sufism (2020)

This thesis proposes a comparison of the individuation process in Jungian psychology and the purification of the nafs (the self) in Sufism. The premises for my argument are the lack of literature between Jungian psychology and Sufism despite the obvious potential of comparative materials, while Jung’s relation to other religious traditions is relatively well documented. The methodology will establish a blueprint within the debate between psychology and religion, with some guidelines for a cross-cultural and interdisciplinary study. I initiate my research with a biographical analysis to highlight the existing traces of Sufism in Jung’s milieu, which is permeated by an Orientalist outlook that influenced his writings as well as his personal, social and historical environment. The main purpose of the biographical analysis is to understand the context for the existing literature, but it will also expose some guidelines for my own comparison. My main contribution is therefore a comprehensive comparison based on a conceptual analysis of some fundamental notions for the individuation process in Jungian psychology and the purification of the nafs in Sufism. The comparative and conceptual methodology allows the negotiation of similarities and differences with a sensible treatment of the psychological and mystical knowledge presented within their respective contexts. This conceptual analysis determines the extent of the crossovers between Jungian psychology and Sufism, while it remains critical regarding their boundaries. The similarities and differences of the comparative analysis ultimately define some patterns and principles in the relation between psychology and mysticism. I therefore conclude my thesis with a critical examination of my argument in the broader context of psychology and religion. I discuss the nature and relation of Jungian psychology and Sufism as a mystical tradition and the various aspects of a comparative study, such as interdisciplinarity and cultural awareness.
Performance Comparisons of Localized and Distributed Transmissions Using Iterative Decision-Directed Channel Estimation in DFT-Precoded OFDMA (2012)

Single-carrier (SC)-Frequency Division Multiple Access (FDMA) using discrete Fourier transform (DFT)-precoded orthogonal frequency division multiple access (OFDMA) achieves flexible orthogonal multi-access in the frequency domain while retaining a low peak-to-average power ratio (PAPR). Although the two types of transmission schemes are evaluated including localized and distributed transmissions, only the localized transmission is adopted in the shared channel carrying user traffic data in the Release 8 Long-Term Evolution (LTE). This paper proposes distributed transmission with affinity to resource block (RB) based resource assignment in order to gain the frequency diversity effect for DFT-precoded OFDMA in a frequency-selective fading channel. We apply iterative decision-directed channel estimation (DDCE) to the RB based distributed transmission to decrease the channel estimation (CE) error, which is a major impairment to distributed transmission. We present a comparison based on the average block error rate (BLER) performance levels between the RB based distributed and localized transmission schemes without and with intra-subframe frequency hopping (FH). Through extensive simulation evaluations, we show the effectiveness of the RB based distributed transmission associated with the iterative DDCE in decreasing the required average received SNR satisfying the target average BLER compared to the localized transmission.