gebhart/patrepeval huggingface dataset:
Electronic structure and spin polarization of Mn-containing dilute magnetic III-V semiconductors (2001)

We present ab initio density-functional calculations for the electronic structure of the dilute magnetic semiconductors ${\mathrm{Mn}}_{x}{\mathrm{Ga}}_{1\ensuremath{-}x}\mathrm{As}$ and ${\mathrm{Mn}}_{x}{\mathrm{In}}_{1\ensuremath{-}x}\mathrm{As}$ with a realistic $x=0.063.$ We find that the introduction of Mn perturbs the position of the nearest As atoms, but does not break the tetrahedral symmetry. Neither material is found to be strictly half metallic. However, in both materials the Mn content results in a majority-spin valence-band maximum that is $\ensuremath{\sim}0.5$ eV above the minority-spin valence-band maximum. This large valence-band split is primarily due to the hybridization of As $4p$ and Mn $3d$ orbitals. It results in a significant energy range where holes have a well-defined spin. The effective masses of holes in this range are found to be comparable to those of GaAs and InAs. Hence, in an ideal, disorder-free situation, spin-polarized transport may be explained by conventional transport in the context of a simple band picture. This leads to a theoretical limit of 100% spin injection from these materials. Attaining this limit in a sufficiently ordered material also requires a careful ``engineering'' of the Fermi-level position and a sufficiently low temperature.
Recent progress in semiconductor laser amplifiers (1988)

Recent progress in semiconductor laser amplifiers (SLAs), mainly GaInAsP traveling-wave semiconductor laser amplifiers (TWAs) for use in optical fiber transmission systems, is discussed. The status of antireflection coating on laser-diode facets which are indispensable for TWAs is discussed. Reported data on small-signal gain, signal-gain saturation, and noise are summarized and discussed in relation to active-layer parameters. Common amplification using SLAs for the amplification of various multiplexed signals, including interchannel crosstalk, is also described. A thick, short active-layer structure for a broadband high-output-power low-noise TWA with polarization-insensitive signal gain is proposed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
From Small Sweeteners to Sweet Proteins:  Anatomy of the Binding Sites of the Human T1R2_T1R3 Receptor (2005)

The sweet taste receptor, a heterodimeric G protein coupled receptor (GPCR) protein, formed by the T1R2 and T1R3 subunits, recognizes several sweet compounds including carbohydrates, amino acids, peptides, proteins, and synthetic sweeteners. Its similarity with the metabotropic glutamate mGluR1 receptor allowed us to build homology models. All possible dimers formed by combinations of the human T1R2 and T1R3 subunits, modeled on the A (closed) or B (open) chains of the extracellular ligand binding domain of the mGluR1 template, yield four ligand binding sites for low-molecular-weight sweeteners. These sites were probed by docking a set of molecules representative of all classes of sweet compounds and calculating the free energy of ligand binding. These sites are not easily accessible to sweet proteins, but docking experiments in silico showed that sweet proteins can bind to a secondary site without entering the deep cleft. Our models account for many experimental observations on the tastes of sweeteners, including sweetness synergy, and can help to design new sweeteners.
Adoptive Immunotherapy of Established Pulmonary Metastases with LAK Cells and Recombinant Interleukin-2 (1984)

The activation of human peripheral blood leukocytes or murine splenocytes with interleukin-2 (IL-2) generated cells that were lytic in vitro for a variety of fresh tumor cells. The adoptive transfer of such lymphokine-activated killer (LAK) cells to mice with established pulmonary sarcoma metastases was highly effective in reducing the number (and size) of these tumor nodules when combined with repeated injections of recombinant IL-2. These findings provide a rationale for clinical trials of the infusion of human LAK cells generated with recombinant IL-2 as well as Phase I trials of the infusion of recombinant IL-2 systemically into humans.
Thermal optimization in multi-granularity multi-core floorplanning (2009)

Multi-core microarchitectures require a careful balance between many competing objectives to achieve the highest possible performance. Integrated early analysis is the consideration of all of these factors at an early stage. Toward this goal, this work presents the first adaptive multi-granularity multi-core microarchitecture-level floorplanner that simultaneously optimizes temperature and performance, and considers memory bus length. We include simultaneous optimization at both the module-level and the core/cache-bank level. Related experiments show that our methodology is effective for optimizing multi-core architectures.
Incorporating single‐side sparing in models for predicting parotid dose sparing in head and neck IMRT (2014)

The combined model for predicting parotid sparing that takes into account single-side sparing improves the prediction accuracy over the previous model.
Hemodialysis vascular access: emerging concepts (1996)

Vascular access complications remain a leading cause of morbidity and hospitalization in patients on chronic maintenance hemodialysis. Although arteriovenous fistulas remain the dialysis access of choice, an increasing percentage of patients are dialyzed using synthetic grafts or permanent catheters. The most frequent vascular access complications are the development of stenosis and of thrombosis. In recent years, increasing attention is being paid to screening techniques designed to detect vascular access stenosis prior to thrombosis. Aggressive screening techniques coupled with interventional procedures such as angioplasty may reduce the incidence of graft thrombosis. Once thrombosis has occurred, mechanical or pharmacomechanical thrombolysis in conjunction with angioplasty may be an effective alternative to surgical thrombectomy.
Investigation of the het genes that control heterokaryon incompatibility between members of heterokaryon-compatibility (h-c) groups A and G1 of Aspergillus nidulans (1990)

A chromosome assay method was used to determine the heterokaryon compatibility relationships between strains belonging to heterokaryon-compatibility (h-c) groups A and G1 of Aspergillus nidulans. A hybrid strain (RD15) was isolated following protoplast fusion of strains 65-5 (h-cA) and 7-141 (h-cG1). The morphology of RD15 was severely abnormal compared to diploid strains of A. nidulans produced from heterokaryon-compatible haploid parents. Inocula of RD15 were induced to haploidize on medium containing Benlate and a parasexual progeny sample of 291 haploid segregants was obtained. The progeny strains were genotyped for standard markers. Allelic ratios and pairwise marker segregations were determined. Pairs of progeny strains that carried different alleles for the standard markers on each linkage group in turn were tested for compatibility. Strain pairs that possessed different alleles for the markers on linkage groups II, III, V, VI and VII were incompatible indicating the presence of heterokaryon-incompatible (het) genes on these linkage groups. Backcrosses to an h-cGl strain showed that two het genes were located on linkage group III and confirmed a total of six het gene differences between the h-cA and h-cGl strains.
Large‐scale phenotypic analysis—the pilot project on yeast chromosome III (1997)

In 1993, a pilot project for the functional analysis of newly discovered open reading frames, presumably coding for proteins, from yeast chromosome III was launched by the European Community. In the frame of this programme, we have developed a large-scale screening for the identification of gene/protein functions via systematic phenotypic analysis. To this end, some 80 haploid mutant yeast strains were constructed, each carrying a targeted deletion of a single gene obtained by HIS3 or TRP1 transplacement in the W303 background and a panel of some 100 growth conditions was established, ranging from growth substrates, stress to, predominantly, specific inhibitors and drugs acting on various cellular processes. Furthermore, co-segregation of the targeted deletion and the observed phenotype(s) in meiotic products has been verified. The experimental procedure, using microtiter plates for phenotypic analysis of yeast mutants, can be applied on a large scale, either on solid or in liquid media. Since the minimal working unit of one 96-well microtiter plate allows the simultaneous analysis of at least 60 mutant strains, hundreds of strains can be handled in parallel. The high number of monotropic and pleiotropic phenotypes (62%) obtained, together with the acquired practical experience, have shown this approach to be simple, inexpensive and reproducible. It provides a useful tool for the yeast community for the systematic search of biochemical and physiological functions of unknown genes accounting for about a half of the 6000 genes of the complete yeast genome. © 1997 John Wiley & Sons, Ltd.
A channel engineering combined with channel epitaxy optimization and TED suppression for 0.15 μm n-n gate CMOS technology (2002)

A new channel engineering combined with optimization of channel epitaxy and suppression of TED (transient enhanced diffusion) is proposed for a practical 0.15 /spl mu/m n-n gate CMOS technology. An optimized channel profile with small Vth fluctuation provides an nMOS with no reverse short channel effect and a high performance BCpMOS.
Monitoring Land-Cover Changes: A Machine-Learning Perspective (2016)

Monitoring land-cover changes is of prime importance for the effective planning and management of critical, natural and man-made resources. The growing availability of remote sensing data provides ample opportunities for monitoring land-cover changes on a global scale using machine-learning techniques. However, remote sensing data sets exhibit unique domain-specific properties that limit the usefulness of traditional machine-learning methods. This article presents a brief overview of these challenges from the perspective of machine learning and discusses some of the recent advances in machine learning that are relevant for addressing them. These approaches show promise for future research in the detection of land-cover change using machine-learning algorithms.
Postimplantation expression patterns indicate a role for the mouse forkhead/HNF-3 α, β and γ genes in determination of the definitive endoderm, chordamesoderm and neuroectoderm (1993)

The HNF-3 alpha, beta and gamma genes constitute a family of transcription factors that are required for hepatocyte-specific gene expression of a number of genes, e.g. transthyretin, alpha-1 antitrypsin and tyrosine aminotransferase. These genes share a highly conserved DNA-binding domain first found in the Drosophila gene, forkhead, which is required for the normal patterning of the developing gut and central nervous system in Drosophila. In adult mouse tissues, transcripts from HNF-3 alpha and beta have been localised to the liver, intestine and lung, whereas HNF-3 gamma is found in the liver, intestine and testis. In light of the early developmental significance of forkhead in Drosophila, we have compared the patterns of expression of HNF-3 alpha, beta and gamma mRNAs during murine embryogenesis. We find that these genes are sequentially activated during development in the definitive endoderm. HNF-3 beta mRNA is expressed in the node at the anterior end of the primitive streak in all three germ layers and is the first gene of this family to be activated. Subsequently, HNF-3 alpha is transcribed in the primitive endoderm in the region of the invaginating foregut and HNF-3 gamma appears upon hindgut differentiation. These genes have different anterior boundaries of mRNA expression in the developing endoderm and transcripts are found in all endoderm-derived structures that differentiate posterior to this boundary. Therefore, we propose that these genes define regionalization within the definitive endoderm. Furthermore, differential mRNA expression of HNF-3 alpha and beta is detected in cells of the ventral neural epithelium, chordamesoderm and notochord. In the neural epithelium, expression of HNF-3 alpha and beta mRNA becomes localised to cells of the floor plate. We propose that, in addition to their characterised requirement for liver-specific gene expression, HNF-3 alpha and beta are required for mesoderm and neural axis formation. We also conclude that HNF-3 beta is the true orthologue of the Drosophila forkhead gene.
Oxidative Macromolecular Damage in Age-Related Macular Degeneration (2009)

The results indicate that an imbalance between TOS and TAC leads to not only increased lipid damage, but also protein and DNA damage. These first reported results suggest that protein and DNA damage might also play a role in the pathogenesis of AMD.
Effect of training on the dose-response relationship for insulin action in men (1989)

Seven endurance-trained subjects [maximal O2 consumption (VO2max) 64 +/- 1 (SE) ml.min-1.kg-1] were subjected to three sequential hyperinsulinemic euglycemic clamps 15 h after having performed their last training session (T). Results were compared with findings in seven untrained subjects (VO2max 44 +/- 2 ml.min-1.kg-1) studied both at rest (UT) and after 60 min of bicycle exercise at 150 W (UT-ex). In T and UT-ex compared with UT, sensitivity for insulin-mediated whole-body glucose uptake was higher [insulin concentrations eliciting half-maximal glucose uptake being 44 +/- 2 (T) and 43 +/- 4 (UT-ex) vs. 52 +/- 3 microU/ml (UT), P less than 0.05] and responsiveness was higher [13.4 +/- 1.2 (T) and 10.9 +/- 0.7 (UT-ex) vs. 9.5 +/- 0.7 mg.min-1.kg-1 (UT), P less than 0.05]. Furthermore, responsiveness was higher (P less than 0.05) in T than in UT-ex. Insulin-stimulated O2 uptake and maximal glucose oxidation rate were higher in T than in UT and UT-ex. Insulin-stimulated conversion or glucose to glycogen and muscle glycogen synthase was higher in T than in UT and UT-ex. However, glycogen storage in vastus lateralis muscle was found only in UT-ex. No change in any glucoregulatory hormone or metabolite could explain the increased insulin action in trained subjects. It is concluded that physical training induces an adaptive increase in insulin responsiveness of whole-body glucose uptake, which does not reflect increased glycogen deposition in muscle.(ABSTRACT TRUNCATED AT 250 WORDS)
Immobilization of the Distal Hinge in the Labile Serpin Plasminogen Activator Inhibitor 1 (2003)

The serpin plasminogen activator inhibitor-1 (PAI-1) plays an important role in the regulation of the fibrinolytic activity in blood. In plasma, PAI-1 circulates mainly in the active conformation. However, PAI-1 spontaneously converts to a latent conformation. This conversion comprises drastic conformational changes in both the distal and the proximal hinge region of the reactive center loop. To study the functional and conformational rearrangements associated solely with the mobility of the proximal hinge, disulfide bonds were introduced to immobilize the distal hinge region. These mutants exhibited specific activities comparable with that of PAI-1-wt. However, the engineered disulfide bond had a major effect on the conformational and associated functional transitions. Strikingly, in contrast to PAI-1-wt, inactivation of these mutants yielded a virtually complete conversion to a substrate-like conformation. Comparison of the digestion pattern (with trypsin and elastase) of the mutants and PAI-1-wt revealed that the inactivated mutants have a conformation differing from that of latent and active PAI-1-wt. Unique trypsin-susceptible cleavage sites arose upon inactivation of these mutants. The localization of these exposed residues provides evidence that a displacement of alphahF has occurred, indicating that the proximal hinge is partly inserted between s3A and s5A. In conclusion, immobilization of the distal hinge region in PAI-1 allowed the identification of an "intermediate" conformation characterized by a partial insertion of the proximal hinge region. We hypothesize that locking PAI-1 in this transition state between active and latent conformations is associated with a displacement of alphahF, subsequently resulting in substrate behavior.
αv‐Integrin isoform expression in primary human tumors and brain metastases (2013)

The stronger αv-integrin expression in brain metastases, especially of αvβ3 and αvβ8 integrins, suggests that certain αv integrin are involved in the process of brain metastasis. αv Integrins may be therapeutic targets for patients with metastatic cancer in brain.
Structural analysis and biological significance of the cell wall lytic enzymes ofStreptococcus pneumoniaeand its bacteriophage (1992)

The development of an appropriate technique for the identification of autolysin-defective mutants of pneumococcus has been a fundamental step to carry out studies on the molecular characteristics of the lytic enzymes of Streptococcus pneumoniae and its bacteriophage. Our results show that the principal pneumococcal autolysin (an amidase) is responsible for the separation of the daughter cells at the end of the cell division. On the other hand, this system provides a reliable experimental model to support the extended idea concerning the modular organization of most proteins. The comparative analyses of the deduced amino acid sequences of these enzymes, as well as the construction of functional chimeric phage-bacterial enzymes, demonstrate that the C-terminal domain, which contains a large number of repeated amino acid motifs, is the substrate-binding domain, whereas the N-terminal domain provides enzymatic specificity. We propose that the pneumococcal lytic enzymes have evolved by modular exchange providing examples of the types of novel genes that the bacteria or the phage might create to allow them to become adapted to new environmental situations.
Transcranial Magnetic Stimulation Elicits Coupled Neural and Hemodynamic Consequences (2007)

Transcranial magnetic stimulation (TMS) is an increasingly common technique used to selectively modify neural processing. However, application of TMS is limited by uncertainty concerning its physiological effects. We applied TMS to the cat visual cortex and evaluated the neural and hemodynamic consequences. Short TMS pulse trains elicited initial activation (approximately 1 minute) and prolonged suppression (5 to 10 minutes) of neural responses. Furthermore, TMS disrupted the temporal structure of activity by altering phase relationships between neural signals. Despite the complexity of this response, neural changes were faithfully reflected in hemodynamic signals; quantitative coupling was present over a range of stimulation parameters. These results demonstrate long-lasting neural responses to TMS and support the use of hemodynamic-based neuroimaging to effectively monitor these changes over time.
Factors determining the refractive effects of intrastromal photorefractive keratectomy with the picosecond laser (1997)

Intrastromal PRK does not work as originally envisioned because the amount of evaporated tissue is very small. The greater long-term refractive changes observed in animal experiments and clinical studies must therefore be due to the healing response of the cornea. Because the refractive effects are strongly influenced by the healing response of the cornea, they are poorly predictable.
Effects of helical structures formed by the binding arms of DNAzymes and their substrates on catalytic activity (1998)

As a part of our efforts to clarify structure-function relationships in reactions catalyzed by deoxyribozymes (DNAzymes), which were recently selected in vitro , we synthesized various chimeras and analyzed the kinetics of the corresponding cleavage reactions. We focused on the binding arms and generated helices composed of binding arms and substrates that consisted of RNA and RNA, of RNA and DNA or of DNA and DNA. As expected for the rate limiting chemical cleavage step in reactions catalyzed by DNAzymes, a linear relationship between log( k cat) and pH was observed. In all cases examined, introduction of DNA into the binding helix enhanced the rate of chemical cleavage. Comparison of CD spectra of DNAzyme. substrate complexes suggested that higher levels of B-form-like helix were associated with higher rates of cleavage of the substrate within the complex. To our surprise, the enhancement of catalytic activity that followed introduction of DNA into the binding helix (enhancement by the presence of more B-form-like helix) was very similar to that observed in the case of the hammerhead ribozymes that we had investigated previously. These data, together with other observations, strongly suggest that the reaction mechanism of metal-ion-dependent DNAzymes is almost identical to that of hammerhead ribozymes.
A theoretical approach to chiral capillary electrophoresis with some practical implications (1994)

A simple model has been proposed which explains enantiomeric resolution in capillary electrophoresis in terms of differential interactions with a chiral selector and differential migration of the two enantiomer-chiral selector complexes. The equations derived allow predictions to be made and there is good support for the model in literature data.
Microfluidic Point-of-Care Devices: New Trends and Future Prospects for eHealth Diagnostics (2020)

Point-of-care (PoC) diagnostics is promising for early detection of a number of diseases, including cancer, diabetes, and cardiovascular diseases, in addition to serving for monitoring health conditions. To be efficient and cost-effective, portable PoC devices are made with microfluidic technologies, with which laboratory analysis can be made with small-volume samples. Recent years have witnessed considerable progress in this area with "epidermal electronics", including miniaturized wearable diagnosis devices. These wearable devices allow for continuous real-time transmission of biological data to the Internet for further processing and transformation into clinical knowledge. Other approaches include bluetooth and WiFi technology for data transmission from portable (non-wearable) diagnosis devices to cellphones or computers, and then to the Internet for communication with centralized healthcare structures. There are, however, considerable challenges to be faced before PoC devices become routine in the clinical practice. For instance, the implementation of this technology requires integration of detection components with other fluid regulatory elements at the microscale, where fluid-flow properties become increasingly controlled by viscous forces rather than inertial forces. Another challenge is to develop new materials for environmentally friendly, cheap, and portable microfluidic devices. In this review paper, we first revisit the progress made in the last few years and discuss trends and strategies for the fabrication of microfluidic devices. Then, we discuss the challenges in lab-on-a-chip biosensing devices, including colorimetric sensors coupled to smartphones, plasmonic sensors, and electronic tongues. The latter ones use statistical and big data analysis for proper classification. The increasing use of big data and artificial intelligence methods is then commented upon in the context of wearable and handled biosensing platforms for the Internet of things and futuristic healthcare systems.