gebhart/patrepeval huggingface dataset:
Islands of retroelements are major components of Drosophila centromeres (2019)

Centromeres are essential chromosomal regions that mediate kinetochore assembly and spindle attachments during cell division. Despite their functional conservation, centromeres are among the most rapidly evolving genomic regions and can shape karyotype evolution and speciation across taxa. Although significant progress has been made in identifying centromere-associated proteins, the highly repetitive centromeres of metazoans have been refractory to DNA sequencing and assembly, leaving large gaps in our understanding of their functional organization and evolution. Here, we identify the sequence composition and organization of the centromeres of Drosophila melanogaster by combining long-read sequencing, chromatin immunoprecipitation for the centromeric histone CENP-A, and high-resolution chromatin fiber imaging. Contrary to previous models that heralded satellite repeats as the major functional components, we demonstrate that functional centromeres form on islands of complex DNA sequences enriched in retroelements that are flanked by large arrays of satellite repeats. Each centromere displays distinct size and arrangement of its DNA elements but is similar in composition overall. We discover that a specific retroelement, G2/Jockey-3, is the most highly enriched sequence in CENP-A chromatin and is the only element shared among all centromeres. G2/Jockey-3 is also associated with CENP-A in the sister species D. simulans, revealing an unexpected conservation despite the reported turnover of centromeric satellite DNA. Our work reveals the DNA sequence identity of the active centromeres of a premier model organism and implicates retroelements as conserved features of centromeric DNA.
Infrared face recognition based on blood perfusion and sub-block dct in wavelet domain (2007)

A novel method for infrared face recognition based on blood perfusion and sub-block DCT in wavelet domain is proposed in this paper. Firstly, thermal images are converted into blood perfusion domain by blood perfusion model to obtain consistent facial images to reduce the effect of ambient variations. Secondly blood perfusion data are decomposed using discrete wavelet transform. Then, the component of low frequency sub-bands is partitioned into sub-blocks, to which the DCT is further applied. Each face is represented by an effective feature combination extracted from the sub-blocks in DCT domain. Finally, the 3-NN classifier in Euclidean distance is utilized for recognition. The experiments conducted illustrate that the method proposed in this paper has better performance compared with traditional PCA, DCT and DWT + PCA methods.
ChemInform Abstract: Growth Kinetics of Nanocrystalline ZnO Particles from Colloidal Suspensions. (1999)

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.
Reduction of Pain, Fatigue, Gastrointestinal and Other Symptoms and Improvement in Quality of Life Indicators in Fibromyalgia Patients with Membrane Lipid Replacement Glycerolphospholipids and Controlled-Release Caffeine (2018)

Objectives: A preliminary, open label study was initiated to determine if oral wafers containing a combination of membrane glycerolphospholipids and controlled-release caffeine could reduce self-reported pain, fatigue, and gastrointestinal symptoms and improve quality of life (QOL) indicators in fibromyalgia patients. Methods: Pain, fatigue and other symptoms were determined using validated, patient survey forms completed over an 8-day test period and compared to baseline values. Participants included 21 patients (15 females and 6 males) of average age of 48.5 ± 9.8 years with a diagnosis of fibromyalgia. These patients consumed four daily chewable wafers containing glycerolphospholipids (4.8 g) and one controlled-released caffeine (184 mg) wafer that maintained caffeine levels at approximately one cup of coffee for over 8 h. Results: Participants in the study responded to the combination test supplement within days. By the end of the study there were significant overall improvements (36.1%, p p p p p < 0.001). Regression analysis of the data using a generalized mixed-effects model and calculating R2 values indicated that reductions in pain, fatigue and gastrointestinal symptoms and improvements in quality of life indicators were consistent, and occurred with a low degree of variance. Males responded slightly better to the combination supplement than females but for most parameters these differences were not significant. Conclusions: The combination membrane lipid replacement glycerolphospholipid supplement with controlled-release caffeine was safe and effective and significantly reduced pain, fatigue and gastrointestinal symptoms as well as improved QOL indicators in fibromyalgia patients.
Circadian Timekeeping in Health and Disease (1983)

THE study of circadian (approximately 24-hour) rhythms has within the past decade evolved from a biologic curiosity to a science with enormous implications for clinical medicine. The concurrent mat...
Load balanced 2D and 3D adaptive mesh refinement in OpenFOAM (2019)

An object-oriented approach to load-balanced adaptive mesh refinement in two and three dimensions is presented for OpenFOAM, a mature C++ library for computational fluid dynamics. Such a high-performance computing technique is mandatory for computational efficiency in cases of moving regions of interest for distributed-memory parallel computer architectures where domain decomposition is applied. Moving regions of interest are dynamically deforming and migrating through the domain during simulations and require high spatial resolution of solution features. We present software design and code structure, and detail on our achievements with respect to software usability for engineering applications, as well as on numerous developments and improvements necessary for high stability and runtime performance.
Existence of Nowhere Differentiable Boundaries in a Realistic Map (1990)

Abstract A generic 3-dimensional diffeomorphic map, with constant Jacobian determinant, is proposed and looked at numerically. It contains a lower-dimensional basin boundary along which a chaotic motion takes place. This boundary is nowhere differentiable in one direction. Therefore, nowhere differentiable limit sets exist generically in nature.
Fatigue and its correction in photon counting experiments (1975)

The fatigue characteristics of RCA GaP and EMI venetian blind photomultipliers have been investigated at low anode currents. Methods of reducing the errors from this source are discussed, and a technique which provides an accurate correction in photon counting experiments is given.
Nitrogen Fixation in Termites (1973)

Nitrogen fixation, measured by the reduction of acetylene to ethylene, was found in workers of the dry-wood termite Kalotermes minor. The soldiers and reproductive castes fixed little or no nitrogen. The fixation rates ranged between 24 and 566 micrograms of nitrogen fixed per month per gram (wet weight) of termite. Nitrogen fixation can be a significant source of nitrogen for these termites.
KC-10A Cargo System Mock-Up Test, (1979)

A test was conducted on the KC-10A Cargo Handling System Mock-Up to evaluate the performance of the current design of the powered roller system. The test consisted of running a total of 246 load/unload cycles with various weights loaded on the pallets. Of these load/unload cycles, 135 were single HCU-6/E pallets and the remaining 111 were coupled HCU-6/E pallets (2 in train). These cycles simulate over 2 years of KC-10A palletized cargo operations. The powered roller system functioned very well for the entire spectrum of loads. Single and coupled pallets were loaded laterally or rotated in the doorway easily. This test demonstrated that the system meets or exceeds its design requirements. (Author)
A National Spinal Muscular Atrophy Registry for Real-World Evidence (2020)

Prospective outcome data collected will provide results on safety and effectiveness in a post-therapy approval era. These data are essential to inform improvements in care and access to therapy for all SMA patients.
Policy-driven access control over a distributed firewall architecture (2003)

Motivated by a scientific application, where virtual organisations are dynamically created to achieve specific goals by sharing resources and information, we propose the synthesis of two lines of research: policy-based access control and distributed firewalls. Through this fusion we expect to deliver a scalable method of setting up security infrastructures for Grid computing infrastructures.
Bill Mackowski, of Milford, a former wildlife biologist, sees snowshoes as imbue (2009)

A large number of different L1 element sites are expressed in human somatic tissues, and this expression varies among different individuals. Paradoxically, few elements were tagged at high frequency, indicating that the majority of expressed L1s are transcribed at low levels. Based on our preliminary expression studies of a limited number of elements in a single family, we predict a significant degree of inter-individual transcript-level polymorphism in this class of sequence.
IS-IS extensions for Computed Multicast applied to MPLS based Segment Routing (2016)

This document describes the IS-IS extensions required to support
multicast for MPLS based Segment Routing. In this approach IS-IS
speakers compute their role in multicast tree construction based on
the information in the IS-IS routing information base.
Sparse Inverse of Covariance Matrix of QTL Effects with Incomplete Marker Data (2004)

Gametic models for fitting breeding values at QTL as random effects in outbred populations have become popular because they require few assumptions about the number and distribution of QTL alleles segregating. The covariance matrix of the gametic effects has an inverse that is sparse and can be constructed rapidly by a simple algorithm, provided that all individuals have marker data, but not otherwise. An equivalent model, in which the joint distribution of QTL breeding values and marker genotypes is considered, was shown to generate a covariance matrix with a sparse inverse that can be constructed rapidly with a simple algorithm. This result makes more feasible including QTL as random effects in analyses of large pedigrees for QTL detection and marker assisted selection. Such analyses often use algorithms that rely upon sparseness of the mixed model equations and require the inverse of the covariance matrix, but not the covariance matrix itself. With the proposed model, each individual has two random effects for each possible unordered marker genotype for that individual. Therefore, individuals with marker data have two random effects, just as with the gametic model. To keep the notation and the derivation simple, the method is derived under the assumptions of a single linked marker and that the pedigree does not contain loops. The algorithm could be applied, as an approximate method, to pedigrees that contain loops.
Backside contacted solar cells with heterojunction emitters and laser fired absorber contacts for crystalline silicon on glass (2016)

Backside contacted cells were fabricated on p- and n-type, liquid phase crystallized silicon on glass. The heterojunction emitter and transparent contacting layer were opened locally using an inkjet printer and the absorber was contacted with laser fired point contacts. An analytical resistance model was derived to determine the resistance losses for the point contact geometry. Using test structures and the model it was found that for p-type cells the main contribution to the cell resistance came from the absorber contact and the absorber. Both were strongly reduced by increasing the absorber doping. For n-type cells the main contributions originated from the emitter and emitter-TCO contact, which was improved by changing the emitter type, resulting in an 11.6 % solar cell.
Antiestrogen-binding site ligands induce autophagy in myeloma cells that proceeds through alteration of cholesterol metabolism (2013)

Multiple myeloma (MM) is a malignancy characterized by the accumulation of clonal plasma cells in the bone marrow. Despite extensive efforts to design drugs targeting tumoral cells and their microenvironment, MM remains an incurable disease for which new therapeutic strategies are needed. We demonstrated here that antiestrogens (AEs) belonging to selective estrogen receptor modulators family induce a caspase-dependent apoptosis and trigger a protective autophagy. Autophagy was recognized by monodansylcadaverin staining, detection of autophagosomes by electronic microscopy, and detection of the cleaved form of the microtubule-associated protein light chain 3. Moreover, autophagy was inhibited by drugs such as bafilomycin A1 and 3-methyladenosine. Autophagy was mediated by the binding of AEs to a class of receptors called the antiestrogen binding site (AEBS) different from the classical estrogen nuclear receptors. The binding of specific ligands to the AEBS was accompanied by alteration of cholesterol metabolism and in particular accumulation of sterols: zymostenol or desmosterol depending on the ligand. This was due to the inhibition of the cholesterol-5,6-epoxide hydrolase activity borne by the AEBS. We further showed that the phosphoinositide 3-kinase/AKT/mammalian target of rapamycin pathway mediated autophagy signaling. Moreover, AEBS ligands restored sensitivity to dexamethasone in resistant MM cells. Since we showed previously that AEs arrest MM tumor growth in xenografted mice, we propose that AEBS ligands may have a potent antimyeloma activity alone or in combination with drugs used in clinic.
Yield enhancement of asynchronous logic circuits through 3-dimensional integration technology (2006)

This paper presents a systematic design for yield enhancement of asynchronous logic circuits using 3-D (3-Dimensional) integration technology. In this design, the target asynchronous circuits on one planar device layer which is fabricated with aggressive technology, are built on fault tolerant graph models with extra spare resources, and can be reconfigured by autonomous reconfiguration logic on another planar device layer which is fabricated with conservative technology, in the presence of hard errors. The yield analysis shows that this method can result in 20--30% overall yield enhancement. This design methodology can be conveniently applied to clocked designs without significant changes.
Intra-pixel sensitivity in NIR detectors for NGST (2003)

Intra-Pixel Sensitivity (IPS) is defined as the spatially varying response of the pixel to incoming flux. IPS plays a crucial role when the Point-Spread Function (PSF) is critically, or under-, sampled. Variations in IPS lead to photometric and astrometric errors. The Next Generation Space Telescope (NGST) requires high quality photometry and astrometry, so an accurate estimation of the IPS function is necessary for a successful NGST mission. Photo-electrons generated in a pixel may be detected in the depletion region (detection of the flux) of the same pixel, or might diffuse and end up in the microstructure of the detector, the electric field distribution therein, wavelength of the incident radiation, and diffusion processes of the excess charge carriers generated determines the IPS function of a pixel that can vary from pixel to pixel. The total detected flux is proportional to the convolution of the PSF and the IPS function. If we approximate the profile of the PSF, then the problem of determining the IPS function reduces to deconvolving using the experimentally obtained Sensitivity variation profile and the calculated PSF. We aim to obtain a highly undersampled PSF, scan it over a single pixel on a grid of 10 x 10 points, and retrieving IPS function using deconvolution. We present our results, experiment design, and the scope of further work, using an NGST detector, to estimate the IPS function at various wavelengths.
DNA methyltransferase 3b preferentially associates with condensed chromatin (2010)

In mammals, DNA methylation is catalyzed by DNA methyltransferases (DNMTs) encoded by Dnmt1, Dnmt3a and Dnmt3b. Since, the mechanisms of regulation of Dnmts are still largely unknown, the physical interaction between Dnmt3b and chromatin was investigated in vivo and in vitro. In embryonic stem cell nuclei, Dnmt3b preferentially associated with histone H1-containing heterochromatin without any significant enrichment of silent-specific histone methylation. Recombinant Dnmt3b preferentially associated with nucleosomal DNA rather than naked DNA. Incorporation of histone H1 into nucleosomal arrays promoted the association of Dnmt3b with chromatin, whereas histone acetylation reduced Dnmt3b binding in vitro. In addition, Dnmt3b associated with histone deacetylase SirT1 in the nuclease resistant chromatin. These findings suggest that Dnmt3b is preferentially recruited into hypoacetylated and condensed chromatin. We propose that Dnmt3b is a 'reader' of higher-order chromatin structure leading to gene silencing through DNA methylation.
LIMITS OF INFRARED IMAGING (2011)

The background photon shot noise, induced by the signal itself and all other in-band surroundings, provides the fundamental infrared imaging sensitivity limit (background limited performance or BLIP). Optical diffraction constrains resolution angle to values greater than the ratio of the detection wavelength to the optics diameter. Imaging technology tries to attain BLIP at spatial frequencies approaching the diffraction limit while minimizing system size, weight, power, and life-cycle cost. To minimize costs, detector array technology must raise the detector operating temperature while keeping dark currents and other noise mechanisms below background shot noise. This requires reducing material and process defects. Recently HgCdTe has seen the MWIR-LWIR device dark currents to be limited only by fundamental mechanisms over a wide range of temperatures and wavelengths. Novel materials systems (e.g. Type-II superlattices) in theory have even lower fundamental limits than HgCdTe , but as yet lag in demonstrated performance. At least for now HgCdTe provides a convenient well-characterized benchmark and gives insight into further improvement possibilities Infrared imaging technology must also exploit advanced processing and packaging techniques to reduce detector pitch to a few wavelengths of detected light. Mid- and long-wave infrared imaging arrays with ~15μm detector dimensions are now approaching this goal.
Detection of drug‐resistant HIV minorities in clinical specimens and therapy failure (2008)

By utilizing the replication dynamics of HIV under drug pressure, a rPhenotyping format potently reveals relevant therapy-resistant minority species, even of HIV known to possess reduced replicative fitness. With its rapid turnaround of 8 days and its high sensitivity, our rPhenotyping system may be a valuable diagnostic tool for detecting the early emergence of therapy-threatening HIV minorities or the persistence of residual resistant virus.
Adjuvant Action of Capsular Polysaccharide of Klebsiella pneumoniae on Antibody Response (1976)

ABSTRACT The neutral fraction (neutral CPS‐K) of Klebsiella pneumoniae capsular polysaccharide (CPS‐K) from type 1, Kasuya strain, has already been reported as the active substance responsible for the strong adjuvant effect of CPS‐K. The present results demonstrate that neutral CPS‐K exhibits further common biological activities with lipopolysaccharide (LPS) isolated from Salmonella enteritidis . The intensity of the lethality in mice of neutral CPS‐K by the intraperitoneal route is very similar to that of LPS. Its lethality for mice by the intravenous (i.v.) route is significantly stronger than that of LPS, because the degree of increase in the sensitivity to their lethality by i.v. challenge is smaller for LPS than for neutral CPS‐K. The intensity of the pyrogenicity of neutral CPS‐K in rabbits is approximately one‐tenth of that of LPS as judged by the minimal pyrogenic doses and fever indices. The skin‐preparatory potency of neutral CPS‐K for the dermal Shwartzman phenomenon in rabbits is also approximately one‐tenth of that of LPS compared on the basis of the minimal skin‐preparatory doses. When injected i.v., neutral CPS‐K exhibits a provocative effect on hemorrhagic reactions in skin sites prepared with neutral CPS‐K or LPS.
Cyclist Drag in Team Pursuit: Influence of Cyclist Sequence, Stature, and Arm Spacing (2013)

In team pursuit, the drag of a group of cyclists riding in a pace line is dependent on several factors, such as anthropometric characteristics (stature) and position of each cyclist as well as the sequence in which they ride. To increase insight in drag reduction mechanisms, the aerodynamic drag of four cyclists riding in a pace line was investigated, using four different cyclists, and for four different sequences. In addition, each sequence was evaluated for two arm spacings. Instead of conventional field or wind tunnel experiments, a validated numerical approach (computational fluid dynamics) was used to evaluate cyclist drag, where the bicycles were not included in the model. The cyclist drag was clearly dependent on his position in the pace line, where second and subsequent positions experienced a drag reduction up to 40%, compared to an individual cyclist. Individual differences in stature and position on the bicycle led to an intercyclist variation of this drag reduction at a specific position in the sequence, but also to a variation of the total drag of the group for different sequences. A larger drag area for the group was found when riding with wider arm spacing. Such numerical studies on cyclists in a pace line are useful for determining the optimal cyclist sequence for team pursuit.
Quaternary heterocyclylamino .beta.-lactams: a generic alternative to the classical acylamino side chain (1982)

6 beta-[(1-Substituted-4-pyridinio)amino]penam-3-carboxylates and 7 beta-[(1-substituted-4-pyridinio)amino]ceph-3-em-4-carboxylates have been found to be interesting new classes of antibacterial beta-lactams, readily available by SN2 Ar coupling of fluoro-substituted quaternized pyridines and appropriate amino lactam carboxylic acids. Compared to penicillin G, the penam 12c exhibited a spectrum extended to Gram-negative species, such as Escherichia, Shigella, Klebsiella and Enterobacter, offset by a loss of potency against Gram-positive species. Excluding Pseudomonas, many examples of the cephems showed excellent activity against the above Gram-negative organisms, and in some cases, such as 15i, the spectrum included good performance against the staphylococci and streptococci. With Serratia and many Proteus species, there was an adverse inoculum and medium effect which was not observed in the good Gram-positive reach of the cephem series.
Extended Krylov Subspaces: Approximation of the Matrix Square Root and Related Functions (1998)

We introduce an economical Gram--Schmidt orthogonalization on the extended Krylov subspace originated by actions of a symmetric matrix and its inverse. An error bound for a family of problems arising from the elliptic method of lines is derived. The bound shows that, for the same approximation quality, the diagonal variant of the extended subspaces requires about the square root of the dimension of the standard Krylov subspaces using only positive or negative matrix powers. An example of an application to the solution of a 2.5-D elliptic problem attests to the computational efficiency of the method for large-scale problems.
Prognostic role of CD4 T-cell depletion after frontline fludarabine, cyclophosphamide and rituximab in chronic lymphocytic leukaemia (2019)

Consolidation/maintenance trials based on detectable MRD after FCR should investigate CD4 T-cell numbers both as a selection and a response criterion, and consolidation treatments should target B-cell/T-cell interactions.