gebhart/patrepeval huggingface dataset:
Potential factors impacting season-long expression of Cry1Ac in 13 commercial varieties of Bollgard® cotton (2001)

A yellow-eyed mutant was discovered in a strain of Heliothis virescens, the tobacco budworm, that already exhibited a mutation for yellow scale, y. We investigated the inheritance of these visible mutations as candidate markers for transgenesis. Yellow eye was controlled by a single, recessive, autosomal factor, the same type of inheritance previously known for y. Presence of the recombinant mutants with yellow scales and wild type eyes in test crosses indicated independent segregation of genes for these traits. The recombinant class with wild type scales and yellow eyes was completely absent and there was a corresponding increase of the double mutant parental class having yellow scales and yellow eyes. These results indicated that a single factor for yellow eye also controlled yellow scales independently of y. This gene was named yes, for yellow eye and scale. We hypothesize that yes controls both eye and scale color through a deficiency in transport of pigment precursors in both the ommochrome and melanin pathways. The unlinked gene y likely controls an enzyme affecting the melanin pathway only. Both y and yes segregated independently of AceIn, acetylcholinesterase insensitivity, and sodium channel hscp, which are genes related to insecticide resistance.
Neuropsychological sequelae of diffuse traumatic brain injury (2004)

DAI leads to neuropsychological impairment dominated by executive and memory dysfunction.
The Phenomenon of Reoxygenation and Its Implications for Fractionated Radiotherapy (1972)

The radiobiological oxygen effect is critical in radiotherapy, as all experimental tumors that have been tested contain large proportions (approximately 1–50%) of severely hypoxic cells, and many human tumors are partially hypoxic on histopathological grounds. In designing fractionated dose regimens, it is essential to recognize the special importance of the reoxygenation of preferentially surviving hypoxic cells. Most animal tumors have been shown to reoxygenate rapidly enough that the hypoxic fraction is restored to the preirradiated level within approximately 24 hours. Different tumors may reoxygenate at different rates. It is presently impossible to identify the mechanism(s) responsible for reoxygenation.
Reaction Kinetics of Amino Acid Decomposition in High-Temperature and High-Pressure Water (2004)

Decomposition behavior of five selected amino acids in high-temperature and high-pressure water was studied using a continuous-flow tubular reactor. The reaction was carried out in the temperature range of 200−340 °C at a pressure of 20 MPa. Alanine and its derivatives leucine, phenylalanine, serine, and aspartic acid were used as model amino acids. The effect of temperature on reaction products, pathway, and rate was determined as a function of reaction time. Alanine decomposed into lactic acid and pyruvic acid, then finally mineralized to carbon dioxide with an activation energy of 154 [kJ/mol] at 20 MPa. The degradation rate decreased in the following order: aspartic acid, serine, phenylalanine, leucine, and alanine. The general reaction network of amino acids under hydrothermal conditions takes two main paths: deamination to produce ammonia and organic acids, and decarboxylation to produce carbonic acid and amines. Deamination was the predominant reaction in the decomposition of aspartic acid, an acidic amino acid. Production of glycine and alanine from serine, an oxy amino acid, was also observed.
Chemical modification of Ce(IV)/EDTA-based artificial restriction DNA cutter for versatile manipulation of double-stranded DNA (2007)

A monophosphate group was attached to the terminus of pseudo-complementary peptide nucleic acid (pcPNA), and two of thus modified pcPNAs were combined with Ce(IV)/EDTA for site-selective hydrolysis of double-stranded DNA. The site-selective DNA scission was notably accelerated by this chemical modification of pcPNAs. These second-generation artificial restriction DNA cutters (ARCUTs) differentiated the target sequence so strictly that no scission occurred even when only one DNA base-pair was altered to another. By using two of the activated ARCUTs simultaneously, DNA substrate was selectively cut at two predetermined sites, and the desired fragment was clipped and cloned. The DNA scission by ARCUT was also successful even when the target site was methylated by methyltransferase and protected from the corresponding restriction enzyme. Furthermore, potentiality of ARCUT for manipulation of huge DNA has been substantiated by site-selective scission of genomic DNA of Escherichia coli (composed of 4,600,000 bp) at the target site. All these results indicate promising applications of ARCUTs for versatile purposes.
Treatment of Human B-Cell Precursor Leukemia in SCID Mice by Using a Combination of the Anti-CD19 Immunotoxin B43-PAP with the Standard Chemotherapeutic Drugs Vincristine, Methylprednisolone, and L-Asparaginase (1998)

We have compared the antileukemic activity of the investigational biotherapeutic agent B43-PAP to the antileukemic activities of the standard chemotherapeutic drugs vincristine (VCR), methylprednisolone (PDN), L-asparaginase (L-ASP) as single agents as well as in a 3-drug combination regimen ("VPL") using a SCID mouse model of human B-cell precursor (BCP) acute lymphoblastic leukemia (ALL). When mice (N = 95) were challenged with 1 x 10(6) NALM-6 leukemia cells, all of them died of disseminated leukemia with a median event-free survival (EFS) of 47 +/- 6 days. B43-PAP was more active than VCR, PDN, or L-ASP and the two-drug combinations VCR + B43-PAP, PDN + B43-PAP, or L-ASP + B43-PAP were not significantly more active than B43-PAP. The 120 days EFS outcome results were 46 +/- 13% for B43-PAP (Median EFS = 92 +/- 22 days), 0 +/- 0% for VCR (Median EFS = 49 +/- 1 days), 40 +/- 22% for PDN (Median EFS = 100 +/- 20 days), 0 +/- 0% for L-ASP (Median EFS = 41 +/- 1 days), 60 +/- 22% for VCR + B43-PAP (Median EFS = >120 days), 60 +/- 22% for PDN + B43-PAP (Median EFS = >120 days), and 50 +/- 25% for L-ASP + B43-PAP (Median EFS = 93 +/- 27 days), When mice (N = 61) were challenged with 5 x 10(6) NALM-6 cells, all of them rapidly died of disseminated leukemia with a median EFS of 37 +/- 3 days. The 3-drug combination "VPL" (Median EFS = 75 +/- 23 days) was slightly less active than B43-PAP (Median EFS = 84 +/- 19 days) (P = 0.09). Notably, the combination of "VPL" with B43-PAP (i.e., VPLB) resulted in 100% survival. By comparison, the combination of "VPL" with daunorubicin (i.e., VPLD) (Median EFS = 69 +/- 31 days) was not more active than VPL. To our knowledge, this preclinical study is the first to demonstrate the feasibility and superb antileukemic activity of immunochemotherapy using anti-CD19 immunotoxin in combination with the standard 3-drug combination "VPL" against BCP ALL.
Repair of Mybpc3 mRNA by 5′-trans-splicing in a Mouse Model of Hypertrophic Cardiomyopathy (2013)

RNA trans-splicing has been explored as a therapeutic option for a variety of genetic diseases, but not for cardiac genetic disease. Hypertrophic cardiomyopathy (HCM) is an autosomal-dominant disease, characterized by left ventricular hypertrophy (LVH) and diastolic dysfunction. MYBPC3, encoding cardiac myosin-binding protein C (cMyBP-C) is frequently mutated. We evaluated the 5'-trans-splicing strategy in a mouse model of HCM carrying a Mybpc3 mutation. 5'-trans-splicing was induced between two independently transcribed molecules, the mutant endogenous Mypbc3 pre-mRNA and an engineered pre-trans-splicing molecule (PTM) carrying a FLAG-tagged wild-type (WT) Mybpc3 cDNA sequence. PTMs were packaged into adeno-associated virus (AAV) for transduction of cultured cardiac myocytes and the heart in vivo. Full-length repaired Mybpc3 mRNA represented up to 66% of total Mybpc3 transcripts in cardiac myocytes and 0.14% in the heart. Repaired cMyBP-C protein was detected by immunoprecipitation in cells and in vivo and exhibited correct incorporation into the sarcomere in cardiac myocytes. This study provides (i) the first evidence of successful 5'-trans-splicing in vivo and (ii) proof-of-concept of mRNA repair in the most prevalent cardiac genetic disease. Since current therapeutic options for HCM only alleviate symptoms, these findings open new horizons for causal therapy of the severe forms of the disease.Molecular Therapy-Nucleic Acids (2013) 2, e102; doi:10.1038/mtna.2013.31; published online 2 July 2013.
Cell surface receptors for picornaviruses (1986)

Abstract Picornaviruses can be divided into at least six receptor families based on results of competition binding and receptor antibody studies. It has been proposed that a canyon present within the virion capsid harbors the viral attachment site for this group of viruses. Cell surface proteins involved in viral attachment have been identified for both rhinoviruses and coxsackie B viruses. Several monoclonal antibodies have been isolated which specifically block the binding of some picornaviruses.
Antibodies specific for VB8 receptor peptide suppress experimental autoimmune encephalomyelitis. (1990)

Recent studies from our laboratory have shown, for the first time, that a synthetic peptide from that TCR VB chain used preferentially by encephalitogenic T cells induced the formation of protective, MHC class I-restricted T cells and prevented the development of EAE in Lewis rats. In this report we 1) demonstrate that immunization with the TCR-VB8-39-59 peptide generated peptide-specific antibodies that protect against experimental autoimmune encephalomyelitis induced by either of the two distinct encephalitogenic epitopes of basic protein, and 2) characterize the production and biologic functions of rat and rabbit antibody responses to the TCR peptide. The antibodies in both species increased in titer over time, were highly specific for the immunogen by direct reaction and inhibition assays, stained only VB8+ T cells, and suppressed clinical signs and to lesser extent the number of histologic lesions of experimental autoimmune encephalomyelitis mediated by VB8+ T cells. Coupled with our previous work, these results indicate that both humoral and cellular responses to the TCR-VB8-39-59 peptide can contribute independent immunoregulatory effects on encephalitogenic T lymphocytes that use common V region genes in response to epitopes of myelin basic protein.
Construction, in vitro and in vivo evaluation of an in-house conductance meter for measurement of skin hydration (2012)

Different probes are used in dermato-cosmetic research to measure the electrical properties of the skin. The principle governing the choice of the geometry and material of the measuring probe is not well defined in the literature and some device's measuring principles are not accessible for the scientific community. The purpose of this work was to develop a simple inexpensive conductance meter for the objective in vivo evaluation of skin hydration. The conductance meter probe was designed using the basic equation governing wave propagation along Transverse Electromagnetic transmission lines. It consisted of two concentric copper circular electrodes printed on FR4 dielectric material. The performance of the probe was validated by evaluating its measurement depth, its ability to monitor in vitro water sorption-desorption and in vivo skin hydration effect in comparison to that of the Corneometer CM 825. The measurement depth of the probe, 15 μm, was comparable to that of CM 825. The in vitro readings of the probe correlated strongly with the amount of water adsorbed on filter paper. Skin hydration after application of a moisturizer was monitored effectively by the new probe with good correlation to the results of CM 825. In conclusion, a simple probe for evaluating skin hydration was made from off-the-shelf materials and its performance was validated in comparison to a commercially available probe.
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications (2011)

Bismark is released under the GNU GPLv3+ licence. The source code is freely available from www.bioinformatics.bbsrc.ac.uk/projects/bismark/.
Detection of circulating tumour cells with a hybrid (epithelial/mesenchymal) phenotype in patients with metastatic non-small cell lung cancer (2011)

We showed for the first time the existence of hybrid CTCs with an epithelial/mesenchymal phenotype in patients with NSCLC. Their characterisation should provide further insight on the significance of EMT in CTCs and on the mechanism of metastasis in patients with NSCLC.
CD30 Contains Two Binding Sites with Different Specificities for Members of the Tumor Necrosis Factor Receptor-associated Factor Family of Signal Transducing Proteins (1996)

CD30 is a member of the tumor necrosis factor (TNF) receptor family of proteins. CD30 can regulate proliferation of lymphocytes and may also play an important role in human immunodeficiency virus replication. However, little is known about CD30 signal transduction. We performed a yeast two-hybrid library screen with the cytoplasmic domain of CD30 and isolated multiple independent cDNAs encoding human tumor necrosis factor receptor-associated factor (TRAF) 1, TRAF2, and CRAF1 (TRAF3). The ability of TRAF1, TRAF2, and CRAF1 to associate with CD30 was confirmed using an in vitro coprecipitation assay, further demonstrating that the interaction was specific and direct. The TRAF-binding domain of CD30 was mapped to the COOH-terminal 36 amino acid residues, which contained two independent binding sites. CRAF1 bound only a single site, which contained the sequence PEQET, whereas TRAF1 and TRAF2 were capable of binding to either the PEQET site or an additional downstream domain. These data indicate that the TRAF protein binding pattern of CD30 differs from other TNF receptor family members and suggest that signaling specificity through TNF receptor family proteins may be achieved through differences in their abilities to bind TRAF proteins.
Sorting Through Confusing Messages: The Art of HAART (2002)

Washington University School of Medicine, St. Louis, Missouri, U.S.A. Address correspondence and reprint requests to William G. Powderly, Division of Infectious Diseases, Washington University School of Medicine, Box 8051, St. Louis, MO 63110, U.S.A.; e-mail: [email protected]
Accurate Blood Flow Measurements: Are Artificial Tracers Necessary? (2012)

Imaging-based blood flow measurement techniques, such as particle image velocimetry, have become an important tool in cardiovascular research. They provide quantitative information about blood flow, which benefits applications ranging from developmental biology to tumor perfusion studies. Studies using these methods can be classified based on whether they use artificial tracers or red blood cells to visualize the fluid motion. We here present the first direct comparison in vivo of both methods. For high magnification cases, the experiments using red blood cells strongly underestimate the flow (up to 50% in the present case), as compared to the tracer results. For medium magnification cases, the results from both methods are indistinguishable as they give the same underestimation of the real velocities (approximately 33%, based on in vitro reference measurements). These results suggest that flow characteristics reported in literature cannot be compared without a careful evaluation of the imaging characteristics. A method to predict the expected flow averaging behavior for a particular facility is presented.
New Modalities for Challenging Targets in Drug Discovery (2017)

Our ever-increasing understanding of biological systems is providing a range of exciting novel biological targets, whose modulation may enable novel therapeutic options for many diseases. These targets include protein-protein and protein-nucleic acid interactions, which are, however, often refractory to classical small-molecule approaches. Other types of molecules, or modalities, are therefore required to address these targets, which has led several academic research groups and pharmaceutical companies to increasingly use the concept of so-called "new modalities". This Review defines for the first time the scope of this term, which includes novel peptidic scaffolds, oligonucleotides, hybrids, molecular conjugates, as well as new uses of classical small molecules. We provide the most representative examples of these modalities to target large binding surface areas such as those found in protein-protein interactions and for biological processes at the center of cell regulation.
Sit-Down & Stand-Up Awareness Algorithm for the Pedestrian Dead Reckoning (2009)

Young Min Yoo (email: ym0903@snu.ac.kr) is Ph.D student in the School of Mechanical and Aerospace Engineering of Seoul National University, Seoul, Korea. He received his B.S, degrees in Information and Control Engineering from Kwangwoon University in 2005. And he received his M.S. degree in the School of Mechanical and Aerospace Engineering of Seoul National University in 2007. His current research topics include the Strapdown Inertial Navigation Systems, BIOGRAPHY
Transmission formalism for supercurrent flow in multiprobe superconductor-semiconductor-superconductor devices (1991)

A theoretical study is given of supercurrent flow in a one-dimensional semiconductor channel coupled to superconductors at both ends. In addition, the channel is coupled to a semiconductor reservoir by means of a junction with variable coupling strength \ensuremath{\varepsilon}. The supercurrent I(cphi) is calculated from the phase-coherent propagation of electronlike and holelike excitations emitted by the superconductor reservoirs, together with electron and hole excitations from the semiconductor reservoir. The effect of temperature and \ensuremath{\varepsilon} on I(cphi) is studied. It is shown that a voltage applied between the semiconductor reservoir and the superconductors modifies the I(cphi) relation, even in the limit \ensuremath{\varepsilon}\ensuremath{\rightarrow}0.
A hybrid approach to optimistic file system directory tree synchronization (2005)

There are two main approaches to optimistic file system synchronization: distributed file systems and file synchronizers. The former type is characterized by a log-based approach that depends on access to file system internals, the latter by a state-based approach that utilizes the standard file system interface, which limits the efficiency of change detection.We propose a hybrid approach that 1) defines a minor extension to the semantics of the file system interface that enables efficient state-based file system change detection and 2) employs selectively instantiated XML documents to make the use of state-based algorithms for optimistic synchronization feasible on large file systems.The hybrid approach is simple, well-suited for current file system architectures, and allows us to leverage existing state-based reconciliation algorithms. An initial implementation shows our approach to be feasible, lightweight, and interoperable and to have satisfactory performance.
Adhesion design maps for bio-inspired attachment systems (2004)

Fibrous surface structures can improve the adhesion of objects to other surfaces. Animals, such as flies and geckos, take advantage of this principle by developing "hairy" contact structures which ensure controlled and repeatable adhesion and detachment. Mathematical models for fiber adhesion predict pronounced dependencies of contact performance on the geometry and the elastic properties of the fibers. In this paper the limits of such contacts imposed by fiber strength, fiber condensation, compliance, and ideal contact strength are modeled for spherical contact tips. Based on this, we introduce the concept of "adhesion design maps" which visualize the predicted mechanical behavior. The maps are useful for understanding biological systems and for guiding experimentation to achieve optimum artificial contacts.
Language model combination and adaptation usingweighted finite state transducers (2010)

In speech recognition systems language model (LMs) are often constructed by training and combining multiple n-gram models. They can be either used to represent different genres or tasks found in diverse text sources, or capture stochastic properties of different linguistic symbol sequences, for example, syllables and words. Unsupervised LM adaptation may also be used to further improve robustness to varying styles or tasks. When using these techniques, extensive software changes are often required. In this paper an alternative and more general approach based on weighted finite state transducers (WFSTs) is investigated for LM combination and adaptation. As it is entirely based on well-defined WFST operations, minimum change to decoding tools is needed. A wide range of LM combination configurations can be flexibly supported. An efficient on-the-fly WFST decoding algorithm is also proposed. Significant error rate gains of 7.3% relative were obtained on a state-of-the-art broadcast audio recognition task using a history dependently adapted multi-level LM modelling both syllable and word sequences.
Tumor Necrosis Factor-α Gene Expression in Mouse Oocytes and Follicular Cells1 (1993)

Ovarian cells that transcribe and translate the gene for tumor necrosis factor alpha (TNF alpha) were identified in the adult cyclic mouse by using in situ hybridization and immunocytochemistry. TNF alpha mRNA was observed in > 97% and protein was contained in approximately 53% of the oocytes of healthy follicles with two or more layers of granulosa cells, but neither was detectable in oocytes of primordial follicles and follicles with a single layer of granulosa cells. In early atretic follicles, only 13% contained TNF alpha protein and 40% contained TNF alpha mRNA. In late stages of atresia, intense immunoreactive TNF alpha was observed in all of the oocytes, but TNF alpha mRNA was present in only 13%. In approximately 85% of follicles, theca and/or granulosa cells exhibited TNF alpha mRNA hybridization signals. Macrophage-like cells within the interstitium were positive for TNF alpha mRNA and protein. In corpora lutea, luteal cells and macrophage-like cells contained TNF alpha message, while only the latter lineage contained immunoreactive TNF alpha. Hybridization signals and immunoreactivity were more intense in older corpora lutea than in corpora lutea of the present cycle. Northern blot analysis revealed a 2.2-kb TNF alpha mRNA in the ovary that was unchanged relative to 28S rRNA (constitutive RNA) during the cycle. Similarly, TNF alpha hybridization signals and immunoreactivity did not appear to change throughout the cycle. These results indicate that TNF alpha gene transcription in the oocyte coincides with the synthesis of immunoreactive TNF alpha and that these complex biochemical processes occur at distinct steps of follicular development in the mouse.(ABSTRACT TRUNCATED AT 250 WORDS)
New surgical treatments for macular degeneration. (2002)

The new surgical techniques described in this article expand the list of new treatments becoming available for people with macular degeneration.
Nanoelectronics and Information Technology: Advanced Electronic Materials and Novel Devices (2003)

From the Publisher:
Providing an introduction to electronic materials and device concepts for the major areas of current and future information technology, the value of this book lies in its focus on the underlying principles. Illustrated by contemporary examples, these basic principles will hold, despite the rapid developments in this field, especially emphasizing nanoelectronics.
There is hardly any field where the links between basic
science and application are tighter than in nanoelectronics & information technology. As an example, the design of resonant tunneling transistors, single electron devices or molecular electronic structures is simply inconceivable without delving deep into quantum mechanics.
This textbook is primarily aimed at students of physics,
electrical engineering and information technology, as well as material science in their 3rd year and higher. It is equally of interest to professionals wanting a broader overview of this hot topic.