gebhart/patrepeval huggingface dataset:
α-Sheet:  The Toxic Conformer in Amyloid Diseases? (2006)

A novel secondary structure, the alpha-sheet, was identified through molecular dynamics (MD) simulations of various proteins associated with amyloid diseases under amyloidogenic conditions. The structure was first predicted by Pauling and Corey, and it has been directly observed in crystal structures of "nonnatural peptides". There are occurrences of alpha-strands and alpha-sheets in the Protein Data Bank, but they are rare. We propose that alpha-sheet is formed during the conformational changes associated with amyloidosis and that it may represent the toxic conformer. Here, structural properties of the alpha-sheet, background information, and experimental support for this novel structure are presented. Finally we speculate about the possible role of this conformation in disease.
Lysosomal-Targeted Two-Photon Fluorescent Probe to Sense Hypochlorous Acid in Live Cells (2017)

A two-photon reversible fluorescent probe L1 was designed and synthesized. The fluorescence intensity of the probe solution was strong, while the fluorescence of the solution was obviously quenched and the color of the solution was changed after the addition of hypochlorous acid, indicating this is "naked-eye sensor" for the detection of HClO. The probe showed great selectivity for hypochlorous acid over other reactive oxygen species (ROS) and anions. Fluorescence titration experiments showed that the probe has a low detection limit of 0.674 μM. Because of a morpholine group introduced to the naphathalimide framework, probe L1 was successfully applied to detect intracellular HClO in lysosome.
Molecular Typing of Treponema pallidum Strains in Western Canada: Predominance of 14d Subtypes (2010)

A single molecular type of T. pallidum, characterized as 14d, caused the majority of the syphilis cases identified in this study. A more discriminatory typing method would be required to determine if these strains are clonal. Treatment of infectious syphilis with macrolide antibiotics should be restricted to patient populations where resistance is rare and clinical and serological follow up of patients is possible.
Retinoblastoma: The Prototypic Hereditary Tumor (2008)

As the first cancer to be described as a genetic disease, retinoblastoma represents the prototypic hereditary tumor. This childhood retinal cancer is initiated by the loss of the RB1 tumor suppressor gene, which has important clinical implications, as highly sensitive mutation detection of mutant RB1 alleles within families accurately identifies individuals at high risk for retinoblastoma and excludes those with normal RB1 and thus directs costly and intense treatment and surveillance only to those who require it. The unique molecular fingerprint of retinoblastoma can be correlated to clinical and histopathological stage. Loss of RB1 initially leads to development of the benign tumor, retinoma. Further genetic insults are necessary for progression to malignancy, including gains of oncogenes NMYC, KIF14, E2F3, and/or DEK, and loss of tumor suppressor genes CDH11 and p75NTR.
Convection and Film Instability Copper Anodes in Hydrochloric Acid (1958)

In the system, when natural convection occurs, there are two steady‐state current plateaus. On the first of these , copper dissolves only in the cuprous form, and the value of the current agrees with that predicted by the Tobias theory of natural convection. On the second plateau, up to 30% of the copper is dissolved as cupric ions. When the circuit is interrupted, the resistance of the CuCl layer decays primarily due to opening of its pores, the pore area increasing linearly with time. Oscillations are found at the anode voltage region below which there is no layer and above which the layer can remain on the electrode indefinitely. A kinetic explanation of oscillations is proposed, and is in accord with the observations.
Survey on practice of venom immunotherapy in France (2016)

Our study shows that most recommendations were fully or partially followed and may need reminding, but many points need to be completed or updated with new tools and knowledge acquired during the last 10 years.
Zur Charakteristik der modernen Ballade (2009)

Wir untersuchten Christoph Meckels Gedichte in Hinblick auf die moderne Ballade. Hier soll eine abschliesende Zusammenfassung mit einem Ruckblick auf die Arbeit gegeben werden. Christoph Meckel ist ein erzahlender Lyriker. Seine erzahlende Gedichte konstituieren sich aus der narrativen Phantasie. Im Gedicht Das Erbe des Sancho Pansa bildet der eine Strophe umfassend Satz eine erzahlerische Einheit wie ein Stuck Cervanteschen Erzahlung, wahrend das Gedicht Ballade vom Lauf der Welt sich in der Dialogfuhrungen der dramatischen Konzeption orientiert. Meckel greift auch in anderen erzahlenden Gedichten immer wieder auf historische und marchenhafte Helden oder “mythische Gestalten und Gotter zuruck und bewirkt damit eine metaphorische Ausweitung einer subjektiv erfahrenen Erkenntnis in eine historische Dimension.” Charakteristisch fur die moderne Darbietungsweise in Meckels Gedichten sind: Ironisches und satirisches Sprachspiel, Personalperspektivierung, subjektives und inneres Bild der Figuren, unregelmasiges Versmas, Reim und Stropheneinteilung, Zwiespalt zwischen einer marchenhaften und phantastischen Traumwelt und einer oden Realitat, fabelhafte und parabolische Indirektheit. Diese Strukturelemente finden sich aber nicht nur in Meckels Balladen, sondern auch in den Gedichten des 19. Jahunderts. Diesen Merkmale begegnet man auch bei traditionellen Balladendichtern, z. B. bei Burger, Goethe, Schiller und auch Heine. Es ware unnotig, ein neues Wort wie modernes Erzahlgedicht” zu schopfen. Die Ballade als literarische Gattung hat eine Geschichte, die keineswegs zum Abschlus gekommen ist. Jede Ballade ist ein Erzahlgedicht, wobei viele Dichter sich der Balladenform bis in die Gegenwart - Meckels Gedichte sind nur ein Beispiel hierfur - bedienen. Viele Balladendichter - wie auch Christoph Meckel - verwenden zudem haufig das Wort Ballade - aber nicht Erzahlgedicht - im Titel ihrer erzahlenden Gedichte.26) Die Balladenforschung sollte sich nicht auf die Klassifizierung der unterschiedlichen Balladenformen, sondern auf die Analyse der einzelnen Texte konzentrieren.
[Possiblities for breast reconstruction following cancer surgery]. (2004)

Cancer of the breast is the most common malignant disease of women, and currently affects approximately 10% of all women. In the large majority of cases, mammary carcinoma can be treated without having to sacrifice the breast. In some 30% of the cases, however, amputation continues to be needed, in particular when a relatively large tumor presents, or when its removal with an adequate safety margin in a relatively small breast would result in appreciable deformation. Reconstruction of the breast is often an important psychological factor, since, as a visible organ, the breast is a determining feature of a woman's physical appearance and her effect on the opposite sex. The availability of various procedures and modern techniques of breast reconstruction make it possible to comply with the individual wishes of the woman concerned.
IDL-2965: A Selective, highly-potent, oral Integrin antagonist for IPF (2019)

<b>Introduction:</b> IPF is a fatal orphan fibrotic lung disease for which next generation treatments are urgently needed. RGD-binding integrins are an attractive therapeutic target involved in TGF-b activation, fibroblast migration, and myofibroblast survival. IDL-2965 is a selective, orally available, small molecule integrin antagonist being developed for IPF and other serious fibrotic diseases. <b>Aims:</b> Preclinical characterization of the potency, selectivity, pharmacokinetics, safety, and antifibrotic activity of IDL-2965. <b>Methods:</b> A robust drug discovery campaign identified integrin antagonists with strong antifibrotic activity and favorable PK. IDL-2965 emerged from these screens and was characterized for potency, selectivity, and antifibrotic efficacy, as well as for safety in a formal toxicology program. <b>Results:</b> Cell-based potency of IDL-2965 was 1.5, 1.4 and 0.4 nM against human αvβ1, αvβ3 and αvβ6, respectively. Oral administration in rat and nonhuman primate provided a t1/2 ≈ 8 hrs. Once-daily oral therapeutic dosing reduced fibrosis in multiple models across organ systems with minimal effective doses ranging from 0.4-3 mg/kg. In a bleomycin model of pulmonary fibrosis, therapeutic dosing of 0.4 mg/kg significantly reduced fibrosis and combination studies with pirfenidone suggest compatibility with current standard of care. 28-day GLP safety studies suggest a large therapeutic index. <b>Conclusions:</b> IDL-2965 is a selective integrin antagonist with significant antifibrotic effect at low, once-daily, oral doses and a favorable safety profile in formal toxicology and safety pharmacology studies. Based on these results a clinical study examining IDL-2965 in healthy subjects and IPF patients will commence in 2019.
Instability of Hematin Used in the Treatment of Acute Hepatic Porphyria (1986)

The acute hepatic porphyrias are diseases in which the production of heme is deficient because of inherited abnormalities in specific enzymes of the heme synthetic pathway.1 The goal of therapy for these diseases is replenishment of cellular heme. This has been attempted clinically with intravenous administration of heme.2 3 4 Because of its poor solubility at neutral pH, heme is prepared as hematin in a bicarbonate solution at a pH of 8. Initial reports indicated that hematin was remarkably effective in severe acute porphyric attacks.2 , 3 However, the results were not uniform, and a more recent study suggested that hematin was frequently ineffective. . . .
The importance of hand hygiene education on primary schoolgirls’ absence due to upper respiratory infections in Saudi Arabia (2018)

To quantify the reduction in absence due to upper respiratory infections (URIs) among primary schoolgirls attending Riyadh's schools after delivering a hand hygiene workshop intervention over a period of 5 weeks. Methods: A cluster randomized trial was conducted among girls attending 4 primary schools between January and March 2018. The participants attended a hand hygiene workshop. The schoolgirls' absences were followed up for 5 weeks. Incidence rate, percentage of absence days, and absence rate were calculated for total and URIs absences. Result: Total number of participating schoolgirls was 496. Upper respiratory infections accounted for 15.3% of absence episodes. Schoolgirls lost 521 days of school and 19.4% of them were URIs-related. Absence rate due to URIs were 12.4 and 23.4 as well as 5.62 and 11.72 per 100 schoolgirls in the control (CG) and experimental (EG) groups, respectively. Percentage of absence days were lower in the experimental group (CG: 0.86% and 1.39% versus EG: 0.39% and 0.72%). Incidence rates of absence due to URIs were 0.54 and 1.02 in CG versus 0.24 and 0.51 in EG per 100 schoolgirls per day. Conclusion: There could be further reduction in school absences if education was accompanied by hand soap dissemination. The study could serve as a pilot for major studies in the future. Sustainability of the intervention can be tested in studies with longer durations.
Nanoparticle-Mediated Visualization and Control of Cellular Membrane Potential: Strategies, Progress, and Remaining Issues (2020)

The interfacing of nanoparticle (NP) materials with cells, tissues, and organisms for a range of applications including imaging, sensing, and drug delivery continues at a rampant pace. An emerging theme in this area is the use of NPs and nanostructured surfaces for the imaging and/or control of cellular membrane potential (MP). Given the important role that MP plays in cellular biology, both in normal physiology and in disease, new materials and methods are continually being developed to probe the activity of electrically excitable cells such as neurons and muscle cells. In this Review, we highlight the current state of the art for both the visualization and control of MP using traditional materials and techniques, discuss the advantageous features of NPs for performing these functions, and present recent examples from the literature of how NP materials have been implemented for the visualization and control of the activity of electrically excitable cells. We conclude with a forward-looking perspective of how we expect to see this field progress in the near term and further into the future.
Risk of Recurrence in Women With Bipolar Disorder During Pregnancy: Prospective Study of Mood Stabilizer Discontinuation (2007)

Discontinuation of mood stabilizer, particularly abruptly, during pregnancy carries a high risk for new morbidity in women with bipolar disorder, especially for early depressive and dysphoric states. However, this risk is reduced markedly by continued mood stabilizer treatment. Treatment planning for pregnant women with bipolar disorder should consider not only the relative risks of fetal exposure to mood stabilizers but also the high risk of recurrence and morbidity associated with stopping maintenance mood stabilizer treatment.
Simultaneous Energy and Water Optimisation in Shale Exploration (2018)

This work presents a mathematical model for the simultaneous optimisation of water and energy usage in hydraulic fracturing using a continuous time scheduling formulation. The recycling/reuse of fracturing water is achieved through the purification of flowback wastewater using thermally driven membrane distillation (MD). A detailed design model for this technology is incorporated within the water network superstructure in order to allow for the simultaneous optimisation of water, operation, capital cost, and energy used. The study also examines the feasibility of utilising the co-produced gas that is traditionally flared as a potential source of energy for MD. The application of the model results in a 22.42% reduction in freshwater consumption and 23.24% savings in the total cost of freshwater. The membrane thermal energy consumption is in the order of 244 × 103 kJ/m3 of water, which is found to be less than the range of thermal consumption values reported for membrane distillation in the literature. Although the obtained results are not generally applicable to all shale gas plays, the proposed framework and supporting models aid in understanding the potential impact of using scheduling and optimisation techniques to address flowback wastewater management.
Partial Likelihood (1975)

A definition is given of partial likelihood generalizing the ideas of conditional and marginal likelihood. Applications include life tables and inference in stochastic processes. It is shown that the usual large-sample properties of maximum likelihood estimates and tests apply when partial likelihood is used.
Network coding from a network flow perspective (2003)

Precise connections between algebraic network coding and network flows are explained in this article. Our combinatorial formulations offer new insights, mathematical simplicity, and lead to a substantially tighter upper bound on the coding field size required for a given connection problem than that in R. Koetter et al.
Biologically derived models of the sunfish for experimental investigations of multi-fin swimming (2011)

The remarkable swimming abilities of bony fish are the result of multiple interacting subsystems, each tuned to perform certain roles. These subsystems, which include the statically unstable body, multiple highly actuated fins, oscillatory neural controllers, and distributed senses, are not often studied as mutually dependent systems. This research program is developing biorobotic models of these systems and integrating the systems into a biorobotic fish so that interdependencies can be explored during free swimming. The robot body was derived from a bluegill sunfish, and has a tunable mass distribution and a mixture of rigid and flexible sections so that dynamical characteristics of the fish body can be explored. Five highly deformable fins have structural properties scaled to those of biological fins and can create gait patterns for steady swimming and maneuvers. A first generation artificial CPG has been programmed for each fin on a network of five low power microcontrollers. Finally, a dedicated biorobotic pectoral fin has been developed and instrumented with distributed sensory systems so relevant physical (e.g., fin curvature) and hydrodynamic (e.g., pressure) data can be identified and used to predict fin force for closed loop control.
Abnormal expression of retinoic acid receptors and keratin 19 by human oral and epidermal squamous cell carcinoma cell lines. (1991)

We have analyzed the expression of the three retinoic acid receptor (RAR) (alpha, beta, gamma) mRNAs and the intermediate filament protein keratin 19 (K19) mRNA in cell lines cultured from oral and epidermal human squamous cell carcinoma (SCC) and from benign, hyperplastic, and hyperkeratotic (leukoplakia) lesions arising in various regions of the oral cavity. Seven of the SCC lines were derived from tumors arising in regions of the oral cavity in which the normal epithelial cells (keratinocytes) express RAR beta transcripts. Seven of the nine SCC lines tested did not exhibit detectable RAR beta mRNA levels, even in response to addition of retinoic acid (RA). The RAR beta gene did not appear to be rearranged or deleted in the five nonexpressing SCC lines examined by Southern analysis. The steady-state RAR gamma mRNA levels were 2- to 4-fold lower in 6 of the 9 SCC lines than in their normal counterparts, whereas the RAR alpha message levels in SCC lines were similar to those of the normal cell strains. The expression of keratin 19 message, which is RA inducible in normal keratinocytes, was also abnormal in many of the SCC cell lines. Some SCC lines, e.g., those derived form tumors of the soft palate epithelium, did not express high levels of K19 message even though normal soft palate keratinocytes expressed high levels of K19 mRNA. Two of the nine SCC lines expressed higher than normal levels of K19 mRNA, and this expression was RA independent. Cells cultured from four oral leukoplakia lesions were also examined and found to express RAR beta mRNA at relatively normal levels, but they expressed RAR gamma message at half the level of epithelial cells cultured from normal tissue. These results show that the correlation between RAR beta gene expression and K19 gene expression that we have observed in the various normal keratinocyte subtypes of the oral cavity (D.L. Crowe et al., manuscript in preparation) is not present in transformed keratinocytes (SCC cells). The lack of apparent RA regulation of the K19 gene in SCC lines may be associated with other aberrations in differentiation which have been identified in SCC cells. Abnormally low expression of the RAR beta receptor may contribute to neoplastic progression in stratified squamous epithelia. It may also determine whether a tumor is responsive to RA as a chemotherapeutic agent.
Antenne "double ailettes" très large bande intégrée sur substrat silicium SOI HR pour des applications millimétriques (2011)

National audience
Integration of GWAS SNPs and tissue specific expression profiling reveal discrete eQTLs for human traits in blood and brain (2012)

Genome-wide association studies have nominated many genetic variants for common human traits, including diseases, but in many cases the underlying biological reason for a trait association is unknown. Subsets of genetic polymorphisms show a statistical association with transcript expression levels, and have therefore been nominated as expression quantitative trait loci (eQTL). However, many tissue and cell types have specific gene expression patterns and so it is not clear how frequently eQTLs found in one tissue type will be replicated in others. In the present study we used two appropriately powered sample series to examine the genetic control of gene expression in blood and brain. We find that while many eQTLs associated with human traits are shared between these two tissues, there are also examples where blood and brain differ, either by restricted gene expression patterns in one tissue or because of differences in how genetic variants are associated with transcript levels. These observations suggest that design of eQTL mapping experiments should consider tissue of interest for the disease or other traits studied.
Supplementary fig 4 from Changes in Peripheral and Local Tumor Immunity after Neoadjuvant Chemotherapy Reshape Clinical Outcomes in Patients with Breast Cancer (2023)

&lt;p&gt;Supplementary Figure 4: sTILs are not prognostic in ER+ or HER2+ disease.&lt;/p&gt;
ABSTRACT Studies of retinal development and regeneration: patterning and re-patterning the retina (2000)

RESUME Abstracts / Resumes 649s / Resumes 649 © 2000 NRC Canada Studies of retinal development and regeneration: patterning and re-patterning the retina T.A. Reh, A. Fischer, S. Fuhrmann, and K. McCabe Department of Biological Structure, University of Washington, Campus Box 357420, Seattle, WA
Gelam (Melaleucaspp.) Honey-Based Hydrogel as Burn Wound Dressing (2011)

A novel cross-linked honey hydrogel dressing was developed by incorporating Malaysian honey into hydrogel dressing formulation, cross-linked and sterilized using electron beam irradiation (25 kGy). In this study, the physical properties of the prepared honey hydrogel and its wound healing efficacy on deep partial thickness burn wounds in rats were assessed. Skin samples were taken at 7, 14, 21, and 28 days after burn for histopathological and molecular evaluations. Application of honey hydrogel dressings significantly enhanced (P < 0.05) wound closure and accelerated the rate of re-epithelialization as compared to control hydrogel and OpSite film dressing. A significant decrease in inflammatory response was observed in honey hydrogel treated wounds as early as 7 days after burn (P < 0.05). Semiquantitative analysis using RT-PCR revealed that treatment with honey hydrogel significantly (P < 0.05) suppressed the expression of proinflammatory cytokines (IL-1α, IL-1β, and IL-6). The present study substantiates the potential efficacy of honey hydrogel dressings in accelerating burn wound healing.
A field trial to assess the effects of rabbit grazing on spring barley (2004)

Summary Spring barley is widely grown throughout the UK and significant yield loss can occur as a result of rabbit grazing. In a 3‐yr trial, spring barley was grown in six enclosures following current agronomic procedures and was subjected to grazing by different population densities of rabbits. The annual yield loss at the end of the trial was 0.5% rabbit −1 ha −1 . The yield loss per rabbit was calculated to be around 25 kg and the financial loss was calculated as £2.00 per rabbit at 1998 prices (approx. £80 tonne −1 ). Models allowing farmers to predict the levels and costs of damage by rabbits to winter wheat and for silage have already been developed. The results from this trial enable farmers to extend their predictions to include spring barley. The implications for this are discussed.