gebhart/patrepeval huggingface dataset:
Structure of the Tetrameric p53 Tumor Suppressor Bound to DNA (2001)

Abstract : The p53 tumor suppressor binds DNA as a tetramer to regulate the transcription of genes involved in cell cycle arrest and apoptosis, and alterations in the DNA-binding core domain of p53 are the most common genetic changes found in breast cancer. The goal of this proposal was to determine the X-ray crystal structure of a p53 tetramer bound to DNA. Towards this goal, we successfully prepared several p53 and short duplex DNA reagents, but have been unable to prepare suitable p53/DNA cocrystals for structure determination. Nonetheless, we have successfully determined the medium resolution (2.7A) structure of the nascent p53 core domain which we reported in the Journal of Biological Chemistry, and have more recently obtained crystal of the p53 core domain that will yield a structure to 2.2A resolution. Future efforts to obtain a structure of the p53 tetramer bound to DNA will involve cocrystallization with longer DNA targets or DNA targets assembled into nucleosome core particles. The structure of tetrameric p53 bound to DNA will provide new insights into the structural basis underlying p53 mutations, and will provide a framework for the structure-based design of drugs that will be useful in the treatment of p53-mediated breast cancer.
Atomic Short Range Order and Pair Interaction of Disordered Au4Mn by Neutron Diffraction (1977)

Atomic diffuse scattering from a single crystal of Au 4 Mn with the disordered fcc structure was observed by neutron diffraction in the three dimensional reciprocal space. A cigar type diffuse pattern along the line of [1, K , 0] with three broad maxima at K =0.27, 0.50 and 0.73 was obtained. After some corrections and an arrangement of the pattern at the equivalent positions in the reciprocal space, the parameters of atomic short range order and pair interaction up to the 50th neighbor were determined by a method presented by Adachi-Nakashima: J. Phys. Soc. Japan 40 (1976) 25. The reproducibilities from the order parameters and the pair interactions thus determined were examined. The former gives a good reproducibility but the latter not. Origins of the pair interaction of this alloy were discussed.
Spatially incoherent illumination as a mechanism for cross-talk suppression in wide-field optical coherence tomography (2004)

Comparison of two illumination modes for wide-field optical coherence tomography has revealed that spatially coherent illumination generates coherent cross talk, causing significant image degradation, and that spatially incoherent illumination, with an adequate interferometer design, provides an efficient mechanism for suppression of coherent cross talk. This is shown by comparison of a pulsed laser with a thermal light source for a U.S. Air Force resolution target covered with a scattering solution made from microbeads as well as for an ex vivo tooth.
Frequent amplifications and deletions of G1/S-phase transition genes, CCND1 and MYC in early breast cancers: A potential role in G1/S escape (2009)

Uncontrolled growth of cancer cells can be related to dysfunctional cell cycle control, including entry into S-phase, initiating cell division. Cyclin CCND3 and CCNE1 along with CDK2 and CDK6 regulate this checkpoint, and genetic changes, detectable by fluorescence in situ hybridization, are hypothesized to increase the aggressiveness of breast cancer, thereby influencing patient survival. Genomic change was investigated in 106 primary breast cancer samples, where the combined gene copy number changes in one of these four cell cycle regulatory factors was observed in 22% of the 98 tumors of successful analysis, distributed with 15 deletions and 7 amplifications. A trend towards decreased survival was observed with the aberrations, suggesting a prognostic potential of this set of markers, which was supported by an association with tumor grade. For validation of the new set of FISH probes for the G1/S-phase cell cycle factors, two additional markers, frequently amplified in breast cancers, were included in this study: The G1/S phase control gene CCND1 and the proliferation marker MYC. Both markers were amplified in 14% and deleted in 5% of the cases. This is the first report of genomic deletions of MYC in breast cancer.
Thermal expansion studies of superconductingU1−xThxBe13(0<~x<~0.052):Implications for the interpretation of theT-xphase diagram (2000)

We report on high-resolution measurements of the coefficient of thermal expansion \ensuremath{\alpha} of the heavy-fermion superconductor ${\mathrm{U}}_{1\ensuremath{-}x}{\mathrm{Th}}_{x}{\mathrm{Be}}_{13}$ for temperatures $0.05\mathrm{K}&lt;~T&lt;~6\mathrm{K}$ and magnetic fields $B&lt;~8\mathrm{T}.$ Particular attention is paid to the properties of the low-temperature normal state and their evolution as a function of thorium concentration. By exploring a wide concentration range, $0&lt;~x&lt;~0.052,$ that encompasses the region ${x}_{c1}=0.019&lt;x&lt;{x}_{c2}=0.045$ where temperature-dependent specific-heat measurements reveal two subsequent phase transitions at ${T}_{c1}&gt;{T}_{c2},$ our study discloses features in the T-x plane that have been overseen by all other techniques applied to this system so far: (i) The substitution of uranium by thorium in ${\mathrm{UBe}}_{13}$ induces an anomaly that manifests itself in a negative $\ensuremath{\alpha}(T)$ contribution to the low-temperature normal-state expansivity. Its distinct field dependence signals a magnetic origin. Analyzing the relative lengths changes associated with this anomaly and that of the phase transition at ${T}_{c2}$ suggests a common (presumably magnetic) nature of both features. (ii) The linear concentration dependence of the second low-energy scale ${T}_{\mathrm{max}},$ which gives rise to a pronounced maximum in $\ensuremath{\alpha}(T)$ of ${\mathrm{UBe}}_{13}$ at 2 K (at $B=0)$ could be followed up---by applying a magnetic field---to concentrations $x&gt;0.03.$ Most remarkably, ${T}_{\mathrm{max}}(x)$ vanishes at $x\ensuremath{\approx}0.043,$ i.e., almost exactly at ${x}_{c2}.$ (iii) Upon increasing x to above 0.03 the normal- to superconducting-state transition at ${T}_{c1}$ progressively loses its signatures in \ensuremath{\alpha}. Our measurements, together with recent specific-heat results by Schreiner et al. [Schreiner et al., Europhys. Lett. 48, 568 (1999)] indicate that superconductivity becomes gapless for $\stackrel{\ensuremath{\rightarrow}}{x}{x}_{c2}.$ Hence, the phase transition seen in specific heat as well as thermal-expansion measurements for samples with $x&gt;{x}_{c2}$ has to be attributed to the ${T}_{c2}$ transition. Concomitant investigations of the ac susceptibility indicate that the normal- to superconducting-state transition for $x&gt;{x}_{c2}$ now coincides with ${T}_{c2}.$ As for the implications of our observations for the interpretation of the various low-temperature anomalies, we discuss two possible scenarios both of which imply an intimate interrelation of superconductivity with the symmetry broken state that forms below ${T}_{c2}.$
Abstract 29: Hydrogen Peroxide Impairs Myogenic Response of Afferent Arterioles from Mice with the Reduce Renal Mass Model of Chronic Kidney Disease (2013)

Background: Impaired autoregulation and systemic hypertension underlie progressive kidney injury in chronic kidney disease (CKD). We reported that the myogenic response (MR) was severely impaired in afferent arterioles (Affs) from mice with reduced renal mass (RRM) and oxidative stress, yet superoxide (O 2 .- ) enhanced MRs of normal mice. Therefore, we tested the hypothesis that an increase in perfusion pressure (PP) enhances the generation of H 2 O 2 selectively in Affs from mice with RRM and that H 2 O 2 causes the impaired MR. Methods and Results: Groups of sham and RRM C57BL/6 mice were fed a high salt (6% NaCl) diet for 3 months. Alternative groups were treated with 2 mM of the redox cycling nitroxide tempol in drinking water for 3 months, which reduced the excretion of both 8-isoprostane (marker of O 2 .- ) and H 2 O 2 . MRs were assessed from the % change in luminal diameter of isolated, perfused Affs after increasing PP from 40 to 80 mmHg, O 2 .- from PEG-SOD inhibitable ethidium:dihydroethidium fluorescence and H 2 O 2 from PEG-catalase (CAT) inhibitable H2DCFDA fluorescence. Results: 1. Compared to sham, increasing PP in Affs from RRM mice increased O 2 .- more (21 ± 2% vs 11 ± 2%, P&lt;0.01), but this was prevented by tempol, and increased H 2 O 2 more (29 ± 8% vs 4 ± 1%, P&lt;0.01), which also was prevented by tempol. 2. Compared to sham, Affs from mice with RRM mice had severely impaired MRs (sham, -14 ± 4% vs RRM, -1 ± 4%, P&lt;0.05), yet this defect was corrected in mice drinking tempol (sham + tempol, -9 ± 6% vs RRM + tempol, -11 ± 2%, NS). 3. Bath addition of PEG-SOD (200 units/ml) attenuated MRs from sham mice (sham + vehicle, -14 ± 4%; sham + SOD, -6 ± 1%; P&lt;0.05), but did not affect responses in RRM mice. 4. Bath addition of PEG-CAT (1000 units/ml) selectively enhanced the MRs in RRM mice (RRM + vehicle -1 ± 4%; RRM + CAT -19 ± 2%; P&lt; 0.01) without effect in sham mice (sham + vehicle, -14 ± 4%; sham + PEG-CAT, -14 ± 2% NS). Conclusions: Excessive H 2 O 2 is released by increased PP of the afferent arterioles only from mice with RRM and accounted for the impaired myogenic response. Tempol, or other drugs that metabolize H 2 O 2 , may preserve renal autoregulation and prevent progressive loss of GFR in CKD.
Supplementary Data 2 from Epithelial-to-Mesenchymal Transition and Autophagy Induction in Breast Carcinoma Promote Escape from T-cell–Mediated Lysis (2023)

&lt;p&gt;PDF file - 72K, SNAI1-6SA cells were sorted by flow cytometry (MoFlo� Astrios� - Beckman Coulter, Inc) based on their ALDH activity&lt;/p&gt;
Cabozantinib (Cabo) in patients (pts) with castrate-resistant prostate cancer (CRPC) metastatic to bone (NCT01428219): Evaluation of bone metastasis microenvironment. (2014)

e16015 Background: Cabo is active in metastatic CRPC. This phase II trial evaluates the effects of Cabo on bone metabolism and tumor activity in prostate cancer bone lesions. Methods: Chemotherapy-naive pts with progressive CRPC and bone metastases accessible to CT-guided biopsy, adequate performance status/organ function underwent bone biopsy, CT and perfusion/diffusion-weighted MRI of bone lesions at baseline and after 6 weeks of Cabo 60 mg daily. Primary endpoint: rate of pts progression-free at 12 weeks (PF12w). Secondary endpoints: safety, PF survival, response proportion/duration, PSA response/time-to-progression. Exploratory endpoints: serum markers of bone metabolism, imaging of bone lesions, immunohistochemistry (IHC) of bone biopsies. A two-stage mini-max design permits early termination after the first 27 evaluable pts (≤12 pts PF12w); alternatively 46 evaluable pts will be accrued with 85% power to detect a PF12w rate <0.45 or >0.65 (5% type I error). Results: 26 pts have been screened, 23 enrolled, 21 started Cabo (8 pts still on Cabo, 6 of them >12 weeks). Median age is 65, median baseline PSA 50.1 ng/ml, median treatment duration 28 (3-88) weeks with 25 dose delays in 15 pts and 18 dose reductions in 14 pts. Grade (G) 3 adverse events (AE) >5%: thromboembolism (14%), elevated lipase (14%), diarrhea (9.5%), no G4/5 AE on Cabo. 14/19 (74%) pts were PF12w; 1 pt had unconfirmed partial response by CT; 6/19 (32%) pts had PSA response, 5/19 (26%) pts had bone scan response (1 complete). Bone biopsy tumor yield was 36% on preliminary analysis; Met, Akt, VEGFR2 IHC and serum markers evaluation is underway. 14 pts had paired MRI data:13 pts PF12w had increased tumor mean apparent diffusion coefficient (ADC) and volume fractions of parametric response map of ADC (PRM_ADC)+ between MRI images; 1 pt not PF12w had insubstantial mean ADC change and the lowest PRM_ADC+ fraction. PRM analysis on Hounsfield Units between CT scans in 13 pts did not reveal substantial bone changes. Conclusions: Based on achieving the primary endpoint of the first stage, study accrual continues. Analysis of biopsy specimens, tumor imaging and bone markers is ongoing. Clinical trial information: NCT01428219.
Plasma Levels of Bevacizumab and Vascular Endothelial Growth Factor After Low-Dose Bevacizumab Treatment for Retinopathy of Prematurity in Infants (2022)

Results of this phase 1 dose de-escalation case series study revealed that bevacizumab doses as low as 0.002 mg were associated with reduced plasma VEGF levels for most infants at 2 and 4 weeks after intravitreal administration; however, no association was observed between total bevacizumab dose administered and reductions in plasma VEGF levels from preinjection to 2 weeks or 4 weeks. Additional studies are needed to evaluate the long-term effects of low-dose bevacizumab on neurodevelopment and retinal structure.
Near-Infrared Autofluorescence in Atherosclerosis Associates With Ceroid and Is Generated by Oxidized Lipid-Induced Oxidative Stress (2021)

[Figure: see text].
Mobile Manipulator Path Planning By A Genetic algorithm (2005)

This article addresses the path-planning problem for a mobile manipulator system that is used to perform a sequence of tasks specified by locations and minimum oriented force capabilities. The problem is to find an optimal sequence of base positions and manipulator configurations for performing a sequence of tasks given a series of task specifications. The formulation of the problem is nonlinear. The feasible regions for the problem are nonconvex and unconnected. Genetic algorithms applied to such problems appear to be very promising while traditional optimization methods cause difficulties. Computer simulations are carried out on a three-degrees-of-freedom manipulator mounted on a two-degrees-of-freedom mobile base to search for the near optimal path-planning solution for performing the sequence of tasks. © 1994 John Wiley & Sons, Inc.
Laboratory-size X-ray Microscope using Wolter Mirror Optics and an Electron-impact X-ray Source for Multi-energy Observation (2018)

An abstract is not available for this content so a preview has been provided. As you have access to this content, a full PDF is available via the ‘Save PDF’ action button.
A New Lymphoid Cell Line, Reh 6, with Characteristics of Non-T and Non-B Cells, Lacking the Epstein-Barr Virus Genome and Derived from Human Acute Lymphoblastic Leukemia (1978)

A new lymphoid cell line, Reh 6, has been established from the peripheral blood of a patient with acute lymphocytic leukemia. Reh 6 cells were assayed for the presence of Epstein-Barr virus (EBV) DNA by nucleic acid hybridization and for Epstein-Barr nuclear antigen (EBNA) by the immunofluorescence test. Reassociation kinetics between in vitro [3H]-labeled EBV DNA and Reh 6 cell DNA indicated the absence of detectable amounts of EBV DNA in Reh 6 cell DNA. In addition, attempts to detect EBNA by the immunofluorescence test in Reh 6 cells were unsuccessful. Thus, this new lymphoid cell line apparently lacks the EBV genome.
The glymphatic system and Alzheimer's disease: possible connection? (2014)

Abstract — Alzheimer’s disease (AD) is the most common cause of dementia in the elderly, accounting for 60-80 % of all dementias. Symptoms of AD include memory loss (initially short term, later on long term as well), changes in mood and sun-downing. Magnetic resonance imaging (MRI) shows diffuse cortical atrophy and enlargement of the lateral ventricles due to neuronal cell loss. At the cellular level, neuroinflammation, activation of microglia, deposition of beta amyloid (Aβ) in the brain parenchyma and cerebral vasculature, and increases in the permeability of the blood-brain barrier (BBB) have all been observed as well. A newly developed theory purports that the glymphatic system of the brain may play a significant role in AD pathogenesis. This paper presents an initial mathematical model of the glymphatic system and studies how changes of transporter density and deposition of Aβ at the BBB changes clearance of Aβ. Changes in local neuronal cell density were also modeled. This represents one of the first attempts to computationally study the role of the glymphatic system in AD. Keywords-Alzheimer’s disease, math model, glymphatic system, LRP1, Aβ clearance I.
BRIC-60: Biological Research in Canisters (BRIC)-60 (2016)

The Biological Research in Canisters (BRIC) is an anodized-aluminum cylinder used to provide passive stowage for investigations evaluating the effects of space flight on small organisms. Specimens flown in the BRIC 60 mm petri dish (BRIC-60) hardware include Lycoperscion esculentum (tomato), Arabidopsis thaliana (thale cress), Glycine max (soybean) seedlings, Physarum polycephalum (slime mold) cells, Pothetria dispar (gypsy moth) eggs and Ceratodon purpureus (moss).
WARP (2008)

The flexible interface between the medium access layer and the custom physical layer of the Rice University Wireless Open-Access Research Platform (WARP) provides a high performance research tool for clean-slate cross layer designs. As we target a community platform, we have implemented various basic PHY and MAC technologies over WARP. Moreover, we are implementing cross-layer schemes such as rate adaptation and crosslayer MIMO MAC protocols. In this demo, we demonstrate the flexibility of the interaction between the the WARP PHY and MAC layers by showing the capability to instantaneously change the modulation scheme, disabling/enabling MAC features such as carrier sensing or RTS/CTS 4-way handshake, and different multi-rate schemes.
A 7m-range, 4.3mW/Ch. Ultrasound ASIC with Universal Energy Recycling TX for All-Weather Metamorphic Robotic 3D Vision System (2021)

A 64-Ch. ultrasound ASIC in 180nm 1P6M standard CMOS is presented for metamorphic robotic machine 3D vision, with 7mrange object detection capability, low-power (4.3mW/Ch.), small form-factor $(5\times 5\times 5cm^{3})$, and lightweight (100g). The proposed Universal Energy Recycling TX (UERTX) driver circuit saves energy by 81% compared to the conventional class-D driver.
S0490 Systematic Review of Anticholinergic Drugs Used in the Treatment of Gastrointestinal Conditions (2020)

INTRODUCTION: Anticholinergic drugs are commonly used for GI disease. For example, about 1 million prescriptions are written annually for hyoscyamine. However, their use does not appear to be confirmed by high quality evidenced-based medicine. To explore evidence for the efficacy and safety of anticholinergic drugs used for gastrointestinal (GI) disorders. We also focused on risk for cognitive side effects, dementia and falls. METHODS: A literature search using Cochrane library, CINAHL, Google Scholar, Ovid and MEDLINE was conducted of all English language published literature to the present. Randomized controlled trials (RCTs), observational, cross-sectional studies, and case series dating from 1975 to 2020 were eligible for review. Quality criteria included participant range was 20–2000 individuals, age range from 12–90 years old, duration range of 1–13 months. Quality-based diagnoses included Infantile Colic, Functional Abdominal Pain, and IBS meeting Manning, Rome I, II, III or IV criteria. Studies needed to include the use of any of the following anticholinergic drugs: Dicyclomine, Hyoscine, Hyoscyamine and Atropine. Outcomes of interest were efficacy of anticholinergic drugs and side effects. Critical appraisals of the included studies were performed by three independent reviewers. Data were extracted onto standardized forms. The study was registered with PROSPERO. RESULTS: Nine articles met initial criteria for review (Figure 1). Of these, 8 were issued before 1991. Selected studies had a duration of 1 to 13 months. None of the articles used appropriate diagnostic criteria listed above, (Table 1). Most reported a variety of adverse reactions, including cognitive side effects. The most common reported adverse reactions were dry mouth, dizziness and blurry vision. A summary of the articles is included in Table 2. CONCLUSION: Despite widespread use of anticholinergic drugs for GI disorders, there is no high-quality data on efficacy, and limited information on their potential side effects. The benefit of anticholinergics for GI disorders using standard diagnostic criteria appears to be unproven. Potential adverse effects require further documentation. At present, anticholinergic drugs are not recommended for the management of GI conditions.Table 1.: Data Quality AssessmentTable 2.: Summary of Results and Side Effects of Studies IncludedFigure 1.: Flow Diagram.
Synthesis of valuable benzenoid aromatics from bioderived feedstock (2023)

Abstract Aromatic chemicals play indispensable roles in our daily lives, having broad applications in household goods, textiles, healthcare, electronics and automotive, but their production currently relies on fossil resources that have heavy environmental burdens. Synthesis of aromatic chemicals from bio-based resources would be a viable approach to improve their sustainability. However, very few methods are available for achieving this goal. Here we present a strategy to synthesize aromatics from 5-hydroxymethylfurfural (HMF), an organic compound derived from sugars under mild conditions. HMF was first converted in two high-yielding steps into 2,5-dioxohexanal (DOH), a novel C6-compound containing three carbonyl groups. Subsequently, acid-catalysed intramolecular aldol condensation of DOH in the presence of secondary amines selectively produced a range of bio-based 4-dialkylamino substituted phenols and 1,4-di-(dialkylamino)benzenes (Wurster’s blue analogues) in 15–88% yields. In the absence of amines, the industrially important hydroquinone was also synthesized from DOH under acidic conditions. Using a similar approach where 4,5-dioxohexanal was the intermediate, we were also able to prepare catechol, a compound with important industrial applications, from HMF. The proposed approach can pave the way for the production of sustainable aromatic chemicals and move their industrial applications closer to achieving a bioeconomy.
Hydrogen bond donors in drug design (2021)

This presentation focuses on the differences between hydrogen bond donors (HBDs) and hydrogen bond acceptors (HBAs) in the context of drug design. Analysis of alkane/water partition coefficients shows that HBDs are typically less strongly solvated than HBAs, implying that desolvation penalty is not generally a plausible explanation for HBD-specific ADME liabilities. <br>
The Protein Structure Initiative Structural Genomics Knowledgebase (2009)

The Protein Structure Initiative (PSI) has produced more than 3300 protein structures in a high throughput manner. In order to achieve this, new technologies for all aspects of the structure determination and analysis pipeline have been developed. The strategies used for target selection by PSI centers have resulted in the structural determination of many novel sequences, and an increase in the structural coverage of protein families. The PSI Structural Genomics Knowledgebase (PSI SGKB) gives centralized access to the structures, annotations, models, protein production protocols, materials and technologies catalyzed by the PSI efforts. In collaboration with the Nature Publishing Group, the PSI SGKB expanded to become the Structural Genomics Gateway that provides a research library, editorials about new research advances and technologies, news, and an events calendar to present a broader view of structural biology and structural genomics. A description of how this resource can be used for enabling biological research will be given. The PSI SGKB is funded by the NIGMS.