gebhart/patrepeval huggingface dataset:
Intracellular localization and loss of copper responsiveness of Mnk, the murine homologue of the Menkes protein, in cells from blotchy (Mo blo) and brindled (Mo br) mouse mutants (1999)

Menkes disease is an X-linked copper deficiency disorder that results from mutations in the ATP7A ( MNK ) gene. A wide range of disease-causing mutations within ATP7A have been described, which lead to a diversity of phenotypes exhibited by Menkes patients. The mottled locus ( Mo, Atp7a, Mnk ) represents the murine homologue of the ATP7A gene, and the mottled mutants exhibit a diversity of phenotypes similar to that observed among Menkes patients. Therefore, these mutants are valuable models for studying Menkes disease. Two of the mottled mutants are brindled and blotchy and their phenotypes resemble classical Menkes disease and occipital horn syndrome (OHS) in humans, respectively. That is, the brindled mutant and patients with classical Menkes disease are severely copper deficient and have profound neurological problems, while OHS patients and the blotchy mouse have a much milder phenotype with predominantly connective tissue defects. In this study, in an attempt to understand the basis for the brindled and blotchy phenotypes, the copper transport characteristics and intracellular distribution of the Mnk protein were assessed in cultured cells from these mutants. The results demonstrated that the abnormal copper metabolism of brindled and blotchy cells may be related to a number of factors, which include the amount of Mnk protein, the intracellular location of the protein and the ability of Mnk to redistribute in elevated copper. The data also provide evidence for a relationship between the copper transport function and copper-dependent trafficking of Mnk.
Global Impact of sdiA Amplification Revealed by Comprehensive Gene Expression Profiling of Escherichia coli (2001)

In Escherichia coli the amplification of sdiA, a positive activator of ftsQAZ, genes that are essential for septation, results in mitomycin C resistance. To help us understand this resistance phenotype, genes whose expression was altered by increased sdiA dosage were identified using a DNA microarray-based, comprehensive transcript profiling method. The expression of 62 genes was reduced by more than threefold; of these, 41 are involved in motility and chemotaxis. Moreover, the expression of 75 genes, 36 of which had been previously characterized, was elevated at least threefold. As expected, increased sdiA dosage led to significantly elevated sdiA and 'ddlB-ftsQAZ-lpxC operon expression. Transcription of two genes, uvrY and uvrC, located downstream of sdiA and oriented in the same direction, was elevated about 10-fold, although the intervening gene, yecF, of opposite polarity was unaffected by increased sdiA dosage. Three genes (mioC and gidAB) flanking the replication origin, oriC, were transcribed more often when sdiA dosage was high, as were 12 genes within 1 min of a terminus of replication, terB. Transcription of the acrABDEF genes, mapping in three widely spaced loci, was elevated significantly, while several genes involved in DNA repair and replication (e.g., nei, recN, mioC, and mcrC) were moderately elevated in expression. Such global analysis provides a link between septation and the response to DNA-damaging agents.
Design and Solution Structure of a Well-Folded Stack of Two β-Hairpins Based on the Amino-Terminal Fragment of Human Granulin A (2000)

Four amino acid substitutions were introduced into a peptide corresponding to the amino-terminal subdomain (30-31 residues) of human granulin A (HGA) in order to assess the contributions of a hydrophobic framework and other interactions to structure stabilization of the stack of two beta-hairpins. The resulting hybrid peptide, HGA 1-31 (D1V, K3H, S9I, Q20P) with four free cysteines, spontaneously formed a uniquely disulfide-bonded isomer with an expected [1-3, 2-4] disulfide pairing pattern. This peptide was characterized in detail by use of NMR and shown to assume a highly stable structure in solution, in contrast to the amino-terminal 1-30 fragment of human granulin A. The prototype peptide, or HGA 1-30 (C17S, C27S), had lower resistance to chemical reduction and proteolysis, broad NH and H(alpha) proton resonances, lower proton resonance dispersion, and no slowly exchanging amide protons. Two other peptides, HGA 1-30 (C17S, Q20P, C27S) and HGA 1-31 (D1V, K3H, S9I, C17S, C27S), with either Pro20 stabilizing a potential reverse turn or with a hydrophobic cluster consisting of Val1, His3, and Ile9, had sharper and slightly better dispersed NH and H(alpha) proton resonances, but still no slowly exchanging amide protons. The solution structure of HGA 1-31 (D1V, K3H, S9I, Q20P) indicates that it adopts a well-folded conformation of a stack of two beta-hairpins, as found for the amino-terminal subdomain of the prototypic carp granulin-1 with representative beta-hairpin stacks. These results highlight the importance of both hydrophobic and turn-stabilizing interactions for the structural integrity of the hairpin stack scaffold. The conformational stability appears to be maintained by a combination of the well-formed second beta-hairpin and two hydrophobic clusters, one located at the interface between the two beta-hairpins and the other on "top" of the first beta-hairpin. The implications of these findings for the design of conformationally stable hairpin stacks are discussed.
Concatenation of Hamming Codes and Accumulator Codes with High-Order Modulations for High-Speed Decoding (2004)

We propose a concatenated code structure combined with high-order modulations suitable for implementation with iterative decoders operating at gigabit-persecond (Gbps) data rates. The examples considered in this article are serial/parallel concatenations of Hamming and accumulator codes. Performance results are given for binary phase-shift keyed (BPSK) modulation, quadrature phase-shift keyed (QPSK) modulation, 8 phase-shift keyed (8PSK) modulation, and 16 quadrature amplitude modulation (16QAM) over additive white Gaussian noise (AWGN) and Rayleigh fading channels. I.
The Undocumented PC (1994)

From the Publisher:
Knowing about the key hardware elements of a PC allows applications programmers to dramatically speed up the execution time of their program. The Undocumented PC reveals for the first time the undocumented or difficult-to-find programming features of critical PC hardware. In addition, the book provides the only available reference to Input/Output ports, undocumented CPU instructions, fixed memory areas, and much more. You will find each major subsystem of the PC explained in detail, followed by extensive reference sections that show and explain both documented and undocumented BIOS-functions. These are explained in far greater detail than ever before, and cover all the major system architectures including the PC, XT, AT, EISA, and MCA. A value-added disk includes diagnostic and analytical tools such as IO?SPY, a TSR that monitors the current I/O port status on screen; equipment detection routines for the disk, diskette, video, and other important aspects; CPU detection routines to identify the exact CPU, FPU, speed, vendor, and other critical processor information; utilities to identify and test undocumented CPU instructions; demonstration utilities to access CMOS memory, the keyboard controller, and other subsystems.
Complex band structure, decay lengths, and Fermi level alignment in simple molecular electronic systems (2002)

The complex band structure of a periodic system is the conventional band structure extended to complex Bloch k vectors. The k vectors with an imaginary part describe spatially decaying wave functions and arise in, for example, the analysis of impurity and surface states. They also represent the quantum tunneling states which are vehicles of electron transport through a barrier such as a thin oxide layer or a molecule. We present a method for obtaining the complex band structure of a molecule which is composed of repeating units. The complex band structures of some simple organic molecules (n-alkanes, alkenes, and linked benzene rings) will be determined and used to analyze electron conduction through molecules (e.g., octanedithiol) connected between gold electrodes. The form of the complex band structure clearly elucidates the molecule length dependence of the tunneling current and also suggests the energy for alignment of the Fermi level.
Ultra-broad and coherent white light generation in silica glass by focused femtosecond pulses at 1.5 µm (2005)

We report on the observation of efficient and ultra-broadband white light supercontinuum generated by focusing femtosecond pulses from an optical parametric amplifier at 1.5 microm in silica glass. The characteristic white light spectrum is extending from 400 nm up to at least 1750 nm. At sufficiently high input powers stable white light patterns associated with the interference of spatially coherent filamentary sources were observed and analyzed. Unlike focusing with 800 nm pulses from a Ti-sapphire laser, the stable fringes formed for each spectral component were pronounced owing to significantly reduced destructive impact of optical breakdown on filamentation of femtosecond pulses at 1.5 microm. By taking advantage of this property, the formation of optical waveguides in silica glass with considerably broader range of writing parameters as compared to those fabricated with 800 nm pulses, was demonstrated.
Pathogenesis and treatment of Shiga toxin-producing Escherichia coli infections (2008)

Improved understanding of Shiga toxin-producing Escherichia coli pathophysiology and progression to hemolytic uremic syndrome provides the basis for prevention, prophylactic and treatment strategies.
A Molecular Marker for Chloroquine-Resistant Falciparum Malaria (2001)

This study shows an association between the pfcrt T76 mutation in P. falciparum and the development of chloroquine resistance during the treatment of malaria. This mutation can be used as a marker in surveillance for chloroquine-resistant falciparum malaria.
Increasing doses of purified influenza virus hemagglutinin and subvirion vaccines enhance antibody responses in the elderly (1996)

The reactogenicities and immunogenicities of two influenza virus vaccines were compared in a placebo-controlled clinical trial among healthy ambulatory persons > or = 65 years old (mean age, 72 years). Volunteers were assigned randomly to receive 15-, 45-, or 135-micrograms doses of monovalent influenza A/Taiwan (H1N1) hemagglutinin (HA) or subvirion (SV) vaccine intramuscularly or a placebo. Increasing doses of SV vaccine were associated with a higher rate of injection site discomfort (P < 0.05; chi-square test for linear trend), but all doses of both vaccines were well tolerated. Increasing the dose of the HA or the SV vaccine resulted in increasingly higher postimmunization levels of serum hemagglutination inhibition and neutralizing antibody levels (P < 0.001; multiple linear regression). Mean serum antibody titers at 1 month increased two- to threefold with a ninefold increase in dose; the frequencies of fourfold or greater rises in titer likewise increased. An increase in the dose of the HA or the SV vaccine also resulted in increased frequencies of rises in immunoglobulin A or G antibody titers in nasal wash specimens. The frequencies increased approximately twofold for each vaccine with a ninefold increase in the dose. These data suggest that increasing the HA vaccine dose is a promising approach to the development of improved influenza virus vaccines for use in elderly people.
Gut CD103 + dendritic cells express indoleamine 2,3-dioxygenase which influences T regulatory/T effector cell balance and oral tolerance induction (2010)

We identified a new IDO-dependent pathway leading to acquisition of tolerogenic functions in mucosal CD103-expressing DCs, indicating IDO as a possible therapeutic target for gut disorders.
Lysyl oxidase‐like 2 expression is increased in colon and esophageal tumors and associated with less differentiated colon tumors (2007)

Lysyl oxidase-like 2 (LOXL2) belongs to an amine oxidase family whose members have been implicated in crosslink formation in stromal collagens and elastin, cell motility, and tumor development and progression. We previously demonstrated the association between increased LOXL2 expression and invasive/metastatic behavior in human breast cancer cells and mouse squamous and spindle cell carcinomas, interaction between LOXL2 and SNAIL in epithelial-mesenchymal transition, and localization of the LOXL2 gene to 8p21.2-21.3, within a minimally deleted region in several cancers, including colon and esophagus. In the present study, we analyzed LOXL2 expression in colon and esophageal tumors, and explored methylation as a regulator of LOXL2 expression. Immunohistochemistry using normal tissues demonstrated intracellular localization of LOXL2 in colonic enteroendocrine cells and esophageal squamous cells at the luminal surface, but not in mitotically active cells. Tissue array analysis of 52 colon adenocarcinomas and 50 esophageal squamous cell carcinomas revealed presence of LOXL2 expression in 83 and 92% of the samples, respectively, and a significant association between increased number of LOXL2-expressing cells and less-differentiated colon carcinomas. We determined that the methylation status of the 1150 bp 5' CpG island may contribute to the regulation of the gene. Loss of heterozygosity studies, using a microsatellite within intron 4 of the LOXL2 gene, revealed that loss of LOXL2 was unlikely to play a major role in either colon or esophageal tumors. These results suggest that increased LOXL2 expression in colon and esophageal cancer may contribute to tumor progression.
Large deflection micromechanical scanning mirrors for linear scans and pattern generation (2000)

An electrostatically driven silicon micro scanning mirror (MSM) for one-dimensional (1-D) and two-dimensional (2-D) deflection of light is presented. A special configuration of the driving electrodes allows the use of small electrode gaps without restricting the deflection of the plate geometrically. In this paper, the starting of the oscillation and the operation of the scanner is discussed. Experimental results show that scan angles of up to 60/spl deg/ can be achieved at a driving voltage of only 20 V. The 2-D deflection of a laser beam is obtained by a gimbal mounting of the mirror plate. For the fabrication of the devices, SOI-wafers are used as the base material. The mechanical structures are defined by a deep silicon etch. For the electrical isolation of areas on the movable frame, polysilicon-filled trenches are used. The mechanical stability of the scanners is tested. The devices resist shocks of more than 1000 g and show no change of the resonance frequency even after long run tests of 7/spl times/10/sup 9/ periods.
Low-Power Circuits for Brain–Machine Interfaces (2008)

This paper presents work on ultra-low-power circuits for brain-machine interfaces with applications for paralysis prosthetics, stroke, Parkinson's disease, epilepsy, prosthetics for the blind, and experimental neuroscience systems. The circuits include a micropower neural amplifier with adaptive power biasing for use in multi-electrode arrays; an analog linear decoding and learning architecture for data compression; low-power radio-frequency (RF) impedance-modulation circuits for data telemetry that minimize power consumption of implanted systems in the body; a wireless link for efficient power transfer; mixed-signal system integration for efficiency, robustness, and programmability; and circuits for wireless stimulation of neurons with power-conserving sleep modes and awake modes. Experimental results from chips that have stimulated and recorded from neurons in the zebra finch brain and results from RF power-link, RF data-link, electrode-recording and electrode-stimulating systems are presented. Simulations of analog learning circuits that have successfully decoded prerecorded neural signals from a monkey brain are also presented.
The half‐lives of angiotensin II, angiotensin II‐amide, angiotensin III, Sar1‐Ala8‐angiotensin II and renin in the circulatory system of the rat. (1978)

1. Methods are described for estimating the half-life of angiotensin analogues and renin in the rat, from the time course of the blood pressure changes they evoke. 2. The following half-life values were measured: angiotensin II, 16 +/- 1 sec; angiotensin III, 14 +/- 1 sec; angiotensin II-amide, 15 +/- 1 sec; Sar1-Ala8-angiotensin II, 6.4 +/- 0.6 min; renin, 3.0 +/- 0.4 min. The distribution volume of angiotensin was found to be 18 ml./kg body wt. 3. It is inferred that the Asp1 residue does not reduce the rate of angiotensin II catabolism, but that substitution of this residue by sarcosine may inhibit catabolism while substitution by asparagine has no effect. 4. Five experimental criteria were identified which indicate that these methods give reliable estimates of the half-life. It is suggested that these results are more accurate than most previous half-life estimates. 5 When tachyphylaxis to angiotensin II-amide occurs, the pressor activity of the plasma is not reduced.
Surface selective binding of nanoclay particles to polyampholyte protein chains (2009)

Binding of nanoclay (Laponite) to gelatin-A and gelatin-B (both polyampholytes) molecules was investigated at room temperature (25 degrees C) both experimentally and theoretically. The stoichiometric binding ratio between gelatin and Laponite was found to be strongly dependent on the solution ionic strength. Large soluble complexes were formed at higher ionic strengths of the solution, a result supported by data obtained from light scattering, viscosity, and zeta potential measurements. The binding problem was theoretically modeled by choosing a suitable two-body screened Coulomb potential, U(R(+)) = (q(-)/2epsilon)[(Q(-)/R(-))e(-kR(-))-(Q(+)/R(+))e(-kR(+))], where the protein dipole has charges Q(+) and Q(-) that are located at distances R(+) and R(-) from the point Laponite charge q(-) and the dispersion liquid has dielectric constant (epsilon). U(R(+)) accounted for electrostatic interactions between a dipole (protein molecule) and an effective charge (Laponite particle) located at an angular position theta. Gelatin-A and Laponite association was facilitated by a strong attractive interaction potential that led to preferential binding of the biopolymer chains to negatively charged face of Laponite particles. In the case of gelatin-B selective surf ace patch binding dominated the process where the positively charged rim and negatively charged face of the particles were selectively bound to the oppositely charged segments of the biopolymer. The equilibrium separation (R(e)) between the protein and nanoclay particle revealed monovalent salt concentration dependence given by R(e) approximately [NaCl](alpha) where alpha = 0.6+/-0.2 for gelatin-A and alpha = 0.4+/-0.2 for gelatin-B systems. The equilibrium separations were approximately 30% less compared to the gelatin-A system implying preferential short-range ordering of the gelatin-B-nanoclay pair in the solvent.
Remissions in leukemia of childhood following acute infectious disease. Staphylococcus and streptococcus, varicella, and feline panleukopenias (1953)

C during the past seventy-five years have suggested that Severe infections may on occasion favorably modify the course of far-advanred neoplastic disease.'O-l1 Dock, in 1904, cited sixty-five references on the ameliorative effect of acute infections in patients with leukemia and suggested further clinical studies. Wintrobe and Hasenbush" in 1939 again reviewed the literature and added observations on twenty-nine instances of acute infections in eighty-six patients with chronic leukemia. They concluded that "infections in the great majority of cases did not produce remissions in the physical signs or in the blood picture."
An Overview of Bearing Vibration Analysis (2008)

Vibration produced by rolling bearings can be complex and can result from geometrical imperfections during the manufacturing process, defects on the rolling surfaces or geometrical errors in associated components. Noise and vibration is becoming more critical in all types of equipment since it is often perceived to be synonymous with quality and often used for predictive maintenance. In this article the different sources of bearing vibration are considered along with some of the characteristic defect frequencies that may be present. Some examples of how vibration analysis can be used to detect deterioration in machine condition are also given.
In vivo turnover studies of C-reactive protein. (1985)

The in vivo plasma clearance rate of the acute phase reactant C-reactive protein (CRP) was studied in mice and rats. The clearance rate of 125I-human CRP in mice and 125I-rat CRP in rats showed a T1/2 of approximately 4 h. The T1/2 was independent of circulating levels of CRP and was not affected by the presence of C-polysaccharide (CPS), a ligand to which CRP binds. However, in mice receiving sufficient CPS, more radioactivity localized to the spleen compared to mice receiving 125I-CRP only. 125I-CPS was rapidly cleared at the same rate by normal mice and by mice undergoing an acute phase response while rats cleared 125I-CPS more slowly despite having high circulating CRP concentrations. These findings suggest that CRP does not provide a mechanism for extremely rapid clearance of its ligands from the circulation, although the handling and subsequent fate of these ligands may be affected.
Functional repair of motor endplates after botulinum neurotoxin type A poisoning: Biphasic switch of synaptic activity between nerve sprouts and their parent terminals (1999)

Blockade of acetylcholine release by botulinum neurotoxin type A at the neuromuscular junction induces the formation of an extensive network of nerve-terminal sprouts. By repeated in vivo imaging of N-(3-triethyl ammonium propyl)-4-(4-(dibutylamino)styryl) pyridinium dibromide uptake into identified nerve endings of the mouse sternomastoid muscle after a single intramuscular injection of the toxin, inhibition of stimulated uptake of the dye at the terminals was detected within a few days, together with an increase in staining of the newly formed sprouts. After 28 days, when nerve stimulation again elicited muscle contraction, regulated vesicle recycling occurred only in the sprouts [shown to contain certain soluble N-ethylmaleimide-sensitive factor attachment proteins (SNAREs) and to abut acetylcholine receptors] and not at the parent terminals. Therefore, only these sprouts could be responsible for nerve-muscle transmission at this time. However, a second, distinct phase of the rehabilitation process followed with a return of vesicle turnover to the original terminals, accompanied by an elimination of the by then superfluous sprouts. This extension and later removal of "functional" sprouts indicate their fundamental importance in the repair of paralyzed endplates, a finding with ramifications for the vital process of nerve regeneration.