gebhart/patrepeval huggingface dataset:
Surface characterization using chemical force microscopy and the flow performance of modified polydimethylsiloxane for microfluidic device applications (2003)

The widespread interest in micro total analysis systems has resulted in efforts to develop devices in cheaper polymer materials such as polydimethylsiloxane (PDMS) as an alternative to expensive glass and silicon devices. We describe the oxidation of the PDMS surface to form ionizable groups using a discharge from a Tesla coil and subsequent chemical modification to augment electroosmotic flow (EOF) within the microfluidic devices. The flow performance of oxidized, amine-modified and unmodified PDMS materials has been determined and directly compared to conventional glass devices. Exact PDMS replicas of glass substrates were prepared using a novel two step micromolding protocol. Chemical force microscopy has been utilized to monitor and measure the efficacy of surface modification yielding information about the acid/base properties of the modified and unmodified surfaces. Results with different substrate materials correlates well with expected flow modifications as a result of surface modification. Oxidized PDMS devices were found to support faster EOF (twice that of native PDMS) similar to glass while those derivatized with 3-aminopropyl triethoxysilane (APTES) showed slower flow rates compared to native PDMS substrates as a result of masking surface charge. Results demonstrate that the surface of PDMS microdevices can be manipulated to control EOF characteristics using a facile surface derivatization methodology allowing surfaces to be tailored for specific microfluidic applications and characterized with chemical force microscopy.
Genetische Ursachen für epidermale Fragilität (2009)

Zusammenfassung Bei epidermaler Fragilität führen geringfügige Verletzungen zur Blasenbildung der Haut und der hautnahen Schleimhäute. Verantwortlich für die Fragilität sind Mutationen in Genen, die Proteine der epidermalen und dermo-epidermalen Adhäsion kodieren. Die meisten Erkrankungen werden in der Gruppe der Epidermolysis bullosa zusammengefasst und sind sowohl klinisch als auch genetisch heterogen. Bei Neugeborenen und Kleinkindern, aber auch bei vielen erwachsenen Patienten kann der Subtyp der Epidermolysis bullosa aufgrund des Phänotyps nicht diagnostiziert werden. Die genaue Diagnosestellung ist nur durch spezifische Laboruntersuchungen, wie das Immunfluoreszenzmapping, die Elektronenmikroskopie und die Mutationsanalyse möglich. Die Behandlung ist symptomatisch und basiert auf allgemeinem Wundmanagement, während bei den schweren Formen mit Multisystembeteiligung interdisziplinäre medizinische Betreuung notwendig ist. Die neuen Erkenntnisse über molekulare Grundlagen und Pathomechanismen der Epidermolysis bullosa ermöglichen die Entwicklung neuartiger molekularen Therapien.
The conserved mosaic prophage protein paratox inhibits the natural competence regulator ComR in Streptococcus (2018)

Horizontal gene transfer is an important means of bacterial evolution. This includes natural genetic transformation, where bacterial cells become "competent" and DNA is acquired from the extracellular environment. Natural competence in many species of Streptococcus, is regulated by quorum sensing via the ComRS receptor-signal pair. The ComR-XIP (mature ComS peptide) complex induces expression of the alternative sigma factor SigX, which targets RNA polymerase to CIN-box promoters to activate genes involved in DNA uptake and recombination. In addition, the widely distributed Streptococcus prophage gene paratox (prx) also contains a CIN-box, and here we demonstrate it to be transcriptionally activated by XIP. In vitro experiments demonstrate that Prx binds ComR directly and prevents the ComR-XIP complex from interacting with DNA. Mutations of prx in vivo caused increased expression of the late competence gene ssb when induced with XIP as compared to wild-type, and Prx orthologues are able to inhibit ComR activation by XIP in a reporter strain which lacks an endogenous prx. Additionally, an X-ray crystal structure of Prx reveals a unique fold that implies a novel molecular mechanism to inhibit ComR. Overall, our results suggest Prx functions to inhibit the acquisition of new DNA by Streptococcus.
In Silico Modeling of Novel Drug Ligands for Treatment of Concussion Associated Tauopathy (2016)

The objective of this study was to develop an in silico screening model for characterization of potential novel ligands from commercial drug libraries able to functionally activate certain olfactory receptors (ORs), which are members of the class A rhodopsin-like family of G protein couple receptors (GPCRs), in the brain of murine models of concussion. We previously found that concussions may significantly influence expression of certain ORs, for example, OR4M1 in subjects with a history of concussion/traumatic brain injury (TBI). In this study, we built a 3-D OR4M1 model and used it in in silico screening of potential novel ligands from commercial drug libraries. We report that in vitro activation of OR4M1 with the commercially available ZINC library compound 10915775 led to a significant attenuation of abnormal tau phosphorylation in embryonic cortico-hippocampal neuronal cultures derived from NSE-OR4M1 transgenic mice, possibly through modulation of the JNK signaling pathway. The attenuation of abnormal tau phosphorylation was rather selective since ZINC10915775 significantly decreased tau phosphorylation on tau Ser202/T205 (AT8 epitope) and tau Thr212/Ser214 (AT100 epitope), but not on tau Ser396/404 (PHF-1 epitope). Moreover, no response of ZINC10915775 was found in control hippocampal neuronal cultures derived from wild type littermates. Our in silico model provides novel means to pharmacologically modulate select ubiquitously expressed ORs in the brain through high affinity ligand activation to prevent and eventually to treat concussion induced down regulation of ORs and subsequent cascade of tau pathology. J. Cell. Biochem. 117: 2241-2248, 2016. © 2016 Wiley Periodicals, Inc.
Depurination As a Yield Decreasing Mechanism in Oligodeoxynucleotide Synthesis (1985)

Abstract The synthesis in our laboratory of very long (80–106 bases) oligodeoxynucleotides using the phosphite method of Matteucci and Caruthers in an automated DNA synthesizer indicates the true efficiency of this multiple step process. The coupling efficiency as measured by trityl cation release i s 99.5–99.8%. However the yield obtained is still below the theoretical yield calculated from the above efficiency. We have attempted t o elucidate yield decreasing mechanisms in long ol igodeoxynucleotide synthesis. Crude reaction mixtures of phosphate-deblocked oligonucleotides which had no 5′-trityl group and which were examined immediately after cleavage from the support show one major species by high resolution PAGE. Harsher hydrolysis generates a new pattern of products superimposed upon the initial ladder representing cleavage at purine residues internal to the full length oligonucleotide. In many cases the cleavage ladder is significantly more intense than the coupling ladder. Hydrolysis a t apurinic sites in ammonium hydroxide at 55° C is apparently quantitative. The implications of this study are that internal depurination does not interfere with chain propagation but directly reduces the isolated yield. The efficiency of the phosphite coupling, oxidation, demethylation, and base deprotection are not the yield limiting steps. Synthesis of even longer fragments may be achievable with a reduction in the depurination o f the propagating chain. More significantly, compounds isolated after proper hydrolysis will not contain any apurinic sites making these compounds suitable for biological use.
N<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mi>K</mml:mi></mml:math>-edge x-ray-absorption study of heteroepitaxial GaN films (1997)

The microstructure of GaN films grown by electron cyclotron resonance (ECR) molecular-beam epitaxy (MBE) and hydride vapor-phase epitaxy (HVPE) is studied using x-ray-absorption measurements at the N $K$ edge. The local microstructure around the N atom is found to be distorted. The nearest neighbors of the N atom are four Ga atoms, ${N}_{1}$ of which are located at a distance ${R}_{1}=1.95\AA{},$ which is expected, and ${N}_{2}$ at a distance ${R}_{2}{=R}_{1}+0.25\AA{}.$ This distortion is more pronounced in the cubic ECR-MBE and the HVPE hexagonal samples where the ratio ${N}_{2}{/N}_{1}$ is equal to 1. In the rest of the samples the distortion is smaller and the ratio ${N}_{2}{/N}_{1}$ takes the value 0.33. Nitrogen deficiency is not detected in the second nearest-neighbor shell and the N atoms are found at the expected distance of 3.11 \AA{}.
Miniband formation in InGaAs quantum dot superlattice with InGaP matrix for application to intermediate-band solar cells (2013)

We report the formation of vertically coupled states in a 20-stack InGaAs QD superlattice with GaAs spacer layers in an InGaP matrix for an application to optimal intermediate-band solar cells. The InGaAs QD superlattices in the InGaP matrix have good optical properties even though the interdot spacing is reduced to 4.5 nm. We confirmed the formation of vertically coupled states by the excitation power dependence in photoluminescence (PL) measurements. The PL peak of a QD superlattice shifts to a shorter wavelength as the excitation power is increased. The blue-shifted energy of the PL peak is 11 meV for a QD superlattice with an interdot spacing of 4.5 nm, whereas the blue shift is not observed for a multistacked QD structure with an interdot spacing of 17 nm. The InGaAs QD superlattices in an InGaP matrix are very attractive for use in realizing the optimal intermediate-band solar cells.
Durability Study on SWNT/Nanofiber Buckypaper Catalyst Support for PEMFCs (2009)

Due to their unique microstructure, buckypaper-supported platinum (Pt) catalysts derived from carbon nanotube and carbon nanofiber have demonstrated a high Pt utilization in proton exchange membrane fuel cells (PEMFCs). [SWNT means single-walled carbon nanotube.] The durability of a buckypaper-supported Pt catalyst was investigated using an accelerated degradation test (ADT) in a mimic cathode environment of PEMFC. Compared to commercial carbon black-supported Pt, Pt/buckypaper showed a better catalyst durability after holding at 1.2 V for 400 h; specifically, almost 80% of the Pt electrochemical surface area was lost for Pt/carbon black, with only a 43% loss for Pt/buckypaper. Transmission electron microscopy and cyclic voltammetry were used to study the Pt degradation mechanism. It was concluded that Pt coarsening and Pt detachment from buckypaper support due to carbon corrosion make the major contribution to the Pt surface area loss under this condition. The Pt loss via detachment from supports after the ADT was calculated as 18% in Pt/buckypaper, while the Pt loss was 69% in Pt/C. It is supposedly due to the higher corrosion resistance of buckypaper because of its high graphitization degree, which is indicated by a slower formation rate of surface oxides in buckypaper than in carbon black. Further durability improvement of the Pt/buckypaper is expected by improving the dispersion of Pt on the buckypaper to reduce Pt sintering.
Sodium Intake and Health: What Should We Recommend Based on the Current Evidence? (2021)

Several health organizations recommend low sodium intake (below 2.3 g/day, 5.8 g/day of salt) for entire populations, on the premise that lowering of sodium intake, irrespective of its level of intake, will lower blood pressure and, in turn, will result in a lower incidence of cardiovascular disease. These guidelines were developed without effective interventions to achieve long term sodium intakes at low levels in free-living individuals and without high-quality evidence that low sodium intake reduces cardiovascular events (compared with average levels of intake). In this review, we examine whether advice to consume low amounts of sodium is supported by robust evidence. We contend that current evidence indicates that most people around the world consume a moderate range of dietary sodium (3 to 5 g/day), that this level of intake is associated with the lowest risk of cardiovascular disease and mortality, and that the risk of adverse health outcomes increases when sodium intakes exceeds 5 g/day or is below 3 g/day. While the current evidence has limitations, it is reasonable, based upon prospective cohort studies, to suggest a mean target of below 5 g/day in populations, while awaiting the results of large randomized controlled trials of sodium reduction on cardiovascular disease and death.
Spectrum sharing and cognitive radio (2009)

Spectrum sharing has been the subject of a 3 year research programme organised by the UK's Virtual Centre of Excellence in Mobile and Personal Communications. Cognitive radio was identified as a key enabling technology to allow spectrum to be shared efficiently between terminals and networks. The project has harnessed the skills of 4 UK Universities working together to understand the potential benefits for its industrial members of cognitive radio technology. This paper discusses some of the work that has been carried out by the Mobile VCE researchers in the field of cognitive radio together with some of the key results and conclusions. The central work has developed algorithms that control the dynamic allocation of radio resources between cooperating network operators as well as spectrum access protocols that allow suitably equipped terminals to sense and use free spectrum. Simulation work has shown that a gain in the efficiency of spectrum use is feasible for both types of spectrum sharing.
ChemInform Abstract: Miscellaneous Nitrogen Derivatives (1997)

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.
Biologic and Molecular Effects of Vitamin D on Bone (1999)

The skeleton provides rigid mechanical support to the body, protects vital organs, and serves as a reservoir of ions, especially for calcium and phosphate required for serum homeostasis. The integrity of the skeleton is maintained by continuous remodeling of bone tissues throughout life in response to a broad spectrum of physiologic signals. As described in Chapter 9, the active hormone 1,25-dihydroxyvitamin D3 (vitamin D) plays a key role in the maintenance of calcium and phosphate blood levels. In response to reduced serum calcium levels, calcium transport is stimulated across the gut and from the renal tubular lumen into the bloodstream. At the same time, calcium is mobilized from bone. Vitamin D actively promotes the release of bone mineral into the circulation by direct effects on the several cellular populations that reside in bone. The hormone influences differentiation and activity of cells of the osteoblast lineage, which form the mineralized bone matrix and cells of the osteoclast lineage, which resorb the mineralized bone (Fig. 1). Vitamin D exerts its effects on these cells by modulating the transcription of a broad spectrum of genes related to these bone cell phenotypes (1). How vitamin D mediates resorption of the bone matrix and subsequent bone formation through complex interactions between different populations of bone cells and at the level of regulation of gene expression is the primary subject of this chapter. The molecular mechanisms contributing to vitamin D-dependent transcription of the bone-specific osteocalcin gene have provided new insights for understanding steroid hormone responses in relation to a broad spectrum of physiologic conditions and phenotypic properties of a cell.
Defining Neurocircuits in Depression (2006)

&lt;p&gt;While many effective treatments are available to treat a major depressive episode, no clinical or biological markers identify which patients are likely to respond to a given treatment or explain why one treatment modality or class of medication is effective when another is not. With these clinical issues in mind, this article presents a synthesis of brain changes associated with clinical response to pharmacotherapy, cognitive-behavior therapy (CBT), and deep brain stimulation (DBS), identified using functional neuroimaging, with findings interpreted in the context of a data-driven depression model. &lt;/p&gt; &lt;h4&gt;ABOUT THE AUTHOR&lt;/h4&gt; &lt;p&gt;Dr. Mayberg is professor, Departments of Psychiatry and Behavioral Sciences and Neurology, Emory University School of Medicine, Atlanta, GA.&lt;/p&gt; &lt;p&gt;Address reprint requests to: Helen Mayberg, MD, Department of Psychiatry, Emory University School of Medicine, 101 Woodruff Circle, WMB 4313, Atlanta GA 30327; or e-mail &lt;a href="mailto:hmayber@emory.edu"&gt;hmayber@emory.edu&lt;/a&gt;.&lt;/p&gt; &lt;p&gt;The research described in this article was supports in part by grants from the Canadian Institutes for Health Research, the National Institutes of Health, and the National Alliance for Research in Schizophrenia and Depression. Dr. Mayberg serves as a consultant for Advanced Neuromodulation Systems on deep brain stimulation.&lt;/p&gt;
Phase Transitions in Complex Networks of Active and Inactive Oscillators (2011)

We study phase transitions in mixed populations of interacting active and inactive oscillators on complex networks. As the ratio of inactive oscillators to the total population increases, the macroscopic oscillatory activity of the whole network decreases and eventually stops at a critical ratio. This phase transition, called an aging transition in [Daido and Nakanishi, 2004], has been studied with simple networks so far. To extend the conventional framework, we analyze aging transitions in complex networks including random and scalefree networks. The critical ratio is theoretically derived through appropriate approximations and numerically verified.
A Case Report of Perianal Paget's Disease Successfully Treated with a Wide Excision and Posterior Femoral V-Y Flap Reconstruction (2006)

症例は82歳の女性で7年前から肛門周囲の発赤, 掻痒感があった. 生検でPaget細胞が認められたため外陰Pagetとの診断で当院に紹介となった. 外陰部を中心として16×15cmの皮膚発赤とびらんを認めた. CTで両鼠径部リンパ節腫脹が認められたが, 99m-Tcを用いたsentinellymph node biopsyではリンパ節転移を認めなかった. 以上より, 外陰Pagetとの診断で手術を施行した. 術前のmappingに従い広範囲腫瘍切除を行った. 肛門方向は歯状線より1cm口側まで切除し術中迅速診断で腫瘍細胞がないことを確認した. 皮膚欠損に対して大腿後面V-Y有茎皮弁を用いた陰部再建とS状結腸人工肛門造設術を施行した. 病理結果は表皮内に限局したPaget細胞であった. 半年後人工肛門を閉鎖, 現在排便状況は正常である. 大腿後面V-Y有茎皮弁を用いた陰部再建は肛門温存の観点からも有効であると考えられた.
Photorefractivity of poly-N-vinylindole-based materials as compared with that of poly-N-vinylcarbazole-based blends (2006)

The asymmetric two-beam coupling technique has been employed to measure the photorefractivity of thin films of polymer blends containing 2,5-dimethyl-4-(p-nitrophenylazo)anisole as the nonlinear optical component. Poly-(1-vinylindole) and poly-(2,3-dimethyl-1-vinylindole) were the photoconductive polymer counterparts. The values of the photorefractivity are reported. It appears that they are comparable with those of similar blends based on the well-known poly-(9-vinylcarbazole) (PVK), here considered as a reference standard. Careful differential scanning calorimetry analyses have been accomplished on the different blends taken into account to rationalize the significantly longer shelf lifetime of the indolyl-based films with respect to the PVK-based blends.
New insights into DNA methylation signatures: SMARCA2 variants in Nicolaides-Baraitser syndrome (2019)

Here we find that a DNAm signature of SMARCA2 pathogenic variants in NCBRS maps to CpGs relevant to disorder pathophysiology, classifies VUS, and is sensitive to the position of the variant in SMARCA2. The patient with an intermediate model score demonstrating a unique genotype-epigenotype-phenotype correlation underscores the potential utility of this signature as a functionally relevant VUS classification system scalable beyond binary "benign" versus "pathogenic" scoring. This is a novel feature of DNAm signatures that could enable phenotypic predictions from genotype data. Our findings also demonstrate that DNAm signatures can be domain-specific, highlighting the precision with which they can reflect genotypic variation.
Characterization of Long-Length, MOCVD-Derived REBCO Coated Conductors (2009)

<para xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> A leading approach to the fabrication of long-length, high-performance <formula formulatype="inline"><tex Notation="TeX">${\rm REBa}_{2}{\hbox {Cu}}_{3}{\hbox {O}}_{7}$</tex></formula> (REBCO) coated conductor is by metal-organic chemical vapor deposition (MOCVD) of REBCO on buffered templates. Templates are produced by ion beam assisted deposition of textured MgO onto polished metal substrates. The overall performance of MOCVD coated conductors achieved to date is impressive, but further improvement is desired. We have used a coordinated set of characterization techniques to identify the underlying causes for critical current (Ic) performance variations in long-length MOCVD conductors. Using electron microscopy and Raman spectroscopy, we studied tape specimens from specially designed experiments performed in SuperPower's MOCVD manufacturing equipment with its six-track “helix” tape path. We find that in multi-pass depositions used to produce thicker REBCO films, the REBCO phase uniformity and texture quality in the first pass play key roles in pass-to-pass microstructure evolution, with nucleation of second phase particles in the first layer promoting misoriented grains that propagate through subsequent layers. These misoriented grains, many growing in close proximity with second phase particles, present current-blocking obstacles that limit Ic performance. Our results show that achieving more uniform deposition in the very first deposited layer plays a critical role that in turn leads to reduced misoriented grain content and REBCO lattice disorder in the second and subsequent layers of the REBCO film. </para>
Biofilm Survival Strategies in Chronic Wounds (2022)

Bacterial biofilms residing in chronic wounds are thought to have numerous survival strategies, making them extremely difficult to eradicate and resulting in long-term infections. However, much of our knowledge regarding biofilm persistence stems from in vitro models and experiments performed in vivo in animal models. While the knowledge obtained from such experiments is highly valuable, its direct translation to the human clinical setting should be undertaken with caution. In this review, we highlight knowledge obtained from human clinical samples in different aspects of biofilm survival strategies. These strategies have been divided into segments of the following attributes: altered transcriptomic profiles, spatial distribution, the production of extracellular polymeric substances, an altered microenvironment, inter-and intra-species interactions, and heterogeneity in the bacterial population. While all these attributes are speculated to contribute to the enhanced persistence of biofilms in chronic wounds, only some of them have been demonstrated to exist in human wounds. Some of the attributes have been observed in other clinical diseases while others have only been observed in vitro. Here, we have strived to clarify the limitations of the current knowledge in regard to this specific topic, without ignoring important in vitro and in vivo observations.