gebhart/patrepeval huggingface dataset:
The Long-term Consequence of Anterior Cruciate Ligament and Meniscus Injuries (2007)

The objectives of this study are to review the long-term consequences of injuries to the anterior cruciate ligament and menisci, the pathogenic mechanisms, and the causes of the considerable variability in outcome. Injuries of the anterior cruciate ligament and menisci are common in both athletes and the general population. At 10 to 20 years after the diagnosis, on average, 50% of those with a diagnosed anterior cruciate ligament or meniscus tear have osteoarthritis with associated pain and functional impairment: the young patient with an old knee. These individuals make up a substantial proportion of the overall osteoarthritis population. There is a lack of evidence to support a protective role of repair or reconstructive surgery of the anterior cruciate ligament or meniscus against osteoarthritis development. A consistent finding in a review of the literature is the often poor reporting of critical study variables, precluding data pooling or a meta-analysis. Osteoarthritis development in the injured joints is caused by intra-articular pathogenic processes initiated at the time of injury, combined with long-term changes in dynamic joint loading. Variation in outcome is reinforced by additional variables associated with the individual such as age, sex, genetics, obesity, muscle strength, activity, and reinjury. A better understanding of these variables may improve future prevention and treatment strategies. In evaluating medical treatment, we now expect large randomized clinical trials complemented by postmarketing monitoring. We should strive toward a comparable level of quality of evidence in surgical treatment of knee injuries. In instances in which a randomized clinical trial is not feasible, natural history and other observational cohort studies need to be as carefully designed and reported as the classic randomized clinical trial, to yield useful information.
The Directory of P450-containing Systems in 1996 (1997)

The Directory of P450-containing Systems on WorldWide Web has been designed to facilitate access to electronic resources for all researchers working in the field of P450-containing and related enzyme systems. Currently, it contains the most up-to-date list of sequences of both the P450 superfamily and proteins mediating electron transfer to P450, i.e. NADPH:P450 reductases, specific NAD(P)H:ferredoxin reductases, cytochromeb5 reductases, ferredoxins and cytochromesb5, and their homologues. All the referenced sequences are provided with accession numbers and links to major sequence databanks: PIR, SWISS-PROT, EMBL/GenBank and PRF. An associated database of steroid substrates and products of P450-dependent reactions has also been developed.
Emitter-coupled spin-transistor logic (2012)

The recent invention of magnetoresistive bipolar spin-transistors makes possible the creation of new spintronic logic families. Here we propose the first logic family exploiting these spin-transistors, extending emitter-coupled logic (ECL) to achieve a greater range of basis logic functions. By placing the wire from the output stage of ECL logic elements near spin-transistors in other parts of a circuit, additional basis logic elements can be realized. These new logic elements support greater logic minimization, resulting in enhanced speed, area, and power characteristics. A novel magnetic shielding structure provides this logic family with the crucial ability to cascade logic stages. This logic family achieves a power-delay product 10 to 25 times smaller than conventional ECL, and can therefore be exploited to increase the performance of very high-speed circuits while broadening the range of design choices for a variety of electronic applications.
Bulk production of singly dispersed carbon nanotubes with prescribed lengths (2005)

The length of carbon nanotubes has a dramatic impact on their electron transport properties. Transport through short (<300 nm) nanotubes is free of acoustic phonon scattering and thus favours ballistic transport, which is highly desirable for memory and logic devices. Production of uniformly short and pristine nanotubes can lead to high-performance nanotube electronics. We have modified the lithography-based technique for cutting nanostructures to efficiently produce solutions of individual nanotubes with average lengths as small as 50 nm. The formation of uniform aqueous films of singly dispersed nanotubes flanked by top and bottom silicon dioxide layers on patternable substrates allows protection of the sidewalls of the nanotubes. Upon plasma etching the cut nanotubes are recovered by water rinsing of the substrates. This method does not alter the optical absorption of the nanotubes, indicating the preservation of their intrinsic properties. This technology offers an affordable alternative to produce bulk quantities of short, singly dispersed and pristine nanotubes for a vast number of applications other than nanoelectronics.
ServerSwitch: A Programmable and High Performance Platform for Data Center Networks (Best Paper Award) (2011)

As one of the fundamental infrastructures for cloud computing, data center networks (DCN) have recently been studied extensively. We currently use pure software-based systems, FPGA based platforms, e.g., NetFPGA, or OpenFlow switches, to implement and evaluate various DCN designs including topology design, control plane and routing, and congestion control. However, software-based approaches suffer from high CPU overhead and processing latency; FPGA based platforms are difficult to program and incur high cost; and OpenFlow focuses on control plane functions at present. In this paper, we design a ServerSwitch to address the above problems. ServerSwitch is motivated by the observation that commodity Ethernet switching chips are becoming programmable and that the PCI-E interface provides high throughput and low latency between the server CPU and I/O subsystem. ServerSwitch uses a commodity switching chip for various customized packet forwarding, and leverages the server CPU for control and data plane packet processing, due to the low latency and high throughput between the switching chip and server CPU. We have built our ServerSwitch at low cost. Our experiments demonstrate that ServerSwitch is fully programmable and achieves high performance. Specifically, we have implemented various forwarding schemes including source routing in hardware. Our in-network caching experiment showed high throughput and flexible data processing. Our QCN (Quantized Congestion Notification) implementation further demonstrated that ServerSwitch can react to network congestions in 23us.
Primary structure of CTP:CMP-3-deoxy-D-manno-octulosonate cytidylyltransferase (CMP-KDO synthetase) from Escherichia coli. (1986)

The gene coding for CTP:CMP-3-deoxy-D-mannooctulosonate cytidylyltransferase (CMP-KDO synthetase), kds B, was previously cloned on a 9-kilobase Pst insert of Escherichia coli DNA into pBR 322 (Goldman, R. C., and Kohlbrenner, W. E. (1985) J. Bacteriol. 163, 256-261). Using a transposon mutagenesis approach we have now located kds B on this insert, which facilitated the isolation and sequencing of a 1.3-kilobase segment of DNA containing kds B and putative RNA polymerase and ribosome binding sites. The primary structure of CMP-KDO synthetase predicted by this nucleotide sequence was verified by amino acid composition and sequence analysis of purified CMP-KDO synthetase and cleavage fragments. Our results show that kds B consists of a 744-base open reading frame coding for a 248-amino acid peptide. The molecular weight of CMP-KDO synthetase calculated from the translated sequence is 27,486, taking into account the loss of the N-terminal methionine. These data define the transcriptional unit of kds B and its translation product in molecular terms, information prerequisite to our understanding of both the mechanism of CMP-KDO formation and the regulation of the KDO metabolic pathway in Gram-negative bacteria.
Transformation of Saccharomyces cerevisiae and other fungi (2010)

Transformation (i.e., genetic modification of a cell by the incorporation of exogenous DNA) is indispensable for manipulating fungi. Here, we review the transformation methods for Saccharomyces cerevisiae, Schizosaccharomyces pombe, Candida albicans, Pichia pastoris and Aspergillus species and discuss some common modifications to improve transformation efficiency. We also present a model of the mechanism underlying S. cerevisiae transformation, based on recent reports and the mechanism of transfection in mammalian systems. This model predicts that DNA attaches to the cell wall and enters the cell via endocytotic membrane invagination, although how DNA reaches the nucleus is unknown. Polyethylene glycol is indispensable for successful transformation of intact cells and the attachment of DNA and also possibly acts on the membrane to increase the transformation efficiency. Both lithium acetate and heat shock, which enhance the transformation efficiency of intact cells but not that of spheroplasts, probably help DNA to pass through the cell wall.
ABC of oral bioavailability: transporters as gatekeepers in the gut (2003)

MDR1 (ABCB1), MRP2 (ABCC2), and BCRP (ABCG2) are members of the family of ATP binding cassette (ABC) transporters. These are plasma membrane transporters that are expressed in various organs. The role of MDR1 and MRP2 in the hepatobiliary system is well defined; both contribute to bile formation by transport of drugs, toxins, and waste products across the canalicular membrane. As they transport exogenous and endogenous substances, they reduce the body load of potentially harmful compounds. The role of ABCG2, which is also expressed in the canalicular membrane of hepatocytes, has not yet been fully characterised. All three proteins are also expressed in the apical membrane of enterocytes where they probably control oral availability of many substances. This important "gatekeeper" function of ABC transporters has been recognised recently and is currently under further investigation. Expression and activity of these transporters in the gut may differ between individuals, due to genetic polymorphisms or pathological conditions. This will lead to individual differences in bioavailability of different drugs, toxins, and (food derived) carcinogens. Recent information on substrates, transport mechanisms, function, and regulation of expression of MDR1, MRP2, and BCRP in different species is summarised in this review.
Neuropoietic cytokines and activin A differentially regulate the phenotype of cultured sympathetic neurons. (1994)

A number of cytokines sharing limited sequence homology have been grouped as a family because of partially overlapping biological activities, receptor subunit promiscuity, and the prediction of a shared secondary structure. Since several of these cytokines regulate gene expression and cell number in the nervous and hematopoietic systems, this specific group is termed the neuropoietic cytokine family. Using a reverse transcription-polymerase chain reaction-based assay system for monitoring the expression of multiple phenotypic markers in cultured sympathetic neurons, we present further evidence that, in addition to cholinergic differentiation factor/leukemia inhibitory factor and ciliary neurotrophic factor, oncostatin M, growth promoting activity, interleukin 6, and interleukin 11 belong in this family. In addition, one member of the transforming growth factor beta superfamily, activin A, shares a selective overlap with the neuropoietic family in the spectrum of neuropeptides that it induces in sympathetic neurons. The particular neuropeptides induced by activin A, however, demonstrate that the activity of this cytokine is distinct from that of the neuropoietic family. Twenty-six other cytokines and growth factors were without detectable activity in this assay.
Effect of dairy manure and sewage sludge on 14C-pesticide degradation in soil (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTEffect of dairy manure and sewage sludge on 14C-pesticide degradation in soilRichard C. Doyle, Donald D. Kaufman, and Gordon W. BurtCite this: J. Agric. Food Chem. 1978, 26, 4, 987–989Publication Date (Print):July 1, 1978Publication History Published online1 May 2002Published inissue 1 July 1978https://pubs.acs.org/doi/10.1021/jf60218a008https://doi.org/10.1021/jf60218a008research-articleACS PublicationsRequest reuse permissionsArticle Views181Altmetric-Citations52LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Expression of Active Human Tissue-Type Plasminogen Activator inEscherichia coli (1998)

The formation of native disulfide bonds in complex eukaryotic proteins expressed in Escherichia coli is extremely inefficient. Tissue plasminogen activator (tPA) is a very important thrombolytic agent with 17 disulfides, and despite numerous attempts, its expression in an active form in bacteria has not been reported. To achieve the production of active tPA in E. coli, we have investigated the effect of cooverexpressing native (DsbA and DsbC) or heterologous (rat and yeast protein disulfide isomerases) cysteine oxidoreductases in the bacterial periplasm. Coexpression of DsbC, an enzyme which catalyzes disulfide bond isomerization in the periplasm, was found to dramatically increase the formation of active tPA both in shake flasks and in fermentors. The active protein was purified with an overall yield of 25% by using three affinity steps with, in sequence, lysine-Sepharose, immobilized Erythrina caffra inhibitor, and Zn-Sepharose resins. After purification, approximately 180 microgram of tPA with a specific activity nearly identical to that of the authentic protein can be obtained per liter of culture in a high-cell-density fermentation. Thus, heterologous proteins as complex as tPA may be produced in an active form in bacteria in amounts suitable for structure-function studies. In addition, these results suggest the feasibility of commercial production of extremely complex proteins in E. coli without the need for in vitro refolding.
Expression and localization of hepatobiliary transport proteins in progressive familial intrahepatic cholestasis† (2005)

Mutations of the bile salt export pump (BSEP) or the multidrug resistance P-glycoprotein 3 (MDR3) are linked to impaired bile salt homeostasis and lead to progressive familial intrahepatic cholestasis (PFIC)-2 and -3, respectively. The regulation of bile salt transporters in PFIC is not known. Expression of hepatobiliary transporters in livers of ten patients with a PFIC phenotype was studied by quantitative reverse transcription polymerase chain reaction, Western blotting, and immunofluorescence microscopy. PFIC was diagnosed by clinical and laboratory findings. All patients could be assigned to PFIC-2 or PFIC-3 by the use of BSEP- and MDR3-specific antibodies and by MDR3 gene-sequencing. Whereas in all PFIC-2 patients, BSEP immunoreactivity was absent from the canalicular membrane, in three PFIC-3 livers, canalicular MDR3 immunoreactivity was detectable. Serum bile salts were elevated to 276 +/- 233 and to 221 +/- 109 micromol/L in PFIC-2 and PFIC-3, respectively. Organic anion transporting polypeptide OATP1B1, OATP1B3, and MRP2 mRNA and protein levels were reduced, whereas sodium taurocholate cotransporting polypeptide (NTCP) was only reduced at the protein level, suggesting a posttranscriptional NTCP regulation. Whereas MRP3 mRNA and protein were not significantly altered, MRP4 messenger RNA and protein were significantly increased in PFIC. In conclusion, PFIC-2 may be reliably diagnosed by immunofluorescence, whereas the diagnosis of PFIC-3 requires gene-sequencing. Several mechanisms may contribute to elevated plasma bile salts in PFIC: reduced bile salt uptake via NTCP, OATP1B1, and OATP1B3, decreased BSEP-dependent secretion into bile, and increased transport back into plasma by MRP4. Upregulation of MRP4, but not of MRP3, might represent an important escape mechanism for bile salt extrusion in PFIC.
Using Digital RNA Counting and Flow Cytometry to Compare mRNA with Protein Expression in Acute Leukemias (2012)

The nCounter technology allows for fast and easy depiction of a mRNA profile from hematologic samples. This technology has the potential to become a valuable tool for the diagnosis of acute leukemias, in addition to multi-color flow cytometry.
cDNA Cloning of an orphan opiate receptor gene family member and its splice variant (1994)

Radioligand binding and cDNA homology studies have suggested the existence of opiate receptors distinct from the recently-cloned mu, delta and kappa receptors. XOR1S, a rat brain cDNA whose predicted translation product displays 67-72% homology with those encoded by mu 1, delta 1 and kappa 1 opiate receptor cDNAs, was constructed from two partial cDNAs identified through cDNA homology approaches. A longer XOR1L variant of this cDNA was also identified by polymerase chain reaction studies using genomic DNA and cDNA from brain and peripheral tissues. XOR1 mRNA is most highly expressed in hypothalamus. COS cell expression of both clones confers neither robust binding of opiate ligands nor reproducible opiate inhibition of forskolin-stimulated adenylate cyclase. These studies identify an orphan clone that helps to define features of the opiate receptor gene family, including apparent differential splicing and expression in peripheral tissues.
Common alleles in candidate susceptibility genes associated with risk and development of epithelial ovarian cancer (2010)

Common germline genetic variation in the population is associated with susceptibility to epithelial ovarian cancer. Microcell-mediated chromosome transfer and expression microarray analysis identified nine genes associated with functional suppression of tumorogenicity in ovarian cancer cell lines; AIFM2, AKTIP, AXIN2, CASP5, FILIP1L, RBBP8, RGC32, RUVBL1 and STAG3. Sixty-three tagging single nucleotide polymorphisms (tSNPs) in these genes were genotyped in 1,799 invasive ovarian cancer cases and 3,045 controls to look for associations with disease risk. Two SNPs in RUVBL1, rs13063604 and rs7650365, were associated with increased risk of serous ovarian cancer [HetOR = 1.42 (1.15-1.74) and the HomOR = 1.63 (1.10-1.42), p-trend = 0.0002] and [HetOR = 0.97 (0.80-1.17), HomOR = 0.74 (0.58-0.93), p-trend = 0.009], respectively. We genotyped rs13063604 and rs7650365 in an additional 4,590 cases and 6,031 controls from ten sites from the United States, Europe and Australia; however, neither SNP was significant in Stage 2. We also evaluated the potential role of tSNPs in these nine genes in ovarian cancer development by testing for allele-specific loss of heterozygosity (LOH) in 286 primary ovarian tumours. We found frequent LOH for tSNPs in AXIN2, AKTIP and RGC32 (64, 46 and 34%, respectively) and one SNP, rs1637001, in STAG3 showed significant allele-specific LOH with loss of the common allele in 94% of informative tumours (p = 0.015). Array comparative genomic hybridisation indicated that this nonrandom allelic imbalance was due to amplification of the rare allele. In conclusion, we show evidence for the involvement of a common allele of STAG3 in the development of epithelial ovarian cancer.
Efficient Solid-State Photoluminescence in New Poly(2,5-dialkoxy-p-phenyleneethynylene)s (1996)

A series of novel poly(2,5-dialkoxy-p-phenyleneethynylene)s (PPEs) has been prepared by the palladium-catalyzed cross-coupling polycondensaton of aryl acetylenes and aryl iodides. Different alkoxy side chains including n-hexadecyloxy, n-octyloxy, (2-ethylhexyl)oxy, (2-methylpropyl)oxy, (3-(dimethylamino)propyl)oxy, and (7-carboxyheptyl)oxy groups were attached to the rigid-rod polymer main chain. With this structural concept, polymers having an identical conjugated backbone but different supramolecular structures in the solid state could be achieved. X-ray diffraction measurements on thin films show that the polymers which have sterically hindered side chains are essentially disordered, while those with only linear side chains can form lamellar structures with significant degrees of long-range order. High photoluminescence (PL) quantum yields, up to 0.86 in solution and 0.36 in the solid state, have been measured for the new materials. While the solution quantum yields are independent of the functionalization, solid-state quantum efficiencies were found to be related to the degree of long-range order in the samples, decreasing with increasing order. The coplanar orientation of the conjugated polymer backbones is assumed to lead to the formation of excimer complexes which provide nonemissive decay channels for the excited states. These nonemissive orientations are more significant in the materials having a greater degree of long-range order.
Comparison between ac and dc current annealing in CoFeSiB glass-covered amorphous microwires (2007)

In this work, we present a study on the magnetic properties of Joule-heated CoFeSiB glass-covered amorphous microwires under applied stress. A comparison between the magnetic properties of four samples is made: (i) as cast, Joule-heated under (ii) dc current or ac current of (iii) 100 Hz or (iv) 500 Hz. The stress modifies the anisotropy and the domain structure in such a way that it can be studied through magnetoimpedance measurements and ferromagnetic resonance (FMR) dispersion relations (DR) extracted from them. From the fitting of the FMR DR, the magnitude and the orientation of the transverse anisotropy field, as well as an insight into the micromagnetic structure of the microwires were obtained. It was concluded that longitudinal anisotropy dominates the microwire behaviour under zero stress. By applying an increasing stress to the microwires, the inner core with longitudinal anisotropy is surrounded by two concentric outer shells with almost circumferential anisotropies. These magnetic configurations can be explained in terms of the residual stress arising from the wire's manufacturing procedure and the additional applied stress.
Complement Regulatory Proteins (2001)

Abstract Complement regulatory proteins are plasma and cell membrane molecules that regulate complement activation and protect host cells against complement damage. Certain diseases, such as hereditary angio‐oedema, membranoproliferative glomerulonephritis and paroxysmal nocturnal haemoglobinuria, are caused by complement regulator deficiency.