gebhart/patrepeval huggingface dataset:
28-Way vertebrate alignment and conservation track in the UCSC Genome Browser (2007)

This article describes a set of alignments of 28 vertebrate genome sequences that is provided by the UCSC Genome Browser. The alignments can be viewed on the Human Genome Browser (March 2006 assembly) at http://genome.ucsc.edu, downloaded in bulk by anonymous FTP from http://hgdownload.cse.ucsc.edu/goldenPath/hg18/multiz28way, or analyzed with the Galaxy server at http://g2.bx.psu.edu. This article illustrates the power of this resource for exploring vertebrate and mammalian evolution, using three examples. First, we present several vignettes involving insertions and deletions within protein-coding regions, including a look at some human-specific indels. Then we study the extent to which start codons and stop codons in the human sequence are conserved in other species, showing that start codons are in general more poorly conserved than stop codons. Finally, an investigation of the phylogenetic depth of conservation for several classes of functional elements in the human genome reveals striking differences in the rates and modes of decay in alignability. Each functional class has a distinctive period of stringent constraint, followed by decays that allow (for the case of regulatory regions) or reject (for coding regions and ultraconserved elements) insertions and deletions.
Occurrence of the Ramsauer effect in the inner-shell ionization of atoms (1976)

Ionization of the K-shell by proton impact is considered using a simple model atomic potential. Differences in cross sections obtained using the atomic and the Coulomb potentials occur mainly through the normalization of the final state wavefunctions. The normalization factor is determined by the Jost function for elastic scattering and the typical Ramsauer-Townsend features of elastic scattering are clearly exhibited in the ionization cross sections.
Trend of digital camera and interchangeable zoom lenses with high ratio based on patent application over the past 10 years (2012)

Although digitalization has tripled consumer-class camera market scale, extreme reductions in prices of fixed-lens cameras has reduced profitability. As a result, a number of manufacturers have entered the market of the System DSC i.e. digital still camera with interchangeable lens, where large profit margins are possible, and many high ratio zoom lenses with image stabilization functions have been released. Quiet actuators are another indispensable component. Design with which there is little degradation in performance due to all types of errors is preferred for good balance in terms of size, lens performance, and the rate of quality to sub-standard products. Decentering, such as that caused by tilting, sensitivity of moving groups is especially important. In addition, image stabilization mechanisms actively shift lens groups. Development of high ratio zoom lenses with vibration reduction mechanism is confronted by the challenge of reduced performance due to decentering, making control over decentering sensitivity between lens groups everything. While there are a number of ways to align lenses (axial alignment), shock resistance and ability to stand up to environmental conditions must also be considered. Naturally, it is very difficult, if not impossible, to make lenses smaller and achieve a low decentering sensitivity at the same time. 4-group zoom construction is beneficial in making lenses smaller, but decentering sensitivity is greater. 5-group zoom configuration makes smaller lenses more difficult, but it enables lower decentering sensitivities. At Nikon, the most advantageous construction is selected for each lens based on specifications. The AF-S DX NIKKOR 18-200mm f/3.5-5.6G ED VR II and AF-S NIKKOR 28-300mm f/3.5-5.6G ED VR are excellent examples of this.
Transient allodynia pain models in mice for early assessment of analgesic activity (2007)

These transient allodynia models are a useful addition to the toolbox of preclinical pain models. They are simple, rapid and reproducible, and will be especially useful for characterizing the pain phenotype of knockout mice.
Analysis of the association between lactotransferrin (LTF) gene polymorphism and dental caries (2010)

Lactotransferrin A/G (exon 2, Lys/Arg) polymorphism was associated with susceptibility to dental caries in 12-year-old students.
Comparing Polychlorinated Biphenyl Concentrations and Patterns in the Saginaw River Using Sediment, Caged Fish, and Semipermeable Membrane Devices (2000)

Three techniques of assessing bioavailable polychlorinated biphenyls (PCBs) in the Saginaw River, MI, were compared: sediments, caged fish, and semipermeable membrane devices (SPMDs). SPMDs and caged fish were placed in the river for 28 days at five sites where sediments were also sampled. The samples were analyzed for PCB congeners to determine concentrations and patterns. Total PCB concentrations ranged from 33 to 280 ng/g (dry weight) in sediments, 46 to 290 ng/g (wet weight) in caged fish, and 77 to 790 ng/g in SPMDs. Previously reported rates of PCB accumulation by SPMDs were used to estimate aqueous concentrations from the PCB concentrations detected in the SPMDs. Sediment-water partition coefficients were used to estimate aqueous PCB concentra tions from sediment. Steady-state bioconcentration factors and depuration rate constants were used to estimate dissolved PCB concentrations from caged channel catfish. Relative PCB patterns from the SPMDs, caged fish, and sediment were compared using principal components analysis. SPMD and sediment samples provide complementary information. Sediments reflect long-term accumula tion and weathering, while SPMDs integrate water concentrations only during the sampling period. Because of higher water solubilities of lower-chlorinated PCBs these predominate in the SPMDs as compared to in the fish and sediments. Contaminant profile differences between caged fish and SPMDs are likely due to metabolism and depuration of certain PCB congeners by fish.
Transparent fluids for 157-nm immersion lithography (2004)

The <i>Journal of Micro/Nanopatterning, Materials, and Metrology</i> (JM3) publishes peer-reviewed papers on the core enabling technologies that address the patterning needs of the electronics industry.
Direct Observation of a Carbene-Alcohol Ylide (2011)

Carboethoxycarbene reacts with methanol-OD to form an ylide. The formation and decay of this ylide was monitored by ultrafast time-resolved IR spectroscopy. The formation and decay of the ylide is linearly dependent on the concentration of methanol-OD in acetonitrile with second-order rate constants of ylide formation (8.4 × 10(9) M(-1) s(-1)) and decay (1.4 × 10(9) M(-1) s(-1)). Similar results were obtained with 1-butanol.
Personalized Glycated Hemoglobin in Diabetes Management: Closing the Gap with Glucose Management Indicator (2023)

Glycated hemoglobin (HbA1c) has played a central role in the management of diabetes since the end of the landmark Diabetes Control and Complications Trial 30 years ago. However, it is known to be subject to distortions related to altered red blood cell (RBC) properties, including changes in cellular lifespan. On occasion, the distortion of HbA1c is associated with a clinical pathological condition affecting RBCs, however, the more frequent scenario is related to interindividual RBC variations that alter HbA1c-average glucose relationship. Clinically, these variations can potentially lead to over- or underestimating glucose exposure of the individual to the extent that may put the person at excess risk of over- or undertreatment. Furthermore, the variable association between HbA1c and glucose levels across different groups of people may become an unintentional driver of inequitable health care delivery, outcomes, and incentives. The subclinical effects within the normal expected physiological range of RBCs can be large enough to alter clinical interpretation of HbA1c and addressing this will help with individualized care and decision making. This review describes a new glycemic measure, personalized HbA1c (pA1c), that may address the clinical inaccuracies of HbA1c by taking into account interindividual variability in RBC glucose uptake and lifespan. Therefore, pA1c represents a more sophisticated understanding of glucose-HbA1c relationship at an individual level. Future use of pA1c, after adequate clinical validation, has the potential to refine glycemic management and the diagnostic criteria in diabetes.
Emotional Perception Deficits in Amyotrophic Lateral Sclerosis (2007)

Emotional recognition deficits occur in bulbar ALS, particularly with emotional facial expressions, and can arise independent of depressive and dementia symptoms or comorbid with depression and dementia. These findings expand the scope of cognitive dysfunction detected in ALS, and bolsters the view of ALS as a multisystem disorder involving cognitive and also motor deficits.
Utility and Safety of Balloon-Assisted Enteroscopy in Small Bowel Crohnʼs Disease: Single - Center Cohort Experience (2016)

Introduction: Balloon-assisted enteroscopy (BAE) has advanced small bowel interrogations for Crohn's disease (CD), both for diagnosis and for therapeutic management of strictures or gastrointestinal bleeding. However, there is a paucity of long-term data on the safety of this procedure, or on its success in reducing the need for surgeries, hospitalizations, or repeat endoscopic interventions. The aim of our study was to assess the overall safety and impact of BAE in the management of small bowel CD. Methods: We performed a retrospective analysis of patients with suspected or established small bowel CD who underwent BAE at our institution between 1/1/2001 and 12/31/2013 for diagnostic CD confirmation, therapeutic intervention (strictures and/or video capsule endoscopy retrieval), or evaluation of gastrointestinal (GI) bleeding. Data were collected on baseline demographic variables, BAE approach, and therapeutic interventions. Additional data on hospitalization for obstructive symptoms after the initial BAE, and the need for further endoscopic dilation or surgical intervention were evaluated over the follow-up period. Adverse events from BAE were recorded. Results: A total of 91 small bowel CD patients underwent 125 BAE procedures during the study period. Median age at diagnosis was 33 years (interquartile range [IQR], 9 - 57), and 51% were females. The indication for BAE was diagnostic in 54 (43%), therapeutic in 43 (34%), GI bleeding in 8, and multiple indications in 20. Antegrade BAE were performed in 57 instances (46%) while 68 were retrograde (54%). Balloon dilation was undertaken in 23 patients (25%) in 32 procedures involving 69 strictures. Median length of stricture was 1.5 centimeters (IQR, 1 - 5) and median diameter was 9 millimeters (5 - 10.3). Median follow-up time was 435 days (IQR, 68 - 1002). Repeat endoscopic dilations were required in 14 patients. Surgery was avoided in 12 of the 23 patients dilated (52%), with no further hospitalizations for small bowel obstruction recorded in 11 of the 12 (92%). Only 1 case of small bowel perforation occurred, and 2 procedures were aborted due to bleeding. Conclusion: Balloon-assisted enteroscopy is safe and efficacious in the diagnosis and management of small bowel Crohn's disease. It is a needed addition to the IBD endoscopic armamentarium.
Oral vaccines (2013)

Oral vaccines are safe and easy to administer and convenient for all ages. They have been successfully developed to protect from many infectious diseases acquired through oral transmission. We recently found in animal models that formulation of oral vaccines in a nanoparticle-releasing microparticle delivery system is a viable approach for selectively inducing large intestinal protective immunity against infections at rectal and genital mucosae. These large-intestine targeted oral vaccines are a potential substitute for the intracolorectal immunization, which has been found to be effective against rectogenital infections but is not feasible for mass vaccination. Moreover, the newly developed delivery system can be modified to selectively target either the small or large intestine for immunization and accordingly revealed a regionalized immune system in the gut. Future applications and research endeavors suggested by the findings are discussed.
Make the right measurement – discovery of an allosteric inhibition site for p300-HAT (2018)

Histone acetyltransferases (HATs) and histone deacetylases (HDACs) catalyze the dynamic and reversible acetylation of proteins, an epigenetic regulatory mechanism associated with multiple cancers. Indeed, HDAC inhibitors are already approved in the clinic. The HAT paralogs p300 and CREB-binding protein (CBP) have been implicated in human pathological conditions including several hematological malignancies and androgen receptor-positive prostate cancer. Others have reported CoA-competitive inhibitors of p300 and CBP with cell-based activity. Here we describe 2 compounds, CPI-0489076 and CPI-0671090, discovered through p300-HAT HTS screening, which inhibit p300-HAT via binding at an allosteric site. We present the high resolution (1.72 and 2.32 ) co-crystal structures of these molecules bound to a previously undescribed allosteric site of p300-HAT.
Systematic Studies on Structural Parameters for Nanotubular Assembly of Hexa-peri-hexabenzocoronenes (2008)

Thirteen different hexa-peri-hexabenzocoronenes (HBCs) I-III were newly synthesized, and their self-assembling behaviors were investigated. Taking into account also the reported behaviors of amphiphilic HBCs, some structural parameters of HBC essential for the tubular assembly were revealed. Points to highlight include (1) the importance of two phenyl groups attached to one side of the HBC unit, (2) essential roles of long paraffinic side chains on the other side of the phenyl groups, and (3) no necessity of hydrophilic oligo(ethylene glycol) side chains. The hierarchical nanotubular structure, rendered by virtue of a synchrotron radiation technique, was virtually identical to our previous proposal, where the nanotubes are composed of helically coiled bilayer tapes with a tilting angle of approximately 45 degrees. Each tape consists of pi-stacked HBC units, where the inner and outer HBC layers are connected by interdigitation of paraffinic side chains. The coiled structure is most likely caused by a steric congestion of the phenyl groups attached to the HBC unit, whose tilting direction may determine the handedness of the helically chiral nanotube.
Coulomb Enhanced Charge Transport in Semicrystalline Polymer Semiconductors (2016)

Polymer semiconductors provide unique possibilities and flexibility in tailoring their optoelectronic properties to match specific application demands. The recent development of semicrystalline polymers with strongly improved charge transport properties forces a review of the current understanding of the charge transport mechanisms and how they relate to the polymer's chemical and structural properties. Here, the charge density dependence of field effect mobility in semicrystalline polymer semiconductors is studied. A simultaneous increase in mobility and its charge density dependence, directly correlated to the increase in average crystallite size of the polymer film, is observed. Further evidence from charge accumulation spectroscopy shows that charges accumulate in the crystalline regions of the polymer film and that the increase in crystallite size affects the average electronic orbitals delocalization. These results clearly point to an effect that is not caused by energetic disorder. It is instead shown that the inclusion of short range coulomb repulsion between charge carriers on nanoscale crystalline domains allows describing the observed mobility dependence in agreement with the structural and optical characterization. The conclusions that are extracted extend beyond pure transistor characterization and can provide new insights into charge carrier transport for regimes and timescales that are relevant to other optoelectronic devices.
ChemInform Abstract: Catalytic Method for the Reduction of Lactones to Lactols. (1996)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
High Throughput Microwave Synthesis of Metal Organic Framework (MOF) Libraries (2007)

The transmission and fluorescence of the compound eye of living, intact blowflies Calliphora erythrocephala, mutant chalky, were studied microspectrophotometrically. Transmission spectra were recorded under four conditions. The fly was either in the normal air environment or in a nitrogen atmosphere, and in both cases the investigated eye was adapted to red and blue light, respectively. The absorbance difference spectra obtained from the two chromatic adapted conditions showed the clear characteristics of the main visual pigment; the difference spectra for the air and the N2 case were virtually identical. The absorbance difference spectrum obtained from the air vs N2 case was very similar to the redox difference spectrum of the pigments in the mitochondrial chain. The redox difference spectra obtained for the two photosteady states were essentially the same. The fluorescence emission spectra induced by UV and blue excitation were measured with the fly in air and in a nitrogen atmosphere, respectively. The UV-induced blue emission under hypoxia, whereas the blue-induced green emission dropped. The changes are typical for a reduction of mitochondrial NADH and flavoproteins, respectively. The transmission and fluorescence measurements corroborates each other and demonstrate mitochondrial activity in photoreceptors in vivo and non-invasively.
Targeting Enterococcus faecalis HMG-CoA reductase with a non-statin inhibitor (2023)

HMG-CoA reductase (HMGR), a rate-limiting enzyme of the mevalonate pathway in Gram-positive pathogenic bacteria, is an attractive target for development of novel antibiotics. In this study, we report the crystal structures of HMGR from Enterococcus faecalis (efHMGR) in the apo and liganded forms, highlighting several unique features of this enzyme. Statins, which inhibit the human enzyme with nanomolar affinity, perform poorly against the bacterial HMGR homologs. We also report a potent competitive inhibitor (Chembridge2 ID 7828315 or compound 315) of the efHMGR enzyme identified by a high-throughput, in-vitro screening. The X-ray crystal structure of efHMGR in complex with 315 was determined to 1.27 Å resolution revealing that the inhibitor occupies the mevalonate-binding site and interacts with several key active site residues conserved among bacterial homologs. Importantly, 315 does not inhibit the human HMGR. Our identification of a selective, non-statin inhibitor of bacterial HMG-CoA reductases will be instrumental in lead optimization and development of novel antibacterial drug candidates.
Wormhole detection using channel characteristics (2012)

The potential applications and pervasive nature of mobile ad-hoc networks (MANETs) has made them an attractive target for attackers. The wireless medium of communication coupled with constrained resources enable attacks which can be executed by a weak adversary. A wormhole is one such attack which poses considerable threat, particularly to routing protocols. In this paper, we devise a novel scheme for detecting a wormhole by utilizing the inherent symmetry of electromagnetic wave propagation in the wireless medium. We demonstrate the loss of this symmetry in case of a wormhole attack and propose a method to detect and flag the adversary. We modify the insecure neighborhood discovery to incorporate authentication. We further extend this scheme to a trust system with low overhead.
Arteriogenesis versus angiogenesis (2017)

Abstract Higher organisms have a cardiovascular circulatory system with blood vessels to supply vital nutrients and oxygen to distant tissues. It is therefore not surprising that vascular disorders are leading causes of mortality. Understanding how new blood vessels form, creates opportunities to cure these life-threatening diseases. After birth, growth of blood vessels mainly occurs via two distinct mechanisms depending on the initial trigger: angiogenesis (referred here as capillary sprouting) is induced primarily by hypoxia, whereas arteriogenesis (referred here as the rapid enlargement of pre-existing collateral arteries, induced by vascular occlusion) is mainly driven by fluid shear stress. Arteriogenesis allows conductance of much larger volumes of blood per unit of time than does the increase in capillary density during angiogenesis. Notwithstanding these major differences, angiogenesis and arteriogenesis share a number of underlying mechanisms, e.g. the involvement of growth factor signalling. This chapter highlights the cellular and molecular events driving the two processes and discusses the therapeutic potential of targeting angiogenesis in cancer and arteriogenesis in cardiovascular diseases.
Anatomical and Quantitative Description of the Transcavernous Approach for Basilar Artery Aneurysms (2007)

Introduction: The management of wide-necked, giant, or unsuccessfully coiled basilar apex aneurysms requires a wide exposure, both for working area and linear visualization of the basilar artery. Cranial-based approaches, such as the transcavernous approach (TcA), have been proposed to deal with such aneurysms; whether abbreviated forms of this approach might provide similar exposure remains controversial. This study examines this issue quantitatively.
Synthesis of A83586C Analogs with Potent Anticancer and β-Catenin/ TCF4/Osteopontin Inhibitory Effects and Insights Into How A83586C Modulates E2Fs and pRb (2009)

The synthesis of three potent new antitumor agents is described: the A83586C-citropeptin hybrid (1), the A83586C-GE3 hybrid (2), and l-Pro-A83586C (3). Significantly, compounds 1 and 2 function as highly potent inhibitors of beta-catenin/TCF4 signaling within cancer cells, while simultaneously downregulating osteopontin (Opn) expression. A83586C antitumor cyclodepsipeptides also inhibit E2F-mediated transcription by downregulating E2F1 expression and inducing dephosphorylation of the oncogenic hyperphosphorylated retinoblastoma protein (pRb).
A New Route to Vitamin E Key‐Intermediates by Olefin Cross‐Metathesis (2006)

Abstract Ru‐Catalyzed olefin cross‐metathesis (CM) has been successfully applied to the synthesis of several phytyl derivatives ( 2b, 2d – f, 3b ) with a trisubstituted CC bond, as useful intermediates for an alternative route to α ‐tocopheryl acetate (vitamin E acetate; 1b ) ( Scheme 1 ). Using the second‐generation Grubbs catalyst RuCl 2 (C 21 H 26 N 2 )(CHPh)PCy 3 (Cy = cyclohexyl; 4a ) and Hoveyda–Grubbs catalyst RuCl 2 (C 21 H 26 N 2 ){CH‐C 6 H 4 (O‐ i Pr)‐2} ( 4b ), the reactions were performed with various C ‐allyl ( 5a – f, 7a,b ) and O ‐allyl ( 8a – d ) derivatives of trimethylhydroquinone‐1‐acetate as substrates. 2,6,10,14‐Tetramethylpentadec‐1‐ene ( 6a ) and derivatives 6c – e of phytol ( 6b ) as well as phytal ( 6f ) were employed as olefin partners for the CM reactions ( Schemes 2 and 5 ). The vitamin E precursors could be prepared in up to 83% isolated yield as ( E / Z )‐mixtures.