gebhart/patrepeval huggingface dataset:
Introduction (1994)

Far-reaching changes can be expected in the Southern African region over the next few years. Since the collapse of Portuguese colonial rule in Angola and Mozambique in the middle 1970s the region has been plunged into political and economic instability. After decades of white minority rule under the system of apartheid, South Africa is set to attain, for the first time in its history, a popularly elected government. This will occur during a period when the end of the Cold War in Europe has lessened super power interest in the region. For some analysts it has now at last become possible to talk about forging a common security policy for the region, possibly on the lines of the Conference for Security and Cooperation in Europe. Such a security policy would take into account not only military and political issues, but also ones of economic welfare and social justice.1 KeywordsForeign PolicySecure GoverningIdeological ConflictSouth African PolicyInkatha Freedom PartyThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
Evaluation of the pregnancy immunotrophism hypothesis by assessment of the reproductive performance of young adult mice of genotype scid/scid.bg/bg (1990)

The hypothesis that enhancement of pregnancy success results from immune recognition of the conceptus was evaluated by studying reproductive performance in a new line of mice deficient in NK cells and lacking B cells and T cells. Doubly mutant mice of genotype scid/scid.bg/bg are both viable and fertile. The numbers of offspring born to pairs of this genotype were not different from numbers born to heterozygous pairs. Differences in prenatal loss could not be found between genotypes by counts of either fetal resorption sites or corpora lutea. The timing of developmental stages and the differentiation of trophoblast, placenta, decidua and metrial gland in scid/scid.bg/bg mice appeared normal. These results suggest either that lymphokine influences on trophoblast cells in vivo do not contribute, in a major way, to pregnancy success or that the important cytokines are derived from uterine cell populations that are not classical, mature B cells, T cells or NK cells.
Soft Tissue Augmentation With Artecoll: 10-Year History,Indications, Techniques, and Complications (2003)

Most of the biologic filler materials that increase the thickness of the corium in a wrinkle line are phagocytosed within a certain time. Therefore, a lasting effect can only be achieved with nonresorbable synthetic substances. Artefill consists of 20 volume percent microspheres of polymethyl-methacrylate and 80 volume percent of bovine collagen. Beneath the crease, the microspheres with their exceptional surface smoothness stimulate fibroblasts to encapsulate each individual one of the 6-million microspheres contained in 1 mL of Artefill. Collagen is merely a carrier substance that prevents the microspheres from agglomerating during tissue ingrowth. The 20 volume percent of microspheres in Artefill provides the scaffold for the 80% volume of connective tissue deposition, a complete replacement of the injected collagen. The filler material beneath a crease acts like a splint and prevents the possibility of its further folding, thereby allowing the diminished thickness of the corium in a crease to recover. This recovery process is well known even in older patients with facial paralysis or after a stroke, whose facial wrinkles and furrows on the paralyzed side disappear over time.
Expression and Differential Intracellular Localization of Two Major Forms of Human 8-Oxoguanine DNA Glycosylase Encoded by Alternatively Spliced OGG1 mRNAs (1999)

We identified seven alternatively spliced forms of human 8-oxoguanine DNA glycosylase (OGG1) mRNAs, classified into two types based on their last exons (type 1 with exon 7: 1a and 1b; type 2 with exon 8: 2a to 2e). Types 1a and 2a mRNAs are major in human tissues. Seven mRNAs are expected to encode different polypeptides (OGG1-1a to 2e) that share their N terminus with the common mitochondrial targeting signal, and each possesses a unique C terminus. A 36-kDa polypeptide, corresponding to OGG1-1a recognized only by antibodies against the region containing helix-hairpin-helix-PVD motif, was copurified from the nuclear extract with an activity introducing a nick into DNA containing 8-oxoguanine. A 40-kDa polypeptide corresponding to a processed form of OGG1-2a was detected in their mitochondria using antibodies against its C terminus. Electron microscopic immunocytochemistry and subfractionation of the mitochondria revealed that OGG1-2a locates on the inner membrane of mitochondria. Deletion mutant analyses revealed that the unique C terminus of OGG1-2a and its mitochondrial targeting signal are essential for mitochondrial localization and that nuclear localization of OGG1-1a depends on the NLS at its C terminus.
Ontology-based integration for relational databases (2006)

In this paper, we show that representation and reasoning techniques used in traditional knowledge engineering and the emerging Semantic Web can play an important role for heterogeneous database integration. Our OntoGrate architecture combines ontology-based schema representation, first order logic inference, and some SQL wrappers to integrate two sample relational databases. We define inferential data integration as the theoretical framework for our approach. The performance evaluation for query answering shows that OntoGrate reformulates conjunctive queries and retrieves over 100,000 answers from a target database in under 30 seconds. In addition to query answering, the system translates 40,000 database facts from source to target in under 30 seconds.
Lab on paper (2008)

Inexpensive and easy-to-use paper-based bioassay represents one practically useful platform for point-of-care diagnostics, particularly for those in developing countries. Microfluidics and point-of-care testing
Mixed-Signal Clock-Skew Calibration Technique for Time-Interleaved ADCs (2008)

Clock-skew errors in time-interleaved (TI) analog-to-digital converters (ADCs) importantly degrade the linearity of such converters. These nearly constant but unknown errors, which must not be confused with random jitter, prevent TI ADCs from performing uniform sampling. This paper proposes a mixed-signal clock-skew calibration technique and explores its limitations to perform a background calibration. Compared to the existing all-digital calibration techniques, ours distinguishes itself by the simplicity of its hardware elements. On the other hand, compared to the all-analog ones, ours keeps the inherent robustness of a digital clock-skew detection. A demonstrator shows the feasibility of our technique. This demonstrator consists of two 10-bit commercial ADCs, a field-programmable gate array to implement a digital clock-skew detector, and an application-specific integrated circuit in a CMOS 0.35-mum technology to implement a digitally trimmable multiphase sampling clock generator. In this highly hostile environment of interconnected discrete components, our demonstrator can correct an initial clock skew of thousands of picoseconds with a granularity of 1.8 ps.
Functional Sarcoplasmic Reticulum for Calcium Handling of Human Embryonic Stem Cell-Derived Cardiomyocytes: Insights for Driven Maturation (2007)

Cardiomyocytes (CMs) are nonregenerative. Self-renewable pluripotent human embryonic stem cells (hESCs) can differentiate into CMs for cell-based therapies. In adult CMs, Ca(2+)-induced Ca(2+) release from the sarcoplasmic reticulum (SR) via the ryanodine receptor (RyR) is key in excitation-contraction coupling. Therefore, proper Ca(2+) handling properties of hESC-derived CMs are required for their successful functional integration with the recipient heart. Here, we performed a comprehensive analysis of CMs differentiated from the H1 (H1-CMs) and HES2 (HES2-CMs) hESC lines and human fetal (F) and adult (A) left ventricular (LV) CMs. Upon electrical stimulation, all of H1-, HES2-, and FLV-CMs generated similar Ca(2+) transients. Caffeine induced Ca(2+) release in 65% of FLV-CMs and approximately 38% of H1- and HES2-CMs. Ryanodine significantly reduced the electrically evoked Ca(2+) transient amplitudes of caffeine-responsive but not -insensitive HES2- and H1-CMs and slowed their upstroke; thapsigargin, which inhibits the sarco/endoplasmic reticulum Ca(2+)-ATPase (SERCA) pump, reduced the amplitude of only caffeine-responsive HES2- and H1-CMs and slowed the decay. SERCA2a expression was highest in ALV-CMs but comparable among H1-, HES2-, and FLV-CMs. The Na(+)-Ca(2+) exchanger was substantially expressed in both HES2- and H1-CMs relative to FLV- and ALV-CMs. RyR was expressed in HES2-, H1-, and FLV-CMs, but the organized pattern for ALV-CMs was not observed. The regulatory proteins junctin, triadin, and calsequestrin were expressed in ALV-CMs but not HES2- and H1-CMs. We conclude that functional SRs are indeed expressed in hESC-CMs, albeit immaturely. Our results may lead to driven maturation of Ca(2+) handling properties of hESC-CMs for enhanced contractile functions. Disclosure of potential conflicts of interest is found at the end of this article.
THE FUNCTION OF HEAT-SHOCK PROTEINS IN STRESS TOLERANCE: DEGRADATION AND REACTIVATION OF DAMAGED PROTEINS (1993)

We have made rapid progress in recent years in identifying the genetic causes of many human diseases. However, despite this recent progress, our mechanistic understanding of these diseases is often incomplete. This is a problem because it limits our ...Read More
Rift Valley Fever Virus Nonstructural Protein NSs Promotes Viral RNA Replication and Transcription in a Minigenome System (2005)

Rift Valley fever virus (RVFV), which belongs to the genus Phlebovirus, family Bunyaviridae, has a tripartite negative-strand genome (S, M, and L segments) and is an important mosquito-borne pathogen for domestic animals and humans. We established an RVFV T7 RNA polymerase-driven minigenome system in which T7 RNA polymerase from an expression plasmid drove expression of RNA transcripts for viral proteins and minigenome RNA transcripts carrying a reporter gene between both termini of the M RNA segment in 293T cells. Like other viruses of the Bunyaviridae family, replication and transcription of the RVFV minigenome required expression of viral N and L proteins. Unexpectedly, the coexpression of an RVFV nonstructural protein, NSs, with N and L proteins resulted in a significant enhancement of minigenome RNA replication. Coexpression of NSs protein with N and L proteins also enhanced minigenome mRNA transcription in the cells expressing viral-sense minigenome RNA transcripts. NSs protein expression increased the RNA replication of minigenomes that originated from S and L RNA segments. Enhancement of minigenome RNA synthesis by NSs protein occurred in cells lacking alpha/beta interferon (IFN-alpha/beta) genes, indicating that the effect of NSs protein on minigenome RNA replication was unrelated to a putative NSs protein-induced inhibition of IFN-alpha/beta production. Our finding that RVFV NSs protein augmented minigenome RNA synthesis was in sharp contrast to reports that Bunyamwera virus (genus Bunyavirus) NSs protein inhibits viral minigenome RNA synthesis, suggesting that RVFV NSs protein and Bunyamwera virus NSs protein have distinctly different biological roles in viral RNA synthesis.
Trace Metal Requirements for Microbial Enzymes Involved in the Production and Consumption of Methane and Nitrous Oxide (2012)

Fluxes of greenhouse gases to the atmosphere are heavily influenced by microbiological activity. Microbial enzymes involved in the production and consumption of greenhouse gases often contain metal cofactors. While extensive research has examined the influence of Fe bioavailability on microbial CO(2) cycling, fewer studies have explored metal requirements for microbial production and consumption of the second- and third-most abundant greenhouse gases, methane (CH(4)), and nitrous oxide (N(2)O). Here we review the current state of biochemical, physiological, and environmental research on transition metal requirements for microbial CH(4) and N(2)O cycling. Methanogenic archaea require large amounts of Fe, Ni, and Co (and some Mo/W and Zn). Low bioavailability of Fe, Ni, and Co limits methanogenesis in pure and mixed cultures and environmental studies. Anaerobic methane oxidation by anaerobic methanotrophic archaea (ANME) likely occurs via reverse methanogenesis since ANME possess most of the enzymes in the methanogenic pathway. Aerobic CH(4) oxidation uses Cu or Fe for the first step depending on Cu availability, and additional Fe, Cu, and Mo for later steps. N(2)O production via classical anaerobic denitrification is primarily Fe-based, whereas aerobic pathways (nitrifier denitrification and archaeal ammonia oxidation) require Cu in addition to, or possibly in place of, Fe. Genes encoding the Cu-containing N(2)O reductase, the only known enzyme capable of microbial N(2)O conversion to N(2), have only been found in classical denitrifiers. Accumulation of N(2)O due to low Cu has been observed in pure cultures and a lake ecosystem, but not in marine systems. Future research is needed on metalloenzymes involved in the production of N(2)O by enrichment cultures of ammonia oxidizing archaea, biological mechanisms for scavenging scarce metals, and possible links between metal bioavailability and greenhouse gas fluxes in anaerobic environments where metals may be limiting due to sulfide-metal scavenging.
Improvement of Gastric Emptying in Diabetic Gastroparesis by Erythromycin (1990)

Erythromycin mimics the effect of the gastrointestinal polypeptide motilin on gastrointestinal motility, probably by binding to motilin receptors and acting as a motilin agonist. Erythromycin may thus have clinical application in patients with disturbances of gastroduodenal motility, such as diabetic gastroparesis. To examine this possibility, we studied the effect of erythromycin on gastric emptying in 10 patients with insulin-dependent diabetes mellitus and gastroparesis. We studied the emptying of liquids and solids simultaneously on separate days after the intravenous administration of erythromycin (200 mg) or placebo, using a double-isotope technique and a double-blind, crossover design. Erythromycin shortened the prolonged gastric-emptying times for both liquids and solids to normal. For example, 120 minutes after the ingestion of a solid meal, mean (+/- SE) retention was 63 +/- 9 percent with placebo and 4 +/- 1 percent with erythromycin, as compared with 9 +/- 3 percent in 10 healthy subjects. The corresponding values 120 minutes after the ingestion of a liquid meal were 32 +/- 4, 9 +/- 3, and 4 +/- 1 percent, respectively. Gastric emptying also improved, but to a lesser degree, in the 10 patients after four weeks of treatment with oral erythromycin (250 mg three times a day). These preliminary results suggest that erythromycin may have therapeutic value in patients with severe diabetic gastroparesis.
Performance of Fourier-based and wavelet-based OFDM for DVB-T systems (2007)

We present a comparative study on Fourier-based OFDM (FFT-OFDM) and wavelet-based OFDM (DWT-OFDM) in DVB-T system (DWT being the discrete wavelet transform).We found that the DWT-OFDM outperforms FFT-OFDM in AWGN and Rayleigh fading channels. For AWGN channel, the gain in term of energy per bit to noise ratio Eb/No was improved by about 5 dB when the system used Haar wavelet compared to FFT-OFDM with a cyclic prefix (CP) of 1/4-th the total OFDM symbol period, for the same BER of 0.001. Other members of Daubechies families such as db8, db16 and db32 also outperformed by the gains of 7 dB, 10 dB and 11 dB, respectively, at the same BER. We also considered Daubechies wavelet db32 and FFT-OFDM with a CP of 1/4-th the total OFDM symbol period in the presence of narrowband interference. In terms of Eb/No, DWT-OFDM surpassed FFT-OFDM by 9 dB at 0.02 BER. It is also shown that the DWT-OFDM of Daubechies db8 and db1 outperform FFT-OFDM in Rayleigh fading, both in multipath flat fading and multipath frequency selective fading. The DWT-OFDMpsilas with db8 and Haar outperformed FFT-OFDM by 7 and 2 dB, respectively, at BER of 0.01 in the flat fading channel. In addition, DWT-OFDM and FFT-OFDM showed about the same performance below 10 dB of Eb/No in frequency selective fading. However, the wavelet-based OFDM showed significant improvement of performance at higher than 10 dB of Eb/No.
Perovskite-based low-cost and high-efficiency hybrid halide solar cells (2014)

A cost-effective and high-throughput material named perovskite has proven to be capable of converting 15.9% of the solar energy to electricity, compared to an efficiency of 3.8% that was obtained only four years ago. It has already outperformed most of the thin-film solar cell technologies that researchers have been studying for decades. Currently, the architecture of perovskite solar cells has been simplified from the traditional dye-sensitized solar cells to planar-heterojunction solar cells. Recently, the performance of perovskite in solar cells has attracted intensive attention and studies. Foreseeably, many transformative steps will be put forward over the coming few years. In this review, we summarize the recent exciting development in perovskite solar cells, and discuss the fundamental mechanisms of perovskite materials in solar cells and their structural evolution. In addition, future directions and prospects are proposed toward high-efficiency perovskite solar cells for practical applications.
Structural classification of zinc fingers: SURVEY AND SUMMARY (2003)

Zinc fingers are small protein domains in which zinc plays a structural role contributing to the stability of the domain. Zinc fingers are structurally diverse and are present among proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins and small molecules. Here we present a comprehensive classification of zinc finger spatial structures. We find that each available zinc finger structure can be placed into one of eight fold groups that we define based on the structural properties in the vicinity of the zinc-binding site. Three of these fold groups comprise the majority of zinc fingers, namely, C2H2-like finger, treble clef finger and the zinc ribbon. Evolutionary relatedness of proteins within fold groups is not implied, but each group is divided into families of potential homologs. We compare our classification to existing groupings of zinc fingers and find that we define more encompassing fold groups, which bring together proteins whose similarities have previously remained unappreciated. We analyze functional properties of different zinc fingers and overlay them onto our classification. The classification helps in understanding the relationship between the structure, function and evolutionary history of these domains. The results are available as an online database of zinc finger structures.
Top-surface-emitting GaAs four-quantum-well lasers emitting at 0.85 μm (1990)

Room temperature CW and pulsed lasing of top-surface-emitting, vertical-cavity, GaAs quantum-well lasers was achieved at ~845 nm. The active gain medium was four 100 Å thick GaAs quantum wells. The whole structure was grown by molecular beam epitaxy. Deep H+-ion implantation followed by annealing was used to control a vertical profile of resistivity for an efficient current injection at the active region. The threshold current was 2.2 mA for CW and pulsed operation using 10 μm diameter lasers. Differential quantum efficiency was about 20%. Minimum threshold current density per quantum well of 360 A/cm2 was obtained.
On filtering false positive transmembrane protein predictions (2002)

While helical transmembrane (TM) region prediction tools achieve high (>90%) success rates for real integral membrane proteins, they produce a considerable number of false positive hits in sequences of known nontransmembrane queries. We propose a modification of the dense alignment surface (DAS) method that achieves a substantial decrease in the false positive error rate. Essentially, a sequence that includes possible transmembrane regions is compared in a second step with TM segments in a sequence library of documented transmembrane proteins. If the performance of the query sequence against the library of documented TM segment-containing sequences in this test is lower than an empirical threshold, it is classified as a non-transmembrane protein. The probability of false positive prediction for trusted TM region hits is expressed in terms of E-values. The modified DAS method, the DAS-TMfilter algorithm, has an unchanged high sensitivity for TM segments ( approximately 95% detected in a learning set of 128 documented transmembrane proteins). At the same time, the selectivity measured over a non-redundant set of 526 soluble proteins with known 3D structure is approximately 99%, mainly because a large number of falsely predicted single membrane-pass proteins are eliminated by the DAS-TMfilter algorithm.
A decision scheme for coronary angiography after acute myocardial infarction. (1989)

It is important to select patients in the convalescent phase of acute myocardial infarction in whom knowledge of coronary anatomy may identify those potentially suitable for intervention aimed at improving prognosis. However, differing guidelines have been proposed, and by applying some of these guidelines to our large database of patients after acute myocardial infarction, several problem areas were identified. These include lack of considering patients with resting ischemia beyond day 5 of hospitalization, management of patients with reduced ventricular function or patients not exercise tested, and the role of coronary angiography in the elderly. Based on this experience and further analysis in 1,848 patients surviving beyond day 5 of hospitalization, a modified decision scheme for coronary angiography was developed and then tested in a second population (n = 780). In the new scheme, patients over 75 years of age are considered individually. Those under 75 years of age with severe resting ischemia in the hospital at any time beyond the first 24 hours (18% mortality between day 6 and year 1), and hospital survivors with a history of previous myocardial infarction and clinical or radiographic signs of left ventricular failure in the hospital (25% 1-year mortality after discharge), are recommended for coronary angiography. Among the remaining patients, some will perform an exercise test, and those with an ischemic response or poor workload (11% 1-year mortality) are also assigned to coronary angiography. When an exercise test is not performed, a resting radionuclide left ventricular ejection fraction is recommended, and coronary angiography is considered if the value lies between 0.20 and 0.44 (12% 1-year mortality). This relatively simple scheme does not make general recommendations in the elderly, considers patients with in-hospital left ventricular failure or reduced left ventricular function or both, and approaches the problem of patients who do not perform an exercise test. This general approach would avoid early coronary angiography in patients with an average 1-year mortality risk after discharge of 3% and recommend coronary angiography in those at increased risk (average mortality rate, 16%) who make up about 55% of this population under 75 years of age.