gebhart/patrepeval huggingface dataset:
Report on the Human Genome Initiative (1987)

The report urges DOE and the Nation to commit to a large. multi-year. multidisciplinary. technological undertaking to order and sequence the human genome. This effort will first require significant innovation in general capability to manipulate DNA. major new analytical methods for ordering and sequencing. theoretical developments in computer science and mathematical biology, and great expansions in our ability to store and manipulate the information and to interface it with other large and diverse genetic databases. The actual ordering and sequencing involves the coordinated processing of some 3 billion bases from a reference human genome. Science is poised on the rudimentary edge of being able to read and understand human genes. A concerted. broadly based. scientific effort to provide new methods of sufficient power and scale should transform this activity from an inefficient one-gene-at-a-time. single laboratory effort into a coordinated. worldwide. comprehensive reading of "the book of man". The effort will be extraordinary in scope and magnitude. but so will be the benefit to biological understanding. new technology and the diagnosis and treatment of human disease.
Processus morphogénétiques (2014)

Enseignement Cours : Maladies neurologiques et psychiatriques, un éclairage développemental (suite) Périodes critiques, définitions Au cours de l’année 2012-2103, nous avons continué notre réflexion sur ce que le développement et l’évolution du système nerveux peuvent nous apprendre sur l’étiologie des maladies neurologiques et psychiatriques. On trouvera dans le résumé de l’année précédente la logique sous-jacente à une telle démarche. Je n’y reviens pas sauf pour souligner que nous avons ac...
Service orchestration and federation for verticals (2018)

The next generation mobile transport networks shall transform into flexible and agile SDN/NFV-based transport and computing platforms, capable of simultaneously supporting the needs of different vertical industries, e.g., automotive, e-health and media, by meeting a diverse range of networking and computing requirements. Network slicing, has emerged as the most promising approach to address this challenge by enabling per-slice management of virtualized resources and provisioning and managing slices tailored to the needs of different vertical industries. Service orchestration is the key enabler for slicing that allows efficient placement of virtual network functions over the infrastructure as well as optimal allocation of virtual resources among all network slices to deliver guaranteed, reliable and scalable services of different verticals. Besides, due to the limited footprint of infrastructure operators, it is also required to enable the interconnection and federation of multiple administrative domains, to effectively allow services to span across several providers. This paper presents the design of Service Orchestrator (SO) in the 5G-TRANSFORMER system, which deals with service orchestration and federation across multiple domains.
Integrated DNA extraction and amplification using electrokinetic pumping in a microfluidic device (2011)

An integrated system employing anion exchange for the extraction of DNA from biological samples prior to polymerase chain reaction DNA amplification has been developed, based on microfluidic methodology utilising electrokinetic pumping. In this system, the biological samples were added directly to chitosan-coated silica beads to facilitate DNA immobilisation. The purified, pre-concentrated DNA was then eluted using a combination of electro-osmotic flow enhanced with electrophoretic mobility, which enable DNA to be transported by both mechanisms into the DNA amplification chamber. Through optimisation of the DNA elution conditions, average DNA extraction efficiencies of 69.1% were achievable. Subsequent DNA amplification performed on the microfluidic system demonstrated not only the ability to use electrokinetic movement to integrate the two processes on a single device, but also that the quality and quantity of DNA eluted was suitable for downstream analysis. This work offers an attractive real-world to chip interface and a route to simpler Lab-on-a-Chip technology which eliminates the need for moving parts.
Total synthesis of [ 15 N]-labelled C6-substituted purines from [ 15 N]-formamide—easy preparation of isotopically labelled cytokinins and derivatives (2018)

Cytokinins (CKs) and their metabolites and derivatives are essential for cell division, plant growth regulation and development. They are typically found at minute concentrations in plant tissues containing very complicated biological matrices. Therefore, defined standards labelled with stable isotopes are required for precise metabolic profiling and quantification of CKs, as well as <i>in vivo</i> elucidation of CK biosynthesis in various plant species. In this work, 11 [<sup>15</sup>N]-labelled C6-purine derivatives were prepared, among them 5 aromatic (<b>4, 5, 6, 7, 8</b>) and 3 isoprenoid (<b>9, 10, 11</b>) CKs. Compared to current methods, optimized syntheses of 6-amino-9H-[<sup>15</sup>N<sub>5</sub>]-purine (adenine) and 6-chloro-9H-[<sup>15</sup>N<sub>4</sub>]-purine (6-chloropurine) were performed to achieve more effective, selective and generally easier approaches. The chemical identity and purity of prepared compounds were confirmed by physico-chemical analyses (TLC; HRMS; HPLC-MS; <sup>1</sup>H, <sup>13</sup>C, <sup>15</sup>N NMR). The presented approach is applicable for the synthesis of any other desired [<sup>15</sup>N<sub>4</sub>]-labelled C6-substituted purine derivatives.
Evaluation of the muscle gene transfer activity of a series of amphiphilic triblock copolymers (2009)

Taken together, the results obtained in the present study show that there is a large flexibility in terms of molecular weight and EO/PO ratio for obtaining increased levels of transgene expression in vivo.
Using Patient-Specific Induced Pluripotent Stem Cells and Wild-Type Mice to Develop a Gene Augmentation-Based Strategy to Treat CLN3 -Associated Retinal Degeneration (2016)

Juvenile neuronal ceroid lipofuscinosis (JNCL) is a childhood neurodegenerative disease with early-onset, severe central vision loss. Affected children develop seizures and CNS degeneration accompanied by severe motor and cognitive deficits. There is no cure for JNCL, and patients usually die during the second or third decade of life. In this study, independent lines of induced pluripotent stem cells (iPSCs) were generated from two patients with molecularly confirmed mutations in CLN3, the gene mutated in JNCL. Clinical-grade adeno-associated adenovirus serotype 2 (AAV2) carrying the full-length coding sequence of human CLN3 was generated in a U.S. Food and Drug Administration-registered cGMP facility. AAV2-CLN3 was efficacious in restoring full-length CLN3 transcript and protein in patient-specific fibroblasts and iPSC-derived retinal neurons. When injected into the subretinal space of wild-type mice, purified AAV2-CLN3 did not show any evidence of retinal toxicity. This study provides proof-of-principle for initiation of a clinical trial using AAV-mediated gene augmentation for the treatment of children with CLN3-associated retinal degeneration.
Tumor Necrosis Factor-α Trimer Disassembly and Inactivation via Peptide-Small Molecule Synergy (2020)

Aberrant signaling by tumor necrosis factor-α (TNFα) is associated with inflammatory diseases that can be treated with engineered proteins that inhibit binding of this cytokine to cell-surface receptors. Despite these clinical successes, there is considerable interest in the development of smaller antagonists of TNFα-receptor interactions. We describe a new 29-residue α/β-peptide, a molecule that contains three β-amino acid residues and three α-aminoisobutryic acid (Aib) residues, that displays potent inhibition of TNFα binding to TNFα receptor 1 (TNFR1) and rescues cells from TNFα-induced death. The complement of nonproteinogenic residues renders this α/β-peptide highly resistant to proteolysis, relative to all-α analogues. The mechanism of inhibitory action of the new 29-mer involves disruption of the trimeric TNFα quaternary structure, which prevents productive binding to TNFα receptors. Unexpectedly, we discovered that peptide-induced trimer disruption can be promoted by structurally diverse small molecules, including a detergent commonly used during selection procedures. The discovery of this synergistic effect provides a new context for understanding previous reports on peptidic antagonists of TNFα-receptor interactions and suggests new avenues for future efforts to block signaling via proteins with an active form that is oligomeric, including other members of the TNFα family.
Measurement of the jet radius and transverse momentum dependence of inclusive jet suppression in lead–lead collisions at sNN=2.76 TeV with the ATLAS detector (2013)

Measurement of the jet radius and transverse momentum dependence of
High speed optical holography of retinal blood flow (2016)

We performed noninvasive video imaging of retinal blood flow in a pigmented rat by holographic interferometry of near-infrared laser light backscattered by retinal tissue, beating against an off-axis reference beam sampled at a frame rate of 39 kHz with a high throughput camera. Local Doppler contrasts emerged from the envelopes of short-time Fourier transforms and the phase of autocorrelation functions of holograms rendered by Fresnel transformation. This approach permitted imaging of blood flow in large retinal vessels (∼30 microns diameter) over 400×400 pixels with a spatial resolution of ∼8 microns and a temporal resolution of ∼6.5 ms.
Ratiometric analysis of in vivo retinal layer thicknesses in multiple sclerosis (2016)

We performed ratiometric analysis of retinal optical coherence tomography images for the first time in multiple sclerosis (MS) patients. The ratiometric analysis identified differences in several retinal layer thickness ratios in the cohort of MS subjects without a history of optic neuritis (ON) compared to healthy control (HC) subjects, and there was no difference in standard retinal nerve fiber layer thickness (RNFLT). The difference in such ratios between HC subjects and those with mild MS-disability, without a difference in RNFLT, further suggests the possibility of using layer ratiometric analysis for detecting early retinal changes in MS. Ratiometric analysis may be useful and potentially more sensitive for detecting disease changes in MS.
Star Polymer Synthesis Using Hexafluoropropylene Oxide as an Efficient Multifunctional Coupling Agent (2004)

Well-defined polyisoprene three-armed star polymers (PI3) were synthesized through a combination of living anionic polymerization and an efficient coupling process using hexafluoropropylene oxide (HFPO). Anionic polymerization of isoprene followed by termination with HFPO yielded three-armed stars with narrow molecular weight distributions. Under optimized conditions, at least 97% of the chains can be coupled. Molecular characterization of the star polymers (SEC, NMR and IR spectroscopy, and MALDI-TOF mass spectrometry) gave data consistent with the star structure and proposed mechanism of formation. The effects of HFPO concentration and the molecular weight of the arm precursors on the extent of star polymer formation were investigated. End-functionalized polyisoprene stars were also prepared and have potential application as trifunctional precursors to branched block copolymers.
9G4 Autoreactivity Is Increased in HIV-Infected Patients and Correlates with HIV Broadly Neutralizing Serum Activity (2012)

The induction of a broadly neutralizing antibody (BNAb) response against HIV-1 would be a desirable feature of a protective vaccine. Vaccine strategies thus far have failed to elicit broadly neutralizing antibody responses; however a minority of HIV-infected patients do develop circulating BNAbs, from which several potent broadly neutralizing monoclonal antibodies (mAbs) have been isolated. The findings that several BNmAbs exhibit autoreactivity and that autoreactive serum antibodies are observed in some HIV patients have advanced the possibility that enforcement of self-tolerance may contribute to the rarity of BNAbs. To examine the possible breakdown of tolerance in HIV patients, we utilized the 9G4 anti-idiotype antibody system, enabling resolution of both autoreactive VH4-34 gene-expressing B cells and serum antibodies. Compared with healthy controls, HIV patients had significantly elevated 9G4+ serum IgG antibody concentrations and frequencies of 9G4+ B cells, a finding characteristic of systemic lupus erythematosus (SLE) patients, both of which positively correlated with HIV viral load. Compared to the global 9G4-IgD--memory B cell population, the 9G4+IgD--memory fraction in HIV patients was dominated by isotype switched IgG+ B cells, but had a more prominent bias toward "IgM only" memory. HIV envelope reactivity was observed both in the 9G4+ serum antibody and 9G4+ B cell population. 9G4+ IgG serum antibody levels positively correlated (r = 0.403, p = 0.0019) with the serum HIV BNAbs. Interestingly, other serum autoantibodies commonly found in SLE (anti-dsDNA, ANA, anti-CL) did not correlate with serum HIV BNAbs. 9G4-associated autoreactivity is preferentially expanded in chronic HIV infection as compared to other SLE autoreactivities. Therefore, the 9G4 system provides an effective tool to examine autoreactivity in HIV patients. Our results suggest that the development of HIV BNAbs is not merely a consequence of a general breakdown in tolerance, but rather a more intricate expansion of selective autoreactive B cells and antibodies.
Worsening of Chronic Heart Failure: Definition, Epidemiology, Management and Prevention. A Clinical Consensus Statement by the Heart Failure Association of the European Society of Cardiology (2023)

Episodes of worsening symptoms and signs characterize the clinical course of patients with chronic heart failure (HF). These events are associated with poorer quality of life, increased risks of hospitalization and death and are a major burden on healthcare resources. They usually require diuretic therapy, either administered intravenously or by escalation of oral doses or with combinations of different diuretic classes. Additional treatments may also have a major role, including initiation of guideline-recommended medical therapy (GRMT). Hospital admission is often necessary but treatment in the emergency service or in outpatient clinics or by primary care physicians has become increasingly used. Prevention of first and recurring episodes of worsening HF is an essential component of HF treatment and this may be achieved through early and rapid administration of GRMT. The aim of the present clinical consensus statement by the Heart Failure Association of the European Society of Cardiology is to provide an update on the definition, clinical characteristics, management and prevention of worsening HF in clinical practice.
Supplementary Fig S1-S7 from Resolving the Spatial and Cellular Architecture of Lung Adenocarcinoma by Multiregion Single-Cell Sequencing (2023)

&lt;p&gt;Supplementary Figures S1-S7 and figure legends&lt;/p&gt;
Simple IP restoration for IP/GbE/10 GbE optical networks (2002)

IP and Ethernet are the dominant transport and link-layer protocols in data networks. In this paper we demonstrate how IP can be used to provide reliable Ethernet transport with fast restoration performance comparable with that achieved in SONET networks.
Acute experimental stress evokes a differential gender‐determined increase in human intestinal macromolecular permeability (2012)

Intestinal macromolecular permeability in response to acute experimental stress is increased in healthy women, a mechanism that may contribute to female oversusceptibility to IBS.
A Study of the Possible Power Extraction from a Point Absorbing Wave Energy Converter (2012)

This thesis presents how experimental results, from wave power research performed offshore at the Lysekil research site, were obtained. The data were used to verify theoretical models as well as evaluate the feasibility of wave power as a future sustainable energy source.The first experiments carried out at the research site was the measurement of the force in a line where one end was connected to a buoy with a diameter of 3 m and the other end to a set of springs with limited stroke length. The system is exposed to high peak forces compared to average forces. The maximum measured force in the line, when the buoy motion is limited by a stiff stopper rope is ten times the average force in that particular sea state.The experiment performed on the first wave energy converter tested at the Lysekil Research Site is described. The infrastructure of the site is presented where the central connection point is the measuring station. The key finding is that it is possible to transform the motions of ocean waves into electrical energy and distribute it to land.Many wave energy converters must be interconnected if large amounts of energy are to be harvested from the waves. The first submerged substation intended for aggregation of energy from wave power converters is described, with focus on the measurement and control system placed inside the substation. During this experiment period the generators were equipped with many different sensors; these measurements are explained in the thesis.The system that aggregates power from the studied wave energy converter is regularly exposed to peak power of up to 20 times the maximum average output from the converter.Vertical and horizontal movement of the buoy has been measured in different ways. The result is that the vertical displacement of the buoy can be measured with a simple accelerometer circuit but it is much more complicated to measure the horizontal displacement. A special method for measuring the horizontal displacement has been implemented by measuring the strain in the enclosure and the force in the line.
Feasibility of transapical aortic valve replacement through a left ventricular apical diverticulum (2013)

Transapical aortic valve replacement is an established technique performed in high-risk patients with symptomatic aortic valve stenosis and vascular disease contraindicating trans-vascular and trans-aortic procedures. The presence of a left ventricular apical diverticulum is a rare event and the treatment depends on dimensions and estimated risk of embolisation, rupture, or onset of ventricular arrhythmias. The diagnosis is based on standard cardiac imaging and symptoms are very rare. In this case report we illustrate our experience with a 81 years old female patient suffering from symptomatic aortic valve stenosis, respiratory disease, chronic renal failure and severe peripheral vascular disease (logistic euroscore: 42%), who successfully underwent a transapical 23 mm balloon-expandable stent-valve implantation through an apical diverticulum of the left ventricle. Intra-luminal thrombi were absent and during the same procedure were able to treat the valve disease and to successfully exclude the apical diverticulum without complications and through a mini thoracotomy. To the best of our knowledge, this is the first time that a transapical procedure is successfully performed through an apical diverticulum.
A multiple-baseline stereo (2002)

A stereo matching method is presented which uses multiple stereo pairs with various baselines to obtain precise depth estimates without suffering from ambiguity. The stereo matching method uses multiple stereo pairs with different baselines generated by a lateral displacement of a camera. Matching is performed by computing the sum of squared-difference (SSD) values. The SSD functions for individual stereo pairs are represented with respect to the inverse depth (rather than the disparity, as is usually done), and then are simply added to produce the sum of SSDs. This resulting function is called the SSSD-in-inverse-depth. The authors define a stereo algorithm, based on the SSSD-in-inverse-depth and then present a mathematical analysis to show how the algorithm can remove ambiguity and increase precision. Experimental results for stereo images are presented to demonstrate the effectiveness of the algorithm.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Supplementary Table 1 from Identification of Small Molecules that Sensitize Resistant Tumor Cells to Tumor Necrosis Factor-Family Death Receptors (2023)

Supplementary Table 1 from Identification of Small Molecules that Sensitize Resistant Tumor Cells to Tumor Necrosis Factor-Family Death Receptors
The 14q restless legs syndrome locus in the French Canadian population (2004)

A new restless legs syndrome locus on chromosome 14 recently has been reported in one family of Italian origin. Our study aimed to replicate this finding and determine the importance of this locus in the French Canadian population. Markers spanning the region were genotyped in 14 large families and linkage assessed using two-point and multipoint logarithm of odds scores. Possible linkage to this locus was found in one of our kindreds providing support for the existence of this locus and indicating that this locus may be responsible for a small fraction of French Canadian restless legs syndrome.
Time delay estimation using difference function (2005)

Time delay estimation (TDE) is used in calculating the direction of arrival (DOA) of speech signals and beamforming. Cross-correlation is a popular method used for TDE. However cross-correlation&apos;s performance degrades in the presence of high noise and reverberation. The YIN algorithm is used to determine the fundamental frequency of music and speech signals. This paper presents an extension of the YIN algorithm that can be used for TDE. Simulations comparing the performance of the unbiased cross-correlation and the modified YIN algorithms in five rooms of different reverberation are presented. The modified YIN algorithm performs better than the unbiased cross-correlation algorithm in high reverberant conditions.
On the growth, structure and dynamics of P3EHT crystals (2020)

We employ X-ray diffraction, NMR and UV-vis spectroscopy techniques to shed light on the structure, molecular mobility and crystallization of a prototypical semiconducting polymer poly(3-(2′-ethylhexyl)thiophene) (P3EHT).