gebhart/patrepeval huggingface dataset:
Altered Chromatin Occupancy of Master Regulators Underlies Evolutionary Divergence in the Transcriptional Landscape of Erythroid Differentiation (2014)

Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary proerythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (∼25% for GATA1, TAL1, and NFE2) but were more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression that is sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites associates with changes in the underlying chromatin structure, driving transcriptional divergence. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the β-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis.
Supplementary Table 1 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients (2023)

Supplementary Table 1 from Characterization of Bone Metastases from Rapid Autopsies of Prostate Cancer Patients
Gene Expression Differences between Low and High Stage Diffuse Large B Cell Lymphoma (DLBCL). (2006)

Abstract Low stage DLBCL patients have better prognosis than those with advanced disease. We searched for differences in gene expression between disease stages to find correlations with tumor stage as possible therapeutic targets. We used 2 microarray datasets from the Leukemia/Lymphoma Molecular Profiling Project containing nodal and extra-nodal de novo DLBCL samples on Lymphochip (LC), spotted arrays of ~7400 and Affymetrix arrays (Affy) of ~45,000 elements. The Affy dataset was a subset of the LC samples. LC elements were median-centered, log2 transformed; Affy elements were array-centered to a 500 average. We compared average gene expression in stage I vs. III/IV, looking for elements with &amp;gt;2-fold differences between low and high stage, with p&amp;lt;.05, excluding Affy elements with an average &amp;lt;100. 35 stage I and 131 stage III/IV samples were analyzed with LC and 34 stage I and 118 stage III/IV samples with Affy. Differentially expressed genes were searched by NCBI Entrez and Stratagene PathwayArchitect software to find common pathways of regulation. From the LC data, 6 genes were identified as differentially expressed, 5 were higher in stage I, 1 was lower in stage I. For the Affy data, 29 genes were differentially expressed, 11 were higher in stage I, 18 were lower in stage I (Table 1). Differences were rarely &amp;gt;3-fold. A subset of these genes, CTGF (connective tissue growth factor), FN1 (fibronectin), INHBA (activin), POSTN (periostin), THBS1 (thrombospondin), and BCL2, are coregulated and/or coregulatory. Many are expressed in the microenvironment and associated with fibrosis, wound healing and Th2 immune response. The presence of these genes at higher levels and their known associations implied a pathway of TGF-β signaling present mainly in the low stage DLBCL. Although TGF-β levels were not different between stages, differences in localization/activation of TGF-β could account for observed differences. In conclusion, there are a small number of stage-specific gene expression differences in DLBCL, and many of these relate to TGF-β signaling in the microenvironment. CTGF and FN1 were previously identified as key prognostic molecules in DLBCL (Rosenwald et al, NEJM 2002). These differences may relate to different prognoses between DLBCL stages and constitute therapeutic targets. Genes Differentially Expressed by Stage higher in stage I higher in stage III/IV LC Affy LC Affy CTGF CTGF IGHM IBRDC2 (2 elements) SERPINA1 MYBPC1 HTR3A POSTN NCR3 BCL2 FN1 INHBA (2 elements) CRYM THBS1 EMP1 SIX1 KLHL14 MGC23911 PP1665 GPM6A (2 elements) FLJ33069 TUBB IgM rheum. factor RF-TT9 CD1C transcribed locus LOC150568 LOC346887 LOC283454 MGC17624 IMAGE:5311619 transcribed locus (2x)
Preliminary investigation of soil chemical and physical properties associated with type‐I fairy ring symptoms in turfgrass (2007)

Abstract Fairy ring is a common disease of turfgrasses worldwide, and necrotic or severely injured turfgrass and soil water repellency are frequently observed in those turfgrass sites exhibiting type‐I fairy ring symptoms. The objective of this research was to evaluate soil chemical and physical properties associated with type‐I fairy ring symptoms in turfgrass. Soil samples were obtained from type‐I fairy ring symptoms on two golf course fairways and one lawn area. Soil analysis from all the three locations revealed concentrations of ammonium–nitrogen, potassium, and sulphur were statistically higher in soil underlying necrotic or bare zones versus soil in healthy turfgrass zones. Soil electrical conductivity (EC) also was higher, while volumetric soil water content was consistently lower in necrotic zones versus soil under healthy turfgrass. Soil water repellency was considered moderate to severe in necrotic zones and mostly wettable to subcritical repellency in soil underlying healthy turfgrass. Soil pH, total nitrogen, magnesium, calcium, cation exchange capacity (CEC), and organic matter content (OM) levels were not consistently different among necrotic and healthy turfgrass zones. The necrotic zones of those type‐I fairy ring areas in turfgrass were most likely associated with a combination of direct and indirect effects of the basidiomycete fungi on soil hydrophobicity and the accumulation of potentially phytotoxic compounds in the turfgrass root zone. Further research is needed to explore the interaction of basidiomycete fungi and the soil chemical and physical environment on turfgrass, and evaluate practices and strategies to control type‐I fairy ring symptoms in turfgrass. Copyright © 2007 John Wiley &amp; Sons, Ltd.
Water-Soluble Copolymers. 64. Effects of pH and Composition on Associative Properties of Amphiphilic Acrylamide/Acrylic Acid Terpolymers (1996)

Acrylamide (AM)/acrylic acid (AA) copolymers and AM/AA/N-(4-hexylphenyl)acrylamide (HPAM, 0.5 mol %) terpolymers with varied AA content have been synthesized by micellar copolymerization. Co- and terpolymers with 5−37 mol % AA and similar hydrodynamic volumes were prepared. Solution viscosity studies of the copolymers as a function of pH and copolymer concentration in deionized water and NaCl solution indicate normal polyelectrolyte behavior. In aqueous solutions, intra- or intermolecular hydrophobic associations may be favored by variation of terpolymer composition. Three-dimensional plots of both I3/I1 (from pyrene probe fluorescence) and viscosity as functions of pH and terpolymer concentration demonstrate the responsive nature of associations in water and in 0.5 M NaCl. Terpolymers containing approximately 9 and 21 mol % AA exhibit intermolecular (open) associations at ≤pH 5 and in the presence of NaCl. The terpolymer containing approximately 37 mol % AA, however, exhibits no intermolecular associations in deionized water even at low pH. Pyrene fluorescence studies of this terpolymer indicate a significantly apolar environment sensed by the probe at pH 4, suggesting that intramolecular (closed) microdomains are formed. Conceptual models based on hydrophobic, ionic, and hydrogen-bonding interactions in these systems are presented.
New Algorithm for Computing Eigenvectors of the Symmetric Eigenvalue Problem (2014)

We describe a design and implementation of a multi-stage algorithm for computing eigenvectors of a dense symmetric matrix. We show that reformulating the existing algorithms is beneficial in terms of performance even if that doubles the computational complexity. Through detailed analysis, we show that the effect of the increase in the asymptotic operation count may be compensated by a much improved performance rate. Our performance results indicate that using our approach achieves very good speedup and scalability even when directly compared with the existing state-of-the-art software.
WE‐A‐330A‐01: Breast CAD in the Digital Era (2006)

Use of output from a computerized analysis of a breast image by radiologists may help them in the tasks of detection or diagnostic, and potentially improve the overall interpretation of breast images and the subsequent patient care. Many factors motivate the attempts to aid or automate radiological diagnosis. Inadequacies in interpretation performance may be due to the presence of image noise or normal anatomical structure as well as to known limitations in the human search and perception process. Developments in breast CAD have led to clinically‐used detection systems in screening mammography and preclinical classification systems for diagnostic breast imaging. Diagnostic breast CAD systems provide output for the characterization of lesions on special‐view mammography, breast sonography, and breast MRI in order to aid in patient management decisions, such as biopsy decisions. As imaging continues to expand in the digital era, computer‐aided diagnosis (CAD) may become an integrated tool in the online diagnostic workup of suspect breast lesions using multi‐modality images and advanced PACS. This presentation reviews research in computerized analysis of mammographic, sonographic, and magnetic resonance breast images for detection and diagnosis. It will include the characterization of lesions and the estimation of the probability of malignancy for use in the diagnostic workup of suspect lesions. CAD systems in diagnostic workup usually involve having the computer extract the margin of the lesion from the surrounding parenchyma, extract characteristics (features) of the lesions, merge these computer‐extracted features into an estimate of the probability of malignancy, and as an option, retrieve automatically similar lesions from an online reference library. The aim of CAD in diagnostic workup is to increase classification sensitivity and specificity as well as to reduce intra‐and inter‐observer variability. While the breadth and depth of CAD is increasing, continued and expanded efforts are needed for collecting and confirming databases, establishing methods for evaluation, integrating effectively and efficiently with PACS and RIS systems, and providing means for clinical evaluation. Learning objectives: 1. To appreciate the development of CAD in multi‐modality imaging for detection and diagnosis of breast cancer. 2. To understand the benefits and challenges as CAD moves into the digital era and is integrated with PACS and HIS. 3. To recognize the necessary steps for advancing and integrating CAD clinically. COI: Maryellen Giger is a shareholder and consultant, and receives research funding from R2 Technology, Inc.
IgE Epitopes of the House Dust Mite Allergen Der p 7 Are Mainly Discontinuous and Conformational (2021)

IgE epitopes of Der p 7 belong to the conformational and discontinuous type whereas sequential Der p 7 peptides lack IgE reactivity. It should thus be possible to construct hypoallergenic vaccines for Der p 7 based on carrier-bound allergen peptides.
Measurement of nondegenerate two-photon absorption spectra of single-crystal polydiacetylene (2004)

We measured nondegenerate two-photon absorption spectra of single-crystal polydiacetylene (PTS) with white-light continuum nonlinear optical spectroscopy. We observed an intermediate state resonance enhancement in qualitative agreement with a three-level model.
Heterobi‐ and ‐trimetallic Ion Pairs of Zirconocene‐Based Isoselective Olefin Polymerization Catalysts with AlMe3 (2015)

Abstract The reactivity towards AlMe 3 of discrete cationic ansa‐zirconocenes 2 a,b that are ubiquitously used in isoselective propylene polymerization and based on [{Ph(H)C(3,6‐ t Bu 2 ‐Flu)(3‐ t Bu‐5‐Et‐Cp)}ZrMe 2 )] {Cp‐Flu} and rac ‐[{Me 2 Si‐(2‐Me‐4‐Ph‐Ind) 2 }ZrMe 2 ] {SBI} was scrutinized. The first example of a structurally characterized Group 4 metallocene AlMe 3 adduct ( 3 b ) is reported. In the presence of excess AlMe 3 , the {SBI}‐based AlMe 3 adduct 3 b undergoes a slow decomposition via CH activation in a bridging methyl unit to yield a new species ( 4 b ) with a trimetallic {Zr(μ‐CH 2 )(μ‐Me)AlMe(μ‐Me)AlMe 2 } core. EXSY NMR data for the process 2 b ⇄ 3 b → 4 b suggest very rapid and reversible binding of an additional AlMe 3 molecule onto AlMe 3 adduct 3 b . The resulting heterotrimetallic species intermediates exchange of methyl groups between different metal centers and slowly undergoes the CH activation reaction towards 4 b .
Cross-Domain 3D Equivariant Image Embeddings (2018)

Spherical convolutional networks have been introduced recently as tools to learn powerful feature representations of 3D shapes. Spherical CNNs are equivariant to 3D rotations making them ideally suited to applications where 3D data may be observed in arbitrary orientations. In this paper we learn 2D image embeddings with a similar equivariant structure: embedding the image of a 3D object should commute with rotations of the object. We introduce a cross-domain embedding from 2D images into a spherical CNN latent space. This embedding encodes images with 3D shape properties and is equivariant to 3D rotations of the observed object. The model is supervised only by target embeddings obtained from a spherical CNN pretrained for 3D shape classification. We show that learning a rich embedding for images with appropriate geometric structure is sufficient for tackling varied applications, such as relative pose estimation and novel view synthesis, without requiring additional task-specific supervision.
A simple andfast technique tocharacterize thegroupdelay properties offilber Bragggratings (2005)

A novel method that usesasimple andfast iterative algorithm torecover thegroup delay ofanyfiber Bragg grating fromits measured transmission spectrum isdescribed. Its benefits overleading techniques inthis field aremuchgreater speed, simplicity, andhigh accuracy eveninthepresence ofsignificant experimental noise. ©2005Optical Society ofAmerica OCIScodes: (060.2340) Fiber optics components; (050.2770) Gratings
Discovery of N -[2-Hydroxy-6-(4-methoxybenzamido)phenyl]-4- (4-methyl-1,4-diazepan-1-yl)benzamide (Darexaban, YM150) as a Potent and Orally Available Factor Xa Inhibitor (2011)

Inhibitors of factor Xa (FXa), a crucial serine protease in the coagulation cascade, have attracted a great deal of attention as a target for developing antithrombotic agents. We previously reported findings from our optimization study of a high-throughput screening (HTS) derived lead compound 1a that resulted in the discovery of potent amidine-containing FXa inhibitors represented by compound 2. We also conducted an alternative optimization study of 1a without incorporating a strong basic amidine group, which generally has an adverse effect on the pharmacokinetic profile after oral administration. Replacement of 4-methoxybenzene with a 1,4-benzodiazepine structure and introduction of a hydroxy group at the central benzene led to the discovery of the potent and orally effective factor Xa inhibitor 14i (darexaban, YM150). Subsequent extensive study revealed a unique aspect to the pharmacokinetic profile of this compound, wherein the hydroxy moiety of 14i is rapidly transformed into its glucuronide conjugate 16 (YM-222714) as an active metabolite after oral administration and it plays a major role in expression of potent anticoagulant activity in plasma. The distinctive, potent activity of inhibitor 14i after oral dosing was explained by this unique pharmacokinetic profile and its favorable membrane permeability. Compound 14i is currently undergoing clinical development for prevention and treatment of thromboembolic diseases.
Numerical Simulation Method for a Liquid-Crystal Aberration Compensation Device (2003)

We have developed a numerical simulation method on the basis of the ray tracing technique to evaluate a liquid-crystal (LC) spherical aberration compensation device for next-generation high-capacity optical memory devices. We numerically evaluated the performance and the tolerance of the LC device and showed its adequate capability to compensate the spherical aberration due to the nonuniformity of the disc cover layer thickness. Using the simulation method, we numerically examined the possibility of using LC devices to compensate the large spherical aberration due to the layer jump of the dual-layer optical disc and determined that the gradation-type LC device can be used for dual-layer optical recording.
Measurement of inclusive jet and dijet cross sections in proton-proton collisions at 7 TeV centre-of-mass energy with the ATLAS detector (2011)

Jet cross sections have been measured for the first time in proton-proton collisions at a centre-of-mass energy of 7 TeV using the ATLAS detector. The measurement uses an integrated luminosity of 17 nb -1 recorded at the Large Hadron Collider. The anti-k t algorithm is used to identify jets, with two jet resolution parameters, R = 0.4 and 0.6. The dominant uncertainty comes from the jet energy scale, which is determined to within 7% for central jets above 60 GeV transverse momentum. Inclusive single-jet differential cross sections are presented as functions of jet transverse momentum and rapidity. Dijet cross sections are presented as functions of dijet mass and the angular variable . The results are compared to expectations based on next-toleading-order QCD, which agree with the data, providing a validation of the theory in a new kinematic regime.
Understanding the Electrochemical Interactions of Coronavirus (2022)

Coronavirus has become a household name over the past two years. Diagnostic tests have seemed to assist early identification and isolation of infected individuals affected by coronavirus, thereby curbing the spread of the disease. Although RT-PCR has been the gold-standard for diagnostic testing, its high turnaround time for results has led to several alternate biosensing technologies being employed for rapid Covid-19 screening. Electrochemical biosensors, being one of those technologies, has the advantage of being miniaturized for point-of-use, and producing rapid and highly sensitive results. Often, these alternate techniques involve the detection of an antigen (eg. spike protein) instead of the nucleic acid material. This leads to a compromise in the detection accuracy while improving the detection time and eliminating the need for amplification. Understanding the working principle of rapid antigen tests is essential for improving the accuracy. In this study, we shed light towards the interaction of coronavirus with our Ultra-Fast Covid-19 Diagnostic Sensor (UFC-19). UFC-19 is a nickel based electrochemical sensor that interacts with SARS-CoV-2 at very short times to produce current responses in a particular analysis window. Chronoamperometry is used for electrochemically characterizing the interaction between the electrocatalyst and hydrogen occupancies on spike protein. This reaction seems to occur at very short time span (~1 ms) as a result of local pH changes at the electrical double layer. UFC-19 can screen for coronavirus in saliva or water and can distinguish coronavirus current response from other viruses like HIV, Influenza or bacteria like E. coli . Although the response is specific to corona viruses, it is not specific to SARS-CoV-2. Hence, it is of utmost importance to selectively distinguish SARS-CoV-2 from other coronaviruses such as SARS-CoV, MERS-CoV or Human-CoV. The kinetics of these coronaviruses are studied using a rotating disk electrode to differentiate how their spike proteins diffuse and interact at the double layer causing pH change. There seems to be a correlation between the dissociation constants, pH changes and diffusion coefficients of the different corona viruses from our preliminary studies. Diffusion coefficients of these corona viruses could provide a possible insight into rate at which the interaction occurs leading a pathway for selective SARS-CoV-2 detection. This insight is key to engineer and improve the accuracy of UFC-19 for SARS-CoV-2 detection and to further extend this technology for other pathogenic organisms.
Opportunities for Research for COVID-19 in the Mission of NIDDK (2020)

The current worldwide pandemic of the coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) continues to cause incredible morbidity and mortality on a global level. Presently, there is no effective pharmacologic therapy nor a vaccine to offer. Given the circumstances and mode of transmission, the coronavirus crisis is expected to remain a significant part of our lives for the foreseeable future, continuing to cause economic hardships, straining our health care system, and changing the way we work and live on a daily basis. From this crisis, we have learned, and will continue to learn, new information almost daily. What we did know prior to the pandemic was that past viral pandemics have clearly demonstrated the association of chronic disease comorbidities with increased risk for morbidity and mortality (1–3). This observation is no different with the current crisis, as a number of chronic diseases appear to be important comorbidities in those with COVID-19 infection (3,4). As recently reported, during 1–30 March 2020, 89.3% of hospitalized adults had one or more underlying conditions. The most commonly reported conditions overall were hypertension (49.7%), obesity (48.3%), chronic lung disease (34.6%), diabetes (28.3%), cardiovascular disease (27.8%), and kidney disease (13.1%) (4), several of which fall within National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) mission areas. It is important from a medical perspective that we fully understand the clinical characteristics of individuals affected, risk factors for mortality and other outcomes, potential underlying health disparities, and other clinical variables in order to be in the best position as a medical community to inform on mitigation strategies and treatment until a vaccine is found.

At present, clinicians managing patients with acute onset of multisystem dysfunction must make urgent decisions with little evidence to guide their practice. …