gebhart/patrepeval huggingface dataset:
A family of expressed antifreeze protein genes from the moth, Choristoneura fumiferana (2002)

The freeze-intolerant insect, Choristoneura fumiferana (spruce budworm), produces multiple antifreeze protein (AFP) isoforms for protection during the overwintering stage. We now report the cloning of AFP genes from insects; Afp-Lu1 encodes a approximately 9-kDa AFP isoform, and Afp-Iu1 encodes a approximately 12-kDa AFP isoform. Both CfAFP genes have similar structures with a single 3- to 3.6-kb intron interrupting the coding region. The second exon of an additional CfAFP gene, 2.7a, encoding a new approximately 9-kDa isoform, was found 3.7 kb upstream of Afp-Lu1 and demonstrates that some AFP family members are linked in tandem. This gene appears to encode an AFP with 68-76% identity to previously isolated CfAFPs. With its eight Cys residues necessary for disulfide bonding and five perfectly conserved 'Thr button' (Thr-Xaa-Thr) ice-binding motifs, it can be modeled as a functional AFP. Southern blot analysis shows that there are approximately 17 genes in this AFP family, with each of the isoforms represented by two to five gene copies. Transcript accumulation from Afp-Lu1 and Afp-Iu1 (or closely related genes) was maximal during the overwintering stage, while 2.7a transcripts were only detected in first instars, larvae that are normally found only in the summer. Contrary to expectations, this differential expression demonstrates that CfAFP gene family transcripts are primarily regulated during development, rather than by seasonally low temperatures.
MyoD Directly Up-regulates Premyogenic Mesoderm Factors during Induction of Skeletal Myogenesis in Stem Cells (2010)

Gain- and loss-of-function experiments have illustrated that the family of myogenic regulatory factors is necessary and sufficient for the formation of skeletal muscle. Furthermore, MyoD required cellular aggregation to induce myogenesis in P19 embryonal carcinoma stem cells. To determine the mechanism by which stem cells can be directed into skeletal muscle, a time course of P19 cell differentiation was examined in the presence and absence of exogenous MyoD. By quantitative PCR, the first MyoD up-regulated transcripts were the premyogenic mesoderm factors Meox1, Pax7, Six1, and Eya2 on day 4 of differentiation. Subsequently, the myoblast markers myogenin, MEF2C, and Myf5 were up-regulated, leading to skeletal myogenesis. These results were corroborated by Western blot analysis, showing up-regulation of Pax3, Six1, and MEF2C proteins, prior to myogenin protein expression. To determine at what stage a dominant-negative MyoD/EnR mutant could inhibit myogenesis, stable cell lines were created and examined. Interestingly, the premyogenic mesoderm factors, Meox1, Pax3/7, Six1, Eya2, and Foxc1, were down-regulated, and as expected, skeletal myogenesis was abolished. Finally, to identify direct targets of MyoD in this system, chromatin immunoprecipitation experiments were performed. MyoD was observed associated with regulatory regions of Meox1, Pax3/7, Six1, Eya2, and myogenin genes. Taken together, MyoD directs stem cells into the skeletal muscle lineage by binding and activating the expression of premyogenic mesoderm genes, prior to activating myoblast genes.
One-dimensional electronic systems in ultrafine mesa-etched single and multiple quantum well wires (1988)

Ultrafine mesa-etched structures with lateral geometrical dimensions of 250 to 550 nm have been prepared in modulation-doped AlGaAs/GaAs heterostructures and multiple quantum well systems. From magnetotransport measurements at low temperatures (T=2.2 K) on these single and multiple quantum well wire structures we find that the lateral carrier confinement leads to the formation of one-dimensional electronic subbands of typically 2 meV energy separation. The width of the electron channel is smaller than the geometrical width, indicating a lateral depletion length of about 100 to 150 nm at the mesa edge.
First neonates with severe acute respiratory syndrome coronavirus 2 infection in Romania (2020)

Even if there are only a few reported cases of neonates infected with COVID-19 and most of them present mild manifestations, newborns need a more careful insight because of the nonspecific symptomatology.
Variable-Loop-Deleted Variants of the Human Immunodeficiency Virus Type 1 Envelope Glycoprotein Can Be Stabilized by an Intermolecular Disulfide Bond between the gp120 and gp41 Subunits (2000)

We have described an oligomeric gp140 envelope glycoprotein from human immunodeficiency virus type 1 that is stabilized by an intermolecular disulfide bond between gp120 and the gp41 ectodomain, termed SOS gp140 (J. M. Binley, R. W. Sanders, B. Clas, N. Schuelke, A. Master, Y. Guo, F. Kajumo, D. J. Anselma, P. J. Maddon, W. C. Olson, and J. P. Moore, J. Virol. 74:627-643, 2000). In this protein, the protease cleavage site between gp120 and gp41 is fully utilized. Here we report the characterization of gp140 variants that have deletions in the first, second, and/or third variable loop (V1, V2, and V3 loops). The SOS disulfide bond formed efficiently in gp140s containing a single loop deletion or a combination deletion of the V1 and V2 loops. However, deletion of all three variable loops prevented formation of the SOS disulfide bond. Some variable-loop-deleted gp140s were not fully processed to their gp120 and gp41 constituents even when the furin protease was cotransfected. The exposure of the gp120-gp41 cleavage site is probably affected in these proteins, even though the disabling change is in a region of gp120 distal from the cleavage site. Antigenic characterization of the variable-loop-deleted SOS gp140 proteins revealed that deletion of the variable loops uncovers cryptic, conserved neutralization epitopes near the coreceptor-binding site on gp120. These modified, disulfide-stabilized glycoproteins might be useful as immunogens.
Synthesis, Nicotinic Acetylcholine Receptor Binding, and Antinociceptive Properties of 2-exo-2-(2‘-Substituted 5‘-pyridinyl)-7-azabicyclo[2.2.1]heptanes. Epibatidine Analogues (2001)

A convenient, high-yield synthesis of 7-tert-butoxycarbonyl-7-azabicyclo[2.2.1]hept-2-ene (5), which involved the addition of tributyltin hydride to 7-tert-butoxycarbonyl-2-p-toluenesulfonyl-7-azabicyclo[2.2.1]hept-2-ene (4) followed by elimination of the tributyltin and p-tolylsulfonyl groups using tetrabutylammonium fluoride was developed. The addition of 2-amino-5-iodopyridine to 5 under reductive Heck conditions provided 7-tert-butoxycarbonyl-2-exo-(2'-amino-5'-pyridinyl)-7-azabicyclo[2.2.1]heptane (6). Compound 6 was the key intermediate used to prepare epibatidine analogues where the 2'-chloro group on the pyridine ring was replaced with a fluorine (1b), bromine (1c), iodine (1d), hydroxy (1e), amino (1f), dimethylamino (1g), trifluoromethanesulfonate (1h), and hydrogen (1i) group. (+)- and (-)-Epibatidine and compounds 1b-d and 1i all possess similar binding affinities at the alpha(4)beta(2) nAChR receptors labeled by [(3)H]epibatidine. Compound 1f has affinity similar to nicotine, whereas compounds 1e, 1g, and 1h have much lower affinity. The binding affinity appears to be dependent upon the electronic nature of the substituent. However, other factors are also involved. None of the compounds possesses appreciable affinity for the alpha(7) nAChR labeled by [(125)I]iodo-MLA. With the exception of 1f and 1g, all the epibatidine analogues are full agonists (tail flick test) in producing antinociception after intrathecal injection in mice.
Novel process for figuring and polishing diamond surfaces (1994)

A novel method for figuring and polishing diamond surfaces is described. It is a three step process, consisting of (1) a diffusion smoothing step using carbon reaction with certain materials at elevated temperatures (such as hot iron, molten rare earth metals, etc.), (2) a laser polishing and figuring step where UV laser ablation actively coupled with in situ interferometry provides the desired diamond figure and (3) an ion beam assisted superpolishing step, where ion beam technology is used to provide the final surface finish.
Design, Synthesis, and Biological Evaluation of Hybrid Molecules Containing α-Methylene-γ-Butyrolactones and α-Bromoacryloyl Moieties (2005)

The synthesis and biological activity of hybrids 8-18 prepared combining alpha-methylene-gamma-butyrolactones and alpha-bromoacryloylamides have been described and their structure-activity relationships discussed. All these heterobifunctional compounds demonstrate good antileukemic activity, significantly superior to that of both alkylating units alone. Using the human leukemia HL-60 cell line, selected compounds 10, 11, 13, and 17 were found to induce morphological changes and internucleosomal DNA fragmentation characteristic of apoptotic cell death.
Gene Therapy Protocols (2001)

Significant advances in gene transfer technology and the completion of sequencing the human genome offer much renewed hope that gene therapy will provide novel approaches to the treatment of inherited and acquired diseases. In this fully updated and revised 2nd edition of the warmly received Gene Therapy Protocols, leading experts from academic and industrial laboratories around the world detail their most effective viral and nonviral methods of gene transfer, as well as discuss their applications in different organ systems. The methods range from those in which new molecular conjugates show great promise for targeting targeting gene transfer and regulating transgene expression, to those used in such exciting applications as the delivery of therapeutic proteins, vaccination, and tissue engineering. In addition, there are completely revised methods based on retroviruses and adenoviruses, as well as new and promising methods based on lentiviruses and adeno-associated viruses. The quantitative aspects of gene therapy are strongly emphasized, and the book reflects the many significant recent improvements in gene transfer efficiency, gene regulation, and vector production. Up-to-date and highly practical, Gene Therapy Protocols, 2nd Edition, offers a rich compilation of the revolutionary advances that have recently occurred in gene transfer technology, with each article providing proven step-by-step laboratory procedures that enable successful therapeutic application
Pathogenic potential of environmental Klebsiella pneumoniae isolates (2004)

Klebsiella pneumoniae is an important opportunistic pathogen and a frequent cause of nosocomial infections. K. pneumoniae infections can occur at nearly any body site; however, urinary tract infections and infections of the respiratory tract predominate. Infections are frequently preceded by gastrointestinal colonization, and the gastrointestinal tract is believed to be the most important reservoir for transmission of the bacteria. In contrast to many other bacterial pathogens, K. pneumoniae is ubiquitous in nature. Several studies have described Klebsiella isolates of environmental origin to be nearly identical to clinical isolates with respect to several phenotypic properties. However, the pathogenic potential of environmental K. pneumoniae isolates is essentially unknown. We have evaluated the virulence of K. pneumoniae strains of environmental and clinical origin directly in animal models, i.e. in urinary tract infection and intestinal colonization models. Furthermore, the ability to adhere to and invade human epithelial cell lines was examined. Although strain-to-strain differences were observed in the individual infection models, overall, strains of environmental origin were found to be as virulent as strains of clinical origin. The ubiquity of K. pneumoniae in nature and the general ability of K. pneumoniae strains to infect susceptible hosts might explain the high frequency of opportunistic infections caused by this species.
Directional local field potentials: A tool to optimize deep brain stimulation (2017)

Local field potentials predict the most efficient stimulation contacts and may provide a useful tool to expedite the selection of the optimal contact for directional DBS. © 2017 The Authors. Movement Disorders published by Wiley Periodicals, Inc. on behalf of International Parkinson and Movement Disorder Society.
Metabolic Mapping of Functional Activity in the Hypothalamo-Neurohypophysial System of the Rat (1979)

Physiological stimulation of the hypothalamo-neurohypophysial system by salt loading of rats resulted in a dramatically increased glucose utilization in the posterior pituitary but not in the paraventricular or supraoptic nuclei. The good correlation between glucose utilization and neural activity in the posterior pituitary (that is, nerve terminals) contrasted with the lack of correlation in the paraventricular and supraoptic nuclei (that is, the sites of the cell bodies of the same neurons). This difference in the metabolic response to functional activity between the two regions of these neurons can be explained by the differences in surface-to-volume ratios of these regions.
Colloquium: Femtosecond optical frequency combs (2003)

Recently there has been a remarkable synergy between the technologies of precision laser stabilization and mode-locked ultrafast lasers. This has resulted in control of the frequency spectrum produced by mode-locked lasers, which consists of a regular comb of sharp lines. Thus such a controlled mode-locked laser is a ``femtosecond optical frequency comb generator.'' For a sufficiently broad comb, it is possible to determine the absolute frequencies of all of the comb lines. This ability has revolutionized optical frequency metrology and synthesis. It has also served as the basis for the recent demonstrations of atomic clocks that utilize an optical frequency transition. In addition, it is having an impact on time-domain applications, including synthesis of a single pulse from two independent lasers. In this Colloquium, we first review the frequency-domain description of a mode-locked laser and the connection between the pulse phase and the frequency spectrum in order to provide a basis for understanding how the absolute frequencies can be determined and controlled. Using this understanding, applications in optical frequency metrology and synthesis and optical atomic clocks are discussed. This is followed by a brief overview of how the comb technology is affecting and will affect time-domain experiments.
Skeletal muscle‐specific immunotoxin for the treatment of focal muscle spasm (1998)

Intramuscular injection of botulinum toxin type A (BTX) is used to treat many disorders characterized by muscular spasms. The utility of BTX, however, is limited by its short duration of action, the development of resistance after repeated injections, and cross-reactivity with autonomic neurons. To overcome these limitations, we engineered an immunotoxin (ITX) to damage skeletal muscle fibers selectively by chemically linking a monoclonal antibody against the nicotinic acetylcholine receptor to the toxin ricin. In vitro, the ITX was 20,000-fold more toxic to myotubes than myoblasts, consistent with the degree of acetylcholine receptor expression. The gastrocnemius muscles of 30 rats were unilaterally injected with a series of protein toxins at various concentrations and examined histopathologically 7 and 30 days later. ITX produced destructive myopathic changes at a dose 300-fold less than the maximum tolerated dose. Assessment of rat muscle strength after unilateral gastrocnemius injections showed that ITX was more effective and had a longer duration of action than BTX. ITXs may have potential for the treatment of involuntary muscle spasms.
Forward Error Correction for DNA Data Storage (2016)

We report on a strong capacity boost in storing digital data in synthetic DNA. In principle, synthetic DNA is an ideal media to archive digital data for very long times because the achievable data density and longevity outperforms today's digital data storage media by far. On the other hand, neither the synthesis, nor the amplification and the sequencing of DNA strands can be performed error-free today and in the foreseeable future. In order to make synthetic DNA available as digital data storage media, specifically tailored forward error correction schemes have to be applied. For the purpose of realizing a DNA data storage, we have developed an efficient and robust forwarderror-correcting scheme adapted to the DNA channel. We based the design of the needed DNA channel model on data from a proof-of-concept conducted 2012 by a team from the Harvard Medical School [1]. Our forward error correction scheme is able to cope with all error types of today's DNA synthesis, amplification and sequencing processes, e.g. insertion, deletion, and swap errors. In a successful experiment, we were able to store and retrieve error-free 22 MByte of digital data in synthetic DNA recently. The found residual error probability is already in the same order as it is in hard disk drives and can be easily improved further. This proves the feasibility to use synthetic DNA as longterm digital data storage media.
Flightin, a novel myofibrillar protein of Drosophila stretch-activated muscles. (1993)

The indirect flight muscles of Drosophila are adapted for rapid oscillatory movements which depend on properties of the contractile apparatus itself. Flight muscles are stretch activated and the frequency of contraction in these muscles is independent of the rate of nerve impulses. Little is known about the molecular basis of these adaptations. We now report a novel protein that is found only in flight muscles and has, therefore, been named flightin. Although we detect only one gene (in polytene region 76D) for flightin, this protein has several isoforms (relative gel mobilities, 27-30 kD; pIs, 4.6-6.0). These isoforms appear to be created by posttranslational modifications. A subset of these isoforms is absent in newly emerged adults but appears when the adult develops the ability to fly. In intact muscles flightin is associated with the A band of the sarcomere, where evidence suggests it interacts with the myosin filaments. Computer database searches do not reveal extensive similarity to any known protein. However, the NH2-terminal 12 residues show similarity to the NH2-terminal sequence of actin, a region that interacts with myosin. These features suggest a role for flightin in the regulation of contraction, possibly by modulating actin-myosin interaction.
Parallel Distributed Processing (1986)

What makes people smarter than computers? These volumes by a pioneering neurocomputing group suggest that the answer lies in the massively parallel architecture of the human mind. They describe a new theory of cognition called connectionism that is challenging the idea of symbolic computation that has traditionally been at the center of debate in theoretical discussions about the mind. The authors' theory assumes the mind is composed of a great number of elementary units connected in a neural network. Mental processes are interactions between these units which excite and inhibit each other in parallel rather than sequential operations. In this context, knowledge can no longer be thought of as stored in localized structures; instead, it consists of the connections between pairs of units that are distributed throughout the network. Volume 1 lays the foundations of this exciting theory of parallel distributed processing, while Volume 2 applies it to a number of specific issues in cognitive science and neuroscience, with chapters describing models of aspects of perception, memory, language, and thought.
IVS8+1 DelG, a Novel Splice Site Mutation Causing DFNA5 Deafness in a Chinese Family (2015)

We identified a novel DFNA5 mutation IVS8+1 delG in a Chinese family which led to skipping of exon 8. This is the sixth DFNA5 mutation relates to hearing loss and the second one in DFNA5 intron 8. Our findings provide further support to the hypothesis that the DFNA5-associated hearing loss represents a mechanism of gain-of-function.
A wireless photoplethysmography signal processing system for long-term monitoring (2016)

This paper has presented a photoplethysmography (PPG) signal processing system based on ensemble empirical mode decomposition (EEMD) method. Traditionally, empirical mode decomposition (EMD) suffers from mode mixing problem during the decomposition process. This paper adopts EEMD to solve the mode mixing problem by adding different sets of white noise and decompose signal into meaningful intrinsic mode functions. The system is implemented on self-designed platform combined with front-end circuit, EEMD chip by TSMC 90nm CMOS technology, and commercial display devices. The results showed that the proposed EEMD processor can effectively solve the mode mixing problem of EMD. It was helpful for non-stationary biomedical signal processing and cardiovascular diseases research.
Temperature Measurement of Carbon Nanotubes Using Infrared Thermography (2008)

Multiwalled carbon nanotubes (MWNTs) have a very high absorbance in the near-infrared (NIR) region of the electromagnetic spectrum. It is demonstrated that the temperature of MWNTs, measured using infrared thermography during NIR laser irradiation, is much higher than that of other carbonaceous materials such as graphite controls. Since most biological materials have a low absorbance in the same region, carbon nanotubes could be used for selective photothermal hyperthermia of biological or nonbiological systems. This study was performed to prove the concept of direct measurement of the temperature distribution of carbon nanotubes when stimulated with laser irradiation. The maximum temperature increase of MWNTs measured with a high-sensitivity infrared camera, continuously irradiated with four 2.5-mW/650-nm lasers, was 7 °C vs a graphite control, while irradiation with a 390-mW/1064-nm laser yielded maximum temperature increases of more than 100 °C above the graphite control. The use of infrared thermography has allowed for specific data on laser-mediated heating kinetics of MWNTs to be presented here for the first time to our knowledge. These results could prove very useful in the design of selective photothermal processes of selectively destroying biological systems of interest.
Thymidylate synthase inhibition after administration of fluorouracil with or without leucovorin in colon cancer patients: implications for treatment with fluorouracil. (1994)

Residual and total TS activity are predictive for response to 5FU. The findings may be applicable for treatment of patients with advanced disease and TS should be evaluated as a prognostic factor in adjuvant chemotherapy studies.
The Ultrastructuhe of the Spiral Ganglion in the Guinea Pig (1967)

The spiral ganglion in the guinea pig is composed of uniform bipolar nerve cell bodies, surrounded by sheaths of compact myelin completed with layers of loose myelin.The perikarya are densely packed with organelles, especially endoplasmic-reticulum, well developed Golgi-zones, mitochondria and osmiophile bodies.A little group of hitherto not described nerve cells differ significantly from the main part of cells in having no myelin sheath but only one single layer of Schwann cell cytoplasma, little endoplasmic reticulum but many neurofilaments. They have a big nucleolus and their axons are very thin without a sheath of compact myelin. Preliminary experiments of strong white noise stimulation do not show significant alteration in the amount of RNA granules in the perikaryon. There seem to be an increasing number of so-called nuclear caps consisting of several layers of endoplasmic reticulum arranged concentric with the nuclear membrane.