gebhart/patrepeval huggingface dataset:
Cloning the Arabidopsis GA1 Locus by Genomic Subtraction (1992)

Arabidopsis thaliana ga l mutants are gibberellin-responsive dwarfs. We used the genomic subtraction technique to clone DNA sequences that are present in wild-type Arabidopsis (ecotype Landsberg erecta, Ler) but are missing in a presumptive g a l deletion mutant, gal-3. The cloned sequences correspond to a 5.0-kb deletion in the gal-3 genome. Three lines of evidence indicated that the 5.0-kb deletion in the gal-3 mutant is located at the GAl locus. First, restriction fragment length polymorphism mapping showed that DNA sequences within the 5.0-kb deletion map to the GAl locus. Second, cosmid clones that contain wild-type DNA inserts spanning the deletion in gal-3 complemented the dwarf phenotype when integrated into the gal-3 genome by Agrobacterium tumefaciens-mediated transformation. Third, we identified molecular lesions in four additional ga l alleles within the 5.0-kb region deleted in mutant gal-3. One of these lesions is a large insertion or inversion located within the most distal intron encoded by the GAl locus. The three other lesions are all single base changes located within the two most distal exons. RNA gel blot analysis indicated that the GAl locus encodes a 2.8-kb mRNA. We calculated a recombination rate of 10-5 cM per nucleotide for the GAl region of the Arabidopsis genome.
Molecular mechanisms of arrhythmias. (1998)

Most arrhythmias occur in patients with structural heart disease, where anatomical factors play an important role. Patients without structural heart disease may also suffer from arrhythmias, and recently the genetic basis for such so-called idiopathic arrhythmias has been elucidated. In the congenital long QT syndrome, characterized by a prolonged QT interval, torsade de pointes and sudden death, three aberrant ionic currents have been identified, resulting in a prolongation of the ventricular action potential, which in its turn may cause early afterdepolarization and torsade de pointes. In LQTS1, mutations in the KvLQT1 gene reduce the slow component of the delayed rectifier Iks; in LQTS, mutations in the Human Ether a-go-go Related Gene (HERG) reduce the rapid component of the delayed rectifier Iks. Both potassium currents are important determinants of repolarization: a reduction in outward currents carried by K+ ions prolongs the action potential. In LQTS3, there are mutation in the NA+ channel gene (SCN5A) which causes the channel to inactivate incompletely; the persistent inward current carried by Na+ ions also prolongs the action potential. In the Brugada syndrome, characterized by right bundle branch block, ST elevation in V1-V3 and sudden death, mutations have been observed in the Na+ channel gene, but it is as yet unclear which functional changes in the NA+ channel are responsible for the typical ECG changes and the arrhythmias. Various cardiac disorders may lead to changes in gene expression that modify channel function. In hypertrophy, the ventricular action potential is prolonged by a decrease in the inward rectifier and the transient outward current. After prolonged episodes of rapid electrical activity, the atrial action potential is shortened, because of a reduction in the Iks type calcium current. Finally, many carriers of mutated genes display no abnormalities on the ECG. It is conceivable that such individuals may show excessive QT prolongation when taking cardiac or noncardiac drugs (such as neuroleptics, antidepressants, antihistamines, antimicrobials, antimalarials) that block potassium currents.
The relationship of plasma glutamine to ammonium and of glycine to acid–base balance in propionic acidaemia (2003)

Hyperammonaemia is a common and serious complication of propionic acidaemia. Treatment of hyperammonaemia with sodium phenylacetate or phenylbutyrate has not been well studied in this disorder. We reviewed the medical records of 5 patients with propionic acidaemia over a 16-year period. We collected information on events where plasma amino acids and ammonium, plasma acids and acid-base balance, or all 3 parameters were obtained simultaneously. All patients were on protein-restricted diet and carnitine throughout the period. In contrast to hyperammonaemia in patients with a urea cycle disorder, plasma glutamine levels were below the normal mean and there was no correlation between plasma ammonium and glutamine levels. The absence of positive correlation between plasma glutamine and ammonium suggests that the routine use of sodium phenylacetate or phenylbutyrate to treat hyperammonaemia in propionic acidaemia should be questioned until further studies are done. Throughout follow-up of our propionic acidaemia patients, we have observed that plasma glycine levels correlated positively with serum bicarbonate. The association of high plasma glycine with good acid-base balance might have a potential role in management and warrants further investigation.
Cooperative Sensing among Cognitive Radios (2006)

Cognitive Radios have been advanced as a technology for the opportunistic use of under-utilized spectrum since they are able to sense the spectrum and use frequency bands if no Primary user is detected. However, the required sensitivity is very demanding since any individual radio might face a deep fade. We propose light-weight cooperation in sensing based on hard decisions to mitigate the sensitivity requirements on individual radios. We show that the "link budget" that system designers have to reserve for fading is a significant function of the required probability of detection. Even a few cooperating users (~10-20) facing independent fades are enough to achieve practical threshold levels by drastically reducing individual detection requirements. Hard decisions perform almost as well as soft decisions in achieving these gains. Cooperative gains in a environment where shadowing is correlated, is limited by the cooperation footprint (area in which users cooperate). In essence, a few independent users are more robust than many correlated users. Unfortunately, cooperative gain is very sensitive to adversarial/failing Cognitive Radios. Radios that fail in a known way (always report the presence/absence of a Primary user) can be compensated for by censoring them. On the other hand, radios that fail in unmodeled ways or may be malicious, introduce a bound on achievable sensitivity reductions. As a rule of thumb, if we believe that 1/N users can fail in an unknown way, then the cooperation gains are limited to what is possible with N trusted users.
Psoralen--long-wave ultraviolet therapy and human cataractogenesis. (1982)

Cataract formation associated with psoralen--long-wave ultraviolet (P-UVA) therapy has been documented in experimental animals. Presumptive P-UVA cataracts in humans have also been reported recently. Cataracts from two patients on P-UVA therapy were subjected to high-resolution phosphorescence spectroscopy. The lens homogenates from these two patients showed phosphorescence peaks identical (in shape and lifetime) with the previously reported 8-methoxypsoralen lens protein photoproduct seen in P-UVA-treated cataractous rat lenses. The data provide objective proof that these phototherapeutic drugs can generate specific P-UVA photoproducts in human lenses. Similar photoproducts have previously been demonstrated in experimental (rat) P-UVA cataracts.
Normal Bone Anatomy and Physiology (2008)

This review describes normal bone anatomy and physiology as an introduction to the subsequent articles in this section that discuss clinical applications of iliac crest bone biopsy. The normal anatomy and functions of the skeleton are reviewed first, followed by a general description of the processes of bone modeling and remodeling. The bone remodeling process regulates the gain and loss of bone mineral density in the adult skeleton and directly influences bone strength. Thorough understanding of the bone remodeling process is critical to appreciation of the value of and interpretation of the results of iliac crest bone histomorphometry. Osteoclast recruitment, activation, and bone resorption is discussed in some detail, followed by a review of osteoblast recruitment and the process of new bone formation. Next, the collagenous and noncollagenous protein components and function of bone extracellular matrix are summarized, followed by a description of the process of mineralization of newly formed bone matrix. The actions of biomechanical forces on bone are sensed by the osteocyte syncytium within bone via the canalicular network and intercellular gap junctions. Finally, concepts regarding bone remodeling, osteoclast and osteoblast function, extracellular matrix, matrix mineralization, and osteocyte function are synthesized in a summary of the currently understood functional determinants of bone strength. This information lays the groundwork for understanding the utility and clinical applications of iliac crest bone biopsy.
Long-range PCR facilitates the identification ofPMS2-specific mutations (2006)

Mutations within the DNA mismatch repair gene, "postmeiotic segregation increased 2" (PMS2), have been associated with a predisposition to hereditary nonpolyposis colorectal cancer (HNPCC; Lynch syndrome). The presence of a large family of highly homologous PMS2 pseudogenes has made previous attempts to sequence PMS2 very difficult. Here, we describe a novel method that utilizes long-range PCR as a way to preferentially amplify PMS2 and not the pseudogenes. A second, exon-specific, amplification from diluted long-range products enables us to obtain a clean sequence that shows no evidence of pseudogene contamination. This method has been used to screen a cohort of patients whose tumors were negative for the PMS2 protein by immunohistochemistry and had not shown any mutations within the MLH1 gene. Sequencing of the PMS2 gene from 30 colorectal and 11 endometrial cancer patients identified 10 novel sequence changes as well as 17 sequence changes that had previously been identified. In total, putative pathologic mutations were detected in 11 of the 41 families. Among these were five novel mutations, c.705+1G>T, c.736_741del6ins11, c.862_863del, c.1688G>T, and c.2007-1G>A. We conclude that PMS2 mutation detection in selected Lynch syndrome and Lynch syndrome-like patients is both feasible and desirable.
Collaboration gets the most out of software (2013)

By centralizing many of the tasks associated with the upkeep of scientific software, SBGrid allows researchers to spend more of their time on research.
Activity of Distamycin A on the Induction of Adaptive Enzymes in Escherichia coli (1966)

SUMMARY We have studied the effect of distamycin A on the synthesis of inducible enzymes in Escherichia coli strain K12. Distamycin A did not inhibit the growth of E. coli K12 when the micro-organism already contained constitutive or inducible enzymes for the metabolism of sugars. The growth of E. coli was prevented when distamycin A was present during the enzymic induction. Distamycin A inhibited the formation of inducible β-galactosidase; the activity of the antibiotic was directly related to its concentration, but independent of the concentration of the inducer. Thus it does not seem that distamycin A causes a decrease of the concentration of inducer. The enzyme synthesized in the presence of subinhibitory concentrations of distamycin A showed the same kinetic behaviour as β-galacto-sidase induced under normal conditions.
2-Methylthioadenosine[beta-32P]diphosphate. An agonist and radioligand for the receptor that inhibits the accumulation of cyclic AMP in intact blood platelets. (1983)

2-Methylthio-ADP and its radioactive analogue [beta-32P]2-methylthio-ADP were synthesized and used to investigate platelet receptors for ADP. 2-Methylthio-ADP induced platelet aggregation and shape change, and inhibited cyclic AMP accumulation in platelets exposed to prostaglandin E1. Compared with ADP, 2-methylthio-ADP was 3-5 times as active as an aggregating agent and 150-200 times as active as an inhibitor of cyclic AMP accumulation. Binding of [beta-32P]2-methylthio-ADP to platelets was measured after centrifuging them through silicone oil to separate platelets from their suspension medium. Binding was reversible, saturable, and specific, with between 400 and 1,200 sites/cell in different platelet preparations. There was no evidence for a second class of binding sites with different affinity. The second order association rate constant was approximately 3.5 X 10(6) M-1 S-1, and the first order dissociation rate was 0.024 s-1, both measured at 23 degrees C. The dissociation equilibrium constant (approximately 15 nM) was about three times higher than the concentration giving half-maximal inhibition of prostaglandin E1-stimulated cyclic AMP accumulation in platelet-rich plasma. Binding was inhibited by ADP (Ki = 3.5 microM), ATP (7 microM), 2-azido-ADP (0.12 microM), inosine diphosphate (IDP, 150 microM), guanosine diphosphate (GDP, 350 microM), and AMP (800 microM). Binding of 2-methylthio-ADP was also blocked by the non-cell-penetrating thiol reagent, p-mercuribenzene sulphonate, a reagent that blocks the inhibition of adenylate cyclase by ADP, but which does not block the ability of ADP to induce aggregation or platelet shape change. The amount of 2-methylthio-ADP bound at saturation was independent of pH in the range 6-8, but the affinity was reduced at pH 6 compared with pH 6.5-8.0. The dissociation constant was not temperature dependent in the range 32 degrees -40 degrees C, whereas the rate of dissociation of 2-methylthio-ADP from platelets after the addition of an excess of ADP approximately doubled over this range. The activation energy for dissociation was approximately 15 kcal/mol. Our results support the conclusion that platelets have a receptor for ADP, which inhibits cyclic AMP accumulation, and which has a sulphydryl group in the binding pocket.
A reverse electrochemical floating-layer technique of SPM tip preparation (2000)

An experimental set-up involving a combination of reverse electrochemical etching and the floating-layer technique of tip preparation is presented. In the model only dc bias is used, avoiding the shortcomings of ac bias. The collection of two tips in a single etching process and mechanical auto-breaking of the circuit are emphasized. This cost and time effective, easy in-laboratory approach yields two sharp tips without paying attention to switching off the circuit. The nature of the tip shape arising from the floating-layer technique has been explained in terms of the electrical field distribution between the electrodes. The addition of some new information together with a few established facts will enrich and enlighten the art of tip preparation.
RNAdb--a comprehensive mammalian noncoding RNA database (2004)

In recent years, there have been increasing numbers of transcripts identified that do not encode proteins, many of which are developmentally regulated and appear to have regulatory functions. Here, we describe the construction of a comprehensive mammalian noncoding RNA database (RNAdb) which contains over 800 unique experimentally studied non-coding RNAs (ncRNAs), including many associated with diseases and/or developmental processes. The database is available at http://research.imb.uq.edu.au/RNAdb and is searchable by many criteria. It includes microRNAs and snoRNAs, but not infrastructural RNAs, such as rRNAs and tRNAs, which are catalogued elsewhere. The database also includes over 1100 putative antisense ncRNAs and almost 20,000 putative ncRNAs identified in high-quality murine and human cDNA libraries, with more to be added in the near future. Many of these RNAs are large, and many are spliced, some alternatively. The database will be useful as a foundation for the emerging field of RNomics and the characterization of the roles of ncRNAs in mammalian gene expression and regulation.
The transcriptional response of Pasteurella multocida to three classes of antibiotics (2009)

This is the first report of the transcriptional response of an avian strain of P. multocida to sub-lethal concentrations of three different classes of antibiotics. We identified common adaptive responses of P. multocida to antibiotic stress. The observed changes in gene expression of known and putative P. multocida virulence factors establish the molecular basis for the therapeutic efficacy of sub-MICs. Our network analysis demonstrates the feasibility and limitations of applying systems modeling to high throughput datasets in 'non-model' bacteria.
Algorithm and implementation of the K-best sphere decoding for MIMO detection (2006)

K-best Schnorr-Euchner (KSE) decoding algorithm is proposed in this paper to approach near-maximum-likelihood (ML) performance for multiple-input-multiple-output (MIMO) detection. As a low complexity MIMO decoding algorithm, the KSE is shown to be suitable for very large scale integration (VLSI) implementations and be capable of supporting soft outputs. Modified KSE (MKSE) decoding algorithm is further proposed to improve the performance of the soft-output KSE with minor modifications. Moreover, a VLSI architecture is proposed for both algorithms. There are several low complexity and low-power features incorporated in the proposed algorithms and the VLSI architecture. The proposed hard-output KSE decoder and the soft-output MKSE decoder is implemented for 4/spl times/4 16-quadrature amplitude modulation (QAM) MIMO detection in a 0.35-/spl mu/m and a 0.13-/spl mu/m CMOS technology, respectively. The implemented hard-output KSE chip core is 5.76 mm/sup 2/ with 91 K gates. The KSE decoding throughput is up to 53.3 Mb/s with a core power consumption of 626 mW at 100 MHz clock frequency and 2.8 V supply. The implemented soft-output MKSE chip can achieve a decoding throughput of more than 100 Mb/s with a 0.56 mm/sup 2/ core area and 97 K gates. The implementation results show that it is feasible to achieve near-ML performance and high detection throughput for a 4/spl times/4 16-QAM MIMO system using the proposed algorithms and the VLSI architecture with reasonable complexity.
ApoA1 Reduces Free Cholesterol Accumulation in Atherosclerotic Lesions of ApoE–Deficient Mice Transplanted With ApoE–Expressing Macrophages (1999)

Along with apolipoprotein (apo) E, which promotes cholesterol efflux from foam cells, apoA1-containing high density lipoprotein (HDL) is thought to facilitate the transport of cholesterol from lesions. This role for apoA1 was tested in vivo by lethally irradiating apoE-deficient and apoE- plus apoA1-deficient mice and reconstituting them with bone marrow cells isolated from wild-type (WT) mice. ApoE, but not apoA1, was synthesized by the transplanted bone marrow-derived cells. Therefore, this transplantation procedure generated apoE-deficient animals with atherosclerotic lesions that contained both apoE and apoA1 (E/A1 mice) and apoE-deficient animals with lesions that contained apoE but no apoA1 (E/A1o mice). As shown previously, the transplanted WT macrophage-derived apoE dramatically lowered the plasma hypercholesterolemia in both groups. On feeding with an atherogenic diet after transplantation, plasma cholesterol levels were raised in both groups of mice, but the levels in the E/A1 mice at 20 weeks were 2- to 3-fold higher than in E/A1o mice. Immunohistochemical staining verified that apoE was abundant in lesions of both groups, whereas apoA1 was detected in the lesions of E/A1 mice only. Despite a 2- to 3-fold lower total plasma cholesterol in the E/A1o mice, the free cholesterol recovered from isolated aortas was approximately 60% higher and the mean lesion area in serial sections of the aortic valves 45% larger. Therefore, apoA1 reduces free cholesterol accumulation in vivo in atherosclerotic lesions.
Innovating to Meet the Demand for Streaming Video (2013)

NJVID, New Jerseyâs statewide digital video portal and repository, was created to provide a sustainable, flexible, and scalable digital video management and delivery infrastructure to serve all educational and cultural heritage institutions in New Jersey. This article describes its implementation and demonstrates the benefits of collaboration to make video more accessible.
Processing and characterization of absorbable polylactide polymers for use in surgical implants (1994)

Absorbable fibers of linear poly-alpha-hydroxy acids have been used successfully in providing temporary scaffolds for tissue regeneration. In some surgical applications, degradation rates for poly(glycolide) (PGA) are too high, but implants of poly(L-lactide) (PLLA) fibers may degrade too slowly for optimal function. Polymers produced by copolymerization of L-lactide with varying amounts of D-lactide may offer an alternative choice for absorbable fiber based implants. Poly(L/D-lactide) stereocopolymers with L/D lactide molar ratios of 95/5, 90/10, and 85/15 were considered. Melt-spun/hot-drawn fibers with L/D molar ratios of 90/10 and 85/15 and draw ratios ranging from 3.0 to 8.9 were further evaluated by mechanical testing, differential scanning calorimetry, birefringence, x-ray diffraction, and in vitro exposure to pH 7.4 phosphate buffered saline at 37 degrees C. Fabrication was reproducible and results indicated that tensile strength, modulus, an birefringence all increased with increasing draw ratio up to a draw ratio of 6.7 and declined thereafter; elongation to failure decreased for the entire range studied. For fibers with a draw ratio of 6.7, there was a 10% relative difference in crystallinity between the 90/10 and 85/15 lactide fibers (90/10 was higher). Wet strength retention after 12 weeks in vitro exposure was approximately 10% for the 90/10 fibers and 30% for the 85/15 fibers. The intermediate wet strength retention of lactide stereocopolymer fibers when compared to reported values for PGA and PLLA fibers, suggests these materials may be useful in absorbable surgical implants for tissue repair and regeneration.
The A ddition o f I nterleukin-6 S oluble R eceptor a nd Transforming G rowth F actor B eta 1 Improves a P reoperative Nomogram f or P redicting B iochemical P rogression i n P atients With C linically L ocalized P rostate C ancer (2003)

Purpose: Several preoperative prostate cancer nomograms have been developed that predict risk of progression using pretreatment prostate-specific antigen (PSA) level, clinical stage, and biopsy Gleason grade. We describe the development and performance of a new nomogram. The nomogram adds new markers to the standard clinical predictors that reflect the biologic behavior of prostate cancer: pretreatment plasma levels of interleukin-6 soluble receptor (IL6SR) and transforming growth factor beta1 (TGF-1). Patients and Methods: Between November 7, 1994 and December 22, 1997, 714 patients with stage cT1c to cT3a prostate cancer and no prior therapy were treated with radical prostatectomy at the Methodist Hospital, Houston TX. Plasma levels of IL6SR and TGF-1 were measured in banked preoperative plasma. With these data, a nomogram was developed to predict the probability of PSA progression within 5 years of surgery. The nomogram was validated with bootstrapping to assess its discrimination and calibration performance. Results: In the multivariable Cox model, PSA (P .004), IL6SR (P < .001), TGF-1 (P < .001), primary Gleason grade (P < .002), and secondary Gleason grade (P .029) were associated with PSA progression, whereas clinical stage (P .696) was not. The nomogram seemed to be well calibrated and had a bootstrap-corrected area under the receiver operating characteristic curve (ie, concordance index) of 0.83. For comparison, a nomogram that omitted IL6SR and TGF-1 achieved a concordance index of only 0.75. Conclusion: We found that pretreatment plasma levels of IL6SR and TGF-1 improved the ability to predict biochemical progression by a prognostically substantial margin. A nomogram including the pretreatment levels of these molecular markers, along with standard clinical markers, has been developed and internally validated. J Clin Oncol 21:3573-3579. © 2003 by American Society of Clinical Oncology.