gebhart/patrepeval huggingface dataset:
Pathway of lysine degradation in Fusobacterium nucleatum (1982)

Lysine was fermented by Fusobacterium nucleatum ATCC 25586 with the formation of about 1 mol each of acetate and butyrate. By the use of [1-14C]lysine or [6-14C]lysine, acetate and butyrate were shown to be derived from both ends of lysine, with acetate being formed preferentially from carbon atoms 1 and 2 and butyrate being formed preferentially from carbon atoms 3 to 6. This indicates that the lysine carbon chain is cleaved between both carbon atoms 2 and 3 and carbon atoms 4 and 5, with the former predominating [1-14C]acetate was also extensively incorporated into butyrate, preferentially into carbon atoms 3 and 4. Cell-free extracts of F. nucleatum were shown to catalyze the reactions of the 3-keto,5-aminohexanoate pathway of lysine degradation, previously described in lysine-fermenting clostridia. The 3-keto,5-aminohexanoate cleavage enzyme was partially purified and shown to have properties much like those of the clostridial enzyme. We conclude that both the pathway and the enzymes of lysine degradation are similar in F. nucleatum and lysine-fermenting clostridia.
Sensing and compensation of femtosecond waveform distortion induced by all-order polarization mode dispersion at selected polarization states (2007)

We demonstrate full characterization of femtosecond pulse distortion induced by all-order polarization mode dispersion (PMD) at selected polarization states via second-harmonic generation (SHG) frequency-resolved optical gating (FROG) measurements at an average power of under 28 nW. By applying the inverse of the measured spectral phase via a programmable pulse shaper, we compress the distorted pulses from more than 3 ps to nearly bandwidth-limited durations of less than 500 fs. Our results show that SHG FROG measurements performed by using fiber-pigtailed aperiodically poled lithium niobate waveguides can serve as a robust and sensitive tool for characterization of PMD-induced spectral phase.
Speed advantage of optimized metal S/D in 25 nm dual-gate fully-depleted CMOS (2003)

With shrinking dimensions, control of extrinsic impedance is becoming increasingly performance limiting. Improvements to source/drain (S/D) technology thus become critical to technology scaling. Metal S/D is a promising approach. A doped S/D device was modeled with a two-component S/D profile: an ultra-steep extension profile offset from the gate edge, and a stronger primary S/D profile aligned to the metal contact. The metal S/D was offset from the gate edge to improve the short channel margin. By reducing series resistance and allowing for lower fringe capacitance, a metal S/D device allows for substantial improvement in speed and/or power. An offset from the metal S/D to the gate should be used to reduce short channel effects. If doped S/D is used, then ultra-low resistance contacts are mandatory.
Human photosynthesis, the ultimate answer to the long term mystery of Kleiber’s law or E = M&lt;sup&gt;3/4&lt;/sup&gt;: Implication in the context of gerontology and neurodegenerative diseases (2013)

Kleiber’s Law or E = M3/4 is a mathematical expression known since 1932 that outlines the relationship between mass (biomass) and the use of energy. It is compelling because it supports a long standing observation that larger animals appear to use energy more efficiently than smaller ones. For example, an elephant’s weight is 200,000 times of a mouse, but uses only about 10,000 fold energy; thus a cat, having a mass of about 100 times of a mouse, only spends roughly 33 fold energy. In other words, the bigger you are, the less energy per gram of tissue you actually need to stay alive. Many facts pertaining to animal size call for a rational explanation. This paper takes into account that the fascinating relationship between mass and energy use for any living thing is governed strictly by a mathematical universal formula across all living species, operating in the tiniest of bacteria to the biggest of whales and sequoia tress. For the first time, we report a capacity for the mammal eukaryotic cell to split, break or dissociate water molecules through melanin. Even though E = M3/4 was discovered eight decades ago, no proper satisfactory explanation exists. Nevertheless, our multiyear detailed study on the “Human Photosynthesis” or first found in the human retina and later in all eukaryotic cells, may finally unravel this mystery, namely, the bigger you are the more surface area you have to absorb electromagnetic radiation and the more potential exists to use that electromagnetic radiation spectra to perform work. We propose a future application of this theory in the context of human diseases, especially age-related disorders, such as retinopathy, cerebrovascular and Alzheimer disease and these implications may not only foster a better understanding of the pathobiology of these devastating diseases but also develop much more effective therapies in the foreseeable future.
Compressively Sensed Video Acquisition in Transmission Electron Microscopy (2017)

Transmission electron microscopy (TEM) is an extremely powerful tool for physical, material, and biological science at the nanoscale. This is especially true for higher-dimensional acquisition modes that produce data beyond the usual two-dimensional images, adding resolution in time, depth (via tomography), scattering angle (through STEM-diffraction, also called 4D STEM), and spectroscopy. Unfortunately, these higher-dimensional modes are extremely bandwidth-hungry. Every added dimension greatly multiplies the number of bytes that need to be captured, with associated increases in acquisition time, sample damage, and equipment expense. This includes, more and more, the equipment needed to transfer, store, and analyze the data. Modern kilohertz-scale cameras are starting to address the issue, but they are not a complete solution, and they can be quite expensive.
The molecular structure and catalytic mechanism of a novel carboxyl peptidase from Scytalidium lignicolum (2004)

The molecular structure of the pepstatin-insensitive carboxyl peptidase from Scytalidium lignicolum, formerly known as scytalidopepsin B, was solved by multiple isomorphous replacement phasing methods and refined to an R factor of 0.230 (R(free) = 0.246) at 2.1-A resolution. In addition to the structure of the unbound peptidase, the structure of a product complex of cleaved angiotensin II bound in the active site of the enzyme was also determined. We propose the name scytalidocarboxyl peptidase B (SCP-B) for this enzyme. On the basis of conserved, catalytic residues identified at the active site, we suggest the name Eqolisin for the enzyme family. The previously uninvestigated SCP-B fold is that of a beta-sandwich; each sheet has seven antiparallel strands. A tripeptide product, Ala-Ile-His, bound in the active site of SCP-B has allowed for identification of the catalytic residues and the residues in subsites S1, S2, and S3, which are important for substrate binding. The most likely hydrolytic mechanism involves nucleophilic attack of a general base (Glu-136)-activated water (OH(-)) on the si-face of the scissile peptide carbonylcarbon atom to form a tetrahedral intermediate. Electrophilic assistance and oxyanion stabilization is provided by the side-chain amide of Gln-53. Protonation of the leaving-group nitrogen is accomplished by the general acid function of the protonated carboxyl group of Glu-136.
A Physical Map of Human Chromosome 7: An Integrated YAC Contig Map with Average STS Spacing of 79 kb (1997)

The construction of highly integrated and annotated physical maps of human chromosomes represents a critical goal of the ongoing Human Genome Project. Our laboratory has focused on developing a physical map of human chromosome 7, a approximately 170-Mb segment of DNA that corresponds to an estimated 5% of the human genome. Using a yeast artificial chromosome (YAC)-based sequence-tagged site (STS)-content mapping strategy, 2150 chromosome 7-specific STSs have been established and mapped to a collection of YACs highly enriched for chromosome 7 DNA. The STSs correspond to sequences generated from a variety of DNA sources, with particular emphasis placed on YAC insert ends, genetic markers, and genes. The YACs include a set of relatively nonchimeric clones from a human-hamster hybrid cell line as well as clones isolated from total genomic libraries. For map integration, we have localized 260 STSs corresponding to Genethon genetic markers and 259 STSs corresponding to markers orders by radiation hybrid (RH) mapping on our YAC contigs. Analysis of the data with the program SEGMAP results in the assembly of 22 contigs that are "anchored" on the Genethon genetic map, the RH map, and/or the cytogenetic map. These 22 contigs are ordered relative to one another, are (in all but 3 cases) oriented relative to the centromere and telomeres, and contain > 98% of the mapped STSs. The largest anchored YAC contig, accounting for most of 7p, contains 634 STSs and 1260 YACs. An additional 14 contigs, accounting for approximately 1.5% of the mapped STSs, are assembled but remain unanchored on either the genetic or RH map. Therefore, these 14 "orphan" contigs are not ordered relative to other contigs. In our contig maps, adjacent STSs are connected by two or more YACs in > 95% of cases. With 2150 mapped STSs, our map provides an average STS spacing of approximately 79 kb. The physical map we report here exceeds the goal of 100-kb average STS spacing and should provide an excellent framework for systematic sequencing of the chromosome.
Intraspecific Arabidopsis Hybrids Show Different Patterns of Heterosis Despite the Close Relatedness of the Parental Genomes (2014)

Heterosis is important for agriculture; however, little is known about the mechanisms driving hybrid vigor. Ultimately, heterosis depends on the interactions of specific alleles and epialleles provided by the parents, which is why hybrids can exhibit different levels of heterosis, even within the same species. We characterize the development of several intraspecific Arabidopsis (Arabidopsis thaliana) F1 hybrids that show different levels of heterosis at maturity. We identify several phases of heterosis beginning during embryogenesis and culminating in a final phase of vegetative maturity and seed production. During each phase, the hybrids show different levels and patterns of growth, despite the close relatedness of the parents. For instance, during the vegetative phases, the hybrids develop larger leaves than the parents to varied extents, and they do so by exploiting increases in cell size and cell numbers in different ratios. Consistent with this finding, we observed changes in the expression of genes known to regulate leaf size in developing rosettes of the hybrids, with the patterns of altered expression differing between combinations. The data show that heterosis is dependent on changes in development throughout the growth cycle of the hybrid, with the traits of mature vegetative biomass and reproductive yield as cumulative outcomes of heterosis at different levels, tissues, and times of development.
A Homozygous Mutation in the Luteinizing Hormone Receptor Causes Partial Leydig Cell Hypoplasia: Correlation between Receptor Activity and Phenotype (1998)

Leydig cell hypoplasia (LCH) is characterized by a decreased response of the Leydig cells to LH. As a result, patients with this syndrome display aberrant male development ranging from complete pseudohermaphroditism to males with micropenis but with otherwise normal sex characteristics. We have evaluated three brothers with a mild form of LCH. Analysis of their LH receptor (LHR) gene revealed a homozygous missense mutation resulting in a substitution of a lysine residue for a isoleucine residue at position 625 of the receptor. In vitro analysis of this mutant LHR, LHR(I625K), in HEK293 cells indicated that the signaling efficiency was significantly impaired, which explains the partial phenotype. We have compared this mutant LHR to two other mutant LHRs, LHR(A593P) and LHR(S616Y), identified in a complete and partial LCH patient, respectively. Although the ligand-binding affinity for all three mutant receptors was normal, the hormonal response of LHR(A593P) was completely absent and that of LHR(S616Y) and LHR(I625K) was severely impaired. Low cell surface expression explained the reduced response of LHR(S616Y), while for LHR(I625K) this diminished response was due to a combination of low cell surface expression and decreased coupling efficiency. For LHR(A593P), the absence of a reduced response resulted from both poor cell surface expression and a complete deficiency in coupling. Our experiments further show a clear correlation between the severity of the clinical phenotype of patients and overall receptor signal capacity, which is a combination of cell surface expression and coupling efficiency.
Characterization of the Nucleoside Triphosphatase Activity of Poliovirus Protein 2C Reveals a Mechanism by Which Guanidine Inhibits Poliovirus Replication (1999)

The highly conserved non-structural protein 2C of picornaviruses is involved in viral genome replication and encapsidation and in the rearrangement of intracellular structures. 2C binds RNA, has nucleoside triphosphatase activity, and shares three motifs with superfamily III helicases. Motifs "A" and "B" are involved in nucleotide triphosphate (NTP) binding and hydrolysis, whereas a function for motif "C" has not yet been demonstrated. Poliovirus RNA replication is inhibited by millimolar concentrations of guanidine hydrochloride (GdnHCl). Resistance and dependence to GdnHCl map to 2C. To characterize the nucleoside triphosphatase activity of 2C, we purified poliovirus recombinant 2C fused to glutathione S-transferase (GST-2C) from Escherichia coli. GST-2C hydrolyzed ATP with a Km of 0.7 mM. Other NTPs, including GTP, competed with ATP for binding to 2C but were poor substrates for hydrolysis. Mutation of conserved residues in motif A and B abolished ATPase activity, as did mutation of the conserved asparagine residue in motif C, an observation indicating the involvement of this motif in ATP hydrolysis. GdnHCl at millimolar concentrations inhibited ATP hydrolysis. Mutations in 2C that confer poliovirus resistant to or dependent on GdnHCl increased the tolerance to GdnHCl up to 100-fold.
Therapy with immunoglobulin: applications for monoclonal antibodies. (2006)

The ability of antibodies to recognize specific antigenic targets and trigger responses from the immune system has made them attractive candidates as therapeutic agents. Monoclonal and recombinant technology have made possible the development of a new class of therapeutic and diagnostic agents that combine the exquisite specificity of antibodies with biologic compatibility and protracted half-lives. This technology is just beginning to be explored and considerable evolution may be expected in the next few decades.
Comparative cognition: Perspectives, challenges, and prospects. (2021)

The publication of the centennial year of the <i>Journal of Comparative Psychology</i> is an occasion to reflect on the state of our discipline. In this article, I focus on one aspect of comparative psychology, namely, comparative cognition. This focus stems from my long-standing interest in comparative cognition. The trends and challenges in comparative cognition share many of the trends and challenges in the broader field of comparative psychology. In the first part of this article, I outline my perspective on the field. Next, I consider challenges. I end with a section on prospects for the future. (PsycInfo Database Record (c) 2021 APA, all rights reserved).
Experience of coronary artery bypass graft on 64 cases (2004)

Objective To review the experience of coronary artery bypass graft (CABG) surgery on 64 patients suffering from coronary artery disease (CAD).Method CABG surgery was performed on 64 patients.The left internal thoracic artery,the left radial artery, and (or) the great saphenous vein were taken up as bypass grafts. Thirty six patients received surgery on arresting hearts with moderate hypothermic cardiopulmonary bypass (CPB).The other 28 patients received surgery off CPB with the cardiac arrester (Octopus) on beating hearts (OPCAB).Results There was no significant difference between the two groups before the operations(P0.05).But different results came out in the time of operation, the time of ICU,the time of the use of vasoactive drugs and the incidence of the post operative complications(P0.05).Not only the syndrome from myocardia ischemia disappeared but the left ventricular ejection fraction (LVEF) increased.Conclusion The OPCAB may prevent the heart as well as the body from injuring by CPB and lower the incidence of the post operative complications.A skilled management of the bypass grafts and a skilled anastomosis are the keys to the success of CABG surgery. [
LK6, a short lived protein kinase in Drosophila that can associate with microtubules and centrosomes (1997)

A number of polyclonal mouse sera were raised against Drosophila proteins that bound to microtubules in vitro (Kellogg et al. (1989) J. Cell Biol. 109, 2977-2991). Some of these sera recognised centrosomes in vivo, and we have been using these to screen expression libraries to isolate cDNAs encoding these putative centrosomal microtubule-associated proteins. Here we report the cloning of one such cDNA that encodes a novel serine/threonine protein kinase called LK6. The protein appears to exist in two forms: an abundant 185 kDa form and a rarer approximately 220 kDa form that interacts with microtubules. At least some of the LK6 protein is located in centrosomes at all stages of the cell cycle in fly embryos. Interestingly, the protein contains a PEST-like sequence and is rapidly turned over in vivo. Constitutive overexpression of LK6 is deleterious to flies and causes defects in microtubule organisation in both eggs and early embryos, whereas constitutive overexpression of a mutant form containing a point mutation that severely impairs the kinase activity is without effect. These findings suggest that LK6 may play a role in regulating microtubule function.
Re: Pimentel et al.—eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome (2001)

Re: Pimentel et al. —eradication of small intestinal bacterial overgrowth reduces symptoms of irritable bowel syndrome
Enhancement of Anticancer Activity in Antineovascular Therapy Is Based on the Intratumoral Distribution of the Active Targeting Carrier for Anticancer Drugs (2006)

We previously observed the enhanced anticancer efficacy of anticancer drugs encapsulated in Ala-Pro-Arg-Pro-Gly-polyethyleneglycol-modified liposome (APRPG-PEG-Lip) in tumor-bearing mice, since APRPG peptide was used as an active targeting tool to angiogenic endothelium. This modality, antineovascular therapy (ANET), aims to eradicate tumor cells indirectly through damaging angiogenic vessels. In the present study, we examined the in vivo trafficking of APRPG-PEG-Lip labeled with [2-(18)F]2-fluoro-2-deoxy-D-glucose ([2-(18)F]FDG) by use of positron emission tomography (PET), and observed that the trafficking of this liposome was quite similar to that of non-targeted long-circulating liposome (PEG-Lip). Then, histochemical analysis of intratumoral distribution of both liposomes was performed by use of fluorescence-labeled liposomes. In contrast to in vivo trafficking, intratumoral distribution of both types of liposomes was quite different: APRPG-PEG-Lip was colocalized with angiogenic endothelial cells that were immunohistochemically stained for CD31, although PEG-Lip was localized around the angiogenic vessels. These results strongly suggest that intratumoral distribution of drug carrier is much more important for therapeutic efficacy than the total accumulation of the anticancer drug in the tumor, and that active delivery of anticancer drugs to angiogenic vessels is useful for cancer treatment.
Alternative route for biosynthesis of amino sugars in Escherichia coli K-12 mutants by means of a catabolic isomerase (1989)

By inserting a lambda placMu bacteriophage into gene glmS encoding glucosamine 6-phosphate synthetase (GlmS), the key enzyme of amino sugar biosynthesis, a nonreverting mutant of Escherichia coli K-12 that was strictly dependent on exogenous N-acetyl-D-glucosamine or D-glucosamine was generated. Analysis of suppressor mutations rendering the mutant independent of amino sugar supply revealed that the catabolic enzyme D-glucosamine-6-phosphate isomerase (deaminase), encoded by gene nagB of the nag operon, was able to fulfill anabolic functions in amino sugar biosynthesis. The suppressor mutants invariably expressed the isomerase constitutively as a result of mutations in nagR, the locus for the repressor of the nag regulon. Suppression was also possible by transformation of glmS mutants with high-copy-number plasmids expressing the gene nagB. Efficient suppression of the glmS lesion, however, required mutations in a second locus, termed glmX, which has been localized to 26.8 min on the standard E. coli K-12 map. Its possible function in nitrogen or cell wall metabolism is discussed.
Modeling and analysis of multichip module power supply planes (1995)

A method that would allow accurate modeling of arbitrarily shaped planes with bypass capacitors has been developed. It is compatible with a SPICE-based modeling method for the rest of the power supply hierarchy and the devices. A modified SPICE is used to accommodate distributed circuits. The distributed circuits are built with microwave analysis software and connected to SPICE by s-parameter files. The modeling process is described and examples of thick and thin-film power supply planes are presented with comparison to measured results. The method is used to explore potential design choices for a large MCM with many simultaneously switching drivers.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
A DNS RR for specifying the location of services (DNS SRV) (1996)

A DNS RR for specifying the