gebhart/patrepeval huggingface dataset:
The Essential Naturalist (2011)

Like nearly every area of scholarly inquiry today, the biological sciences are broken into increasingly narrow fields and subfields, their practitioners divided into ecologists, evolutionary biologists, taxonomists, paleontologists, and much more. But all these splintered pieces have their origins in the larger field of natural history - and in this era when climate change and relentless population growth are irrevocably altering the world around us, perhaps it's time to step back and take a new, fresh look at the larger picture. The Essential Naturalist offers exactly that: a wide-ranging, eclectic collection of writings from more than eight centuries of observations of the natural world, from Leeuwenhoek to E. O. Wilson, from von Humboldt to Rachel Carson. Featuring commentaries by practicing scientists that offer personal accounts of the importance of the long tradition of natural history writing to their current research, the volume serves simultaneously as an overview of the field's long history and as an inspirational starting point for new explorations, for trained scientists and amateur enthusiasts alike.
Infertility surgery (1992)

Tubal and peritoneal factors continue to be a leading cause of infertility. In vitro fertilization, operative laparoscopy, and microsurgery are alternatives, but they are frequently complimentary therapeutic approaches. Proper investigation is the key to select the primary treatment modality. A well-performed hysterosalpingography is most valuable in the initial assessment of the tubes and uterus. Hysterosalpingosonography, radionuclide hysterosalpingography, and falloposcopy are experimental investigative tools that may be useful in selected circumstances. Effective adjuvants to reduce postoperative adhesions continue to elude the surgeon and new substances are being experimented with. In proximal tubal obstruction, selective salpingography and tubal catheterization may differentiate cornual spasm from pathologic tubal occlusion and may be therapeutic when viscous material or endotubal synechia are the cause of obstruction. Microsurgery remains the effective approach for significant lesions such as salpingitis isthmica nodosa, endometriosis, obliterative fibrosis, and chronic follicular salpingitis. Distal tubal occlusion is amenable to treatment via either laparoscopy or microsurgery. The functional status of the oviduct appears to be the most important prognostic factor in subsequent pregnancy outcome.
Overexpression of HOXB4 enhances the hematopoietic potential of embryonic stem cells differentiated in vitro (1996)

Little is known about the molecular mechanisms controlling primitive hematopoietic stem cells, especially during embryogenesis. Homeobox genes encode a family of transcription factors that have gained increasing attention as master regulators of developmental processes and recently have been implicated in the differentiation and proliferation of hematopoietic cells. Several Hox homeobox genes are now known to be differentially expressed in various subpopulations of human hematopoietic cells and one such gene, HOXB4, has recently been shown to positively determine the proliferative potential of primitive murine bone marrow cells, including cells with long-term repopulating ability. To determine if this gene might influence hematopoiesis at the earliest stages of development, embryonic stem (ES) cells were genetically modified by retroviral gene transfer to overexpress HOXB4 and the effect on their in vitro differentiation was examined. HOXB4 overexpression significantly increased the number of progenitors of mixed erythroid/myeloid colonies and definitive, but not primitive, erythroid colonies derived from embryoid bodies (EBs) at various stages after induction of differentiation. There appeared to be no significant effect on the generation of granulocytic or monocytic progenitors, nor on the efficiency of EB formation or growth rate. Analysis of mRNA from EBs derived from HOXB4-transduced ES cells on different days of primary differentiation showed a significant increase in adult beta-globin expression, with no detectable effect on GATA-1 or embryonic globin (beta H-1). Thus, HOXB4 enhances the erythropoietic, and possibly more primitive, hematopoietic differentiative potential of ES cells. These results provide new evidence implicating Hox genes in the control of very early stages in the development of the hematopoietic system and highlight the utility of the ES model for gaining insights into the molecular genetic regulation of differentiation and proliferation events.
Lentiviral Hematopoietic Stem Cell Gene Therapy Benefits Metachromatic Leukodystrophy (2013)

Metachromatic leukodystrophy (MLD) is an inherited lysosomal storage disease caused by arylsulfatase A (ARSA) deficiency. Patients with MLD exhibit progressive motor and cognitive impairment and die within a few years of symptom onset. We used a lentiviral vector to transfer a functional ARSA gene into hematopoietic stem cells (HSCs) from three presymptomatic patients who showed genetic, biochemical, and neurophysiological evidence of late infantile MLD. After reinfusion of the gene-corrected HSCs, the patients showed extensive and stable ARSA gene replacement, which led to high enzyme expression throughout hematopoietic lineages and in cerebrospinal fluid. Analyses of vector integrations revealed no evidence of aberrant clonal behavior. The disease did not manifest or progress in the three patients 7 to 21 months beyond the predicted age of symptom onset. These findings indicate that extensive genetic engineering of human hematopoiesis can be achieved with lentiviral vectors and that this approach may offer therapeutic benefit for MLD patients.
Fat Transport in Lipoproteins — An Integrated Approach to Mechanisms and Disorders (1967)

Glyceride TransportTwo Forms of Plasma Glyceride TransportIn subjects on fat-free diets the plasma lipid concentrations vary little throughout the day and tend to be highest just before breakfast.102 When the diet contains fat the levels of cholesterol and phospholipids in plasma are still relatively constant, but the glyceride concentration, as already intimated, is quite variable. It is lowest during the early morning hours (when blood samples for analysis are usually taken) and rises sharply, reaching a peak about three hours after breakfast. The concentration is boosted again by the midday meal, and after some decline in the afternoon, . . .
Similarities in normal and binocularly rivalrous viewing (1997)

We report here a series of observations-most of which the reader can experience directly-showing that distinct components of patterned visual stimuli (orthogonal lines of a different hue) vary in perception as sets. Although less frequent and often less complete, these perceptual fluctuations in normal viewing are otherwise similar to the binocular rivalry experienced when incompatible scenes are presented dichoptically.
The bone marrow constitutes a reservoir of pericyte progenitors (2006)

Adult bone marrow is a rich reservoir of hematopoietic and mesenchymal stem and progenitor cells. Mobilization and recruitment of bone marrow-derived cells to injured or ischemic tissue or tumors endorse the initiation and maintenance of angiogenic processes in the adult by incorporating endothelial progenitor cells (EPC) into the developing vasculature and by recruiting accessory hematopoietic cells. Recent data have now revealed that the origin of bone marrow-derived vascular cells is not restricted to endothelial cells but also includes pericytes--the perivascular support cells. Several laboratories have now reported the existence of pericyte progenitor cells, and these cells, like EPC, can be mobilized and recruited to the remodeling vasculature under ischemic conditions and in tumors. This review focuses on pericytes in vessel formation and on recent discoveries about their bone marrow origin in the adult.
Scanning Transmission Electron Microscopy of DNA-Protein Complexes (2003)

The scanning transmission electron microscope (STEM) at Brookhaven National Laboratory* (BNL) is nearly unique in its ability not only to image isolated unstained and unshadowed biological molecules but also to obtain quantitative information about them such as their oligomeric state (1) (see Note 1). This makes it ideal, in principle, for looking at protein-DNA complexes and obtaining information about the masses bound. However, there are very stringent requirements on the purity and stability of the samples.
Benefits of CCVT secondary voltage compensation on traveling wave-based fault locators (2014)

In this paper, the influence of the frequency response of coupling capacitor voltage transformers (CCVT) on traveling wave-based fault locators is analyzed, highlighting the benefits of the CCVT secondary voltage compensation when only voltage measurements are available. In order to do so, the frequency response of a well-known 230 kV CCVT model is evaluated and a digital compensator is proposed. Several fault scenarios in a 230 kV power system were simulated via Alternative Transients Program (ATP). In each case, the fault point was estimated using a two-terminal traveling wave-based fault location algorithm, considering as inputs the primary voltages, secondary voltages and secondary voltages corrected by the proposed digital compensator. For a more thorough evaluation, the analyzed fault location method was implemented using two different transient detection algorithms available in the literature. The obtained results indicate that the CCVT frequency response compensation is effective and suitable for traveling wave-based fault locators.
A molecular dynamics investigation of the elastomeric restoring force in elastin (1990)

A repetitive polypentapeptide organized as a connected chain of beta-bends is believed to be an important structural element of elastin, the major elastomer in biological systems. Molecular dynamics simulations were carried out on hydrated polymers of (Val-Pro-Gly-Val- Gly)18 at various extensions. Analysis of the fluctuations of backbone angles in relaxed elastin showed that particularly large-amplitude torsional motions occur in phi and psi angles of residues connecting sequentially adjacent hairpin bends. Many such motions reflect peptide plane librations that result from anticorrelated crankshaft rotations of psi i and phi i+1. These effects were much reduced in stretched polymer models. The conformational entropy of relaxed and stretched elastin models was estimated using a treatment due to Meirovitch, and gave a calculated decrease in entropy of about 1 cal/mol deg when the polymer was stretched to 1.75 times its original length. There are large changes in solvent-accessible surface area during the initial stages of elastin stretching. Collectively these results suggest that hydrophobic interactions make contributions to elastin entropy at low extensions, but that librational mechanisms make larger contributions to the elastic restoring force at longer extensions.
Codon usage in regulatory genes inEscherichia colidoes not reflect selection for ‘rare’ codons (1986)

It has often been suggested that differential usage of codons recognized by rare tRNA species, i.e. "rare codons", represents an evolutionary strategy to modulate gene expression. In particular, regulatory genes are reported to have an extraordinarily high frequency of rare codons. From E. coli we have compiled codon usage data for highly expressed genes, moderately/lowly expressed genes, and regulatory genes. We have identified a clear and general trend in codon usage bias, from the very high bias seen in very highly expressed genes and attributed to selection, to a rather low bias in other genes which seems to be more influenced by mutation than by selection. There is no clear tendency for an increased frequency of rare codons in the regulatory genes, compared to a large group of other moderately/lowly expressed genes with low codon bias. From this, as well as a consideration of evolutionary rates of regulatory genes, and of experimental data on translation rates, we conclude that the pattern of synonymous codon usage in regulatory genes reflects primarily the relaxation of natural selection.
Human 55-kDa receptor for tumor necrosis factor coupled to signal transduction cascades. (1992)

The numerous biological activities of tumor necrosis factor (TNF) appear mediated by two types of receptors of 55 kDa (TR55) and 75 kDa (TR75) molecular mass. To test TR55 for its individual role in signaling across the membrane, a cDNA coding for the human TR55 was stably expressed in murine 70Z/3 pre-B cells, which lack binding sites for, and proved nonresponsive to human TNF. The transfected TR55 showed high affinity ligand binding and active internalization. It is demonstrated that the TNF signaling cascade, i.e. stimulation of protein kinase C, sphingomyelinase, and phospholipase A2, production of the second messengers diacylglycerol and ceramide, can occur completely through exclusive binding of TNF to TR55. The p55 TNF-binding site functions as an autonomous TNF receptor that mediates key signal transduction pathways, which may control the majority of TNF actions.
AB-180 Circulatory Support System: Summary of Development and Phase I Clinical Trial (1998)

The AB-180 Circulatory Support System (AB-180 CSS; Cardiac Assist Technologies, Pittsburgh, PA) is a left ventricular assist system for investigational use in patients with postcardiotomy cardiogenic shock who are refractory to standard treatment with an intra-aortic balloon pump, pharmacologic treatment, or both. The intent of the AB-180 CSS is to provide temporary (up to 14 days) mechanical circulatory support until the heart recovers adequate mechanical function. The system consists of a small implantable centrifugal pump and a controller. A unique infusion system produces a hydrodynamic bearing between rotational and stationary components of the AB-180 CSS pump. This infusion system also provides a source of heparin for localized anticoagulation. Extensive bench and animal work has illustrated anticoagulation requirements, established operating guidelines, and demonstrated safety and efficacy. An investigational device exemption has been granted for a Phase I, five patient feasibility study at Allegheny General Hospital in Pittsburgh, Pennsylvania. To date, the pump has been implanted in one patient. The results from this first case are presented here.
Interaction between the cell‐cycle‐control proteins p34cdc2 and p9CKShs2 (1992)

A universal intracellular factor, the 'M-phase-promoting factor' (MPF), displaying histone H1 kinase activity and constituted of at least two subunits, p34cdc2 and cyclin Bcdc13, triggers the G2----M transition of the cell cycle in all organisms. The yeast p13suc1 and p18CKS1 subunits and their functionally interchangeable human homologues, p9CKShs1 and p9CKShs2, directly interact with p34cdc2 and may actually be part of the MPF complex. We have chemically synthesized p9CKShs2 and several of its peptide domains in order to investigate the binding of p9CKShs2 and p34cdc2. Several arguments support the hypothesis that the N-terminal half (peptide B) and the C-terminal half (peptide E) each contain a p34cdc2-binding site and that these two binding domains cooperate in establishing a stable p9CKShs2-p34cdc2 complex: (a) only the combination of peptides B + E, and not B or E alone, is able to elute the cdc2 kinase from p9CKShs1-Sepharose beads; (b) only immobilized peptides B + E, and not immobilized B or E, bind the cdc2 kinase; (c) only the peptides B + E combination, and not B or E alone, can compete with p9CKShs1 for cdc2 kinase binding; (d) only when supplemented with E or B free peptide does the cdc2 kinase bind to B- or E-Sepharose beads, respectively. No binding occurs in the absence of free peptide. This additivity cannot be attributed to the formation of a B-E complex mimicking the full-length p9CKShs2. The cyclin B subunit is not required for the formation of the p9CKShs2-p34cdc2 complex through these two binding domains. The implications of the existence of two cooperative p34cdc2-binding domains in p9CKShs2 on the structure of the active M-phase-specific kinase is discussed.
In Vivo Gene Delivery and Stable Transduction of Nondividing Cells by a Lentiviral Vector (1996)

A retroviral vector system based on the human immunodeficiency virus (HIV) was developed that, in contrast to a murine leukemia virus-based counterpart, transduced heterologous sequences into HeLa cells and rat fibroblasts blocked in the cell cycle, as well as into human primary macrophages. Additionally, the HIV vector could mediate stable in vivo gene transfer into terminally differentiated neurons. The ability of HIV-based viral vectors to deliver genes in vivo into nondividing cells could increase the applicability of retroviral vectors in human gene therapy.
An experimental model of idiopathic pneumonia syndrome after bone marrow transplantation: I. The roles of minor H antigens and endotoxin (1996)

Idiopathic pneumonia syndrome (IPS) refers to diffuse, non-infectious pneumonia that occurs after allogeneic bone marrow transplantation (BMT). We have developed a model of IPS using a well-characterized murine BMT system (B10.BR-->CBA) in which lung injury after BMT can be induced by minor histocompatibility (H) antigenic differences between donor and host. Lung pathology and broncho-alveolar lavage (BAL) fluid were analyzed in transplant recipients before and after both syngeneic and allogeneic BMT. At 2 weeks after BMT, no specific pathologic abnormalities were noted; at 6 weeks, both pneumonitis and mononuclear cell infiltration around vessels and bronchioles were observed only in mice receiving allogeneic BMT. This injury was associated with elevated BAL fluid levels of endotoxin (lipopolysaccharide [LPS]), neutrophils, and tumor necrosis factor alpha. No pathologic organisms were isolated from the respiratory tract of any animal. We also tested the role of endotoxin in the development of this injury. Injection of LPS 6 weeks after transplantation caused profound lung injury only in mice with moderate graft-versus-host disease; dramatic increases in BAL neutrophils and tumor necrosis factor alpha were observed, with alveolar hemorrhage occurring in 4 of 12 of these mice but in no other group. We conclude that (1) this murine BMT system is a potentially useful model of clinical IPS; (2) minor H differences between donor and recipient can be important stimuli in the pathogenesis of IPS; and (3) endotoxin in BAL fluid is associated with lung injury, and excess endotoxin can cause the development of alveolar hemorrhage in this model.
Virus-specific, CD8+ major histocompatibility complex class I-restricted cytotoxic T lymphocytes in lymphocytic choriomeningitis virus-infected beta2-microglobulin-deficient mice (1997)

Following infection with lymphocytic choriomeningitis virus (LCMV), normal adult mice generate virus-specific, major histocompatibility complex (MHC) class I-restricted cytotoxic T lymphocytes (CTL) which clear the virus after intraperitoneal infection or cause death following intracranial (i.c.) infection. We have investigated the response of beta2-microglobulin-deficient (beta2m-) mice of the H-2d haplotype (KOD mice) to LCMV infection. Unlike H-2b beta2m- mice, which generate CD4+ MHC class II-restricted CTL in response to LCMV, KOD mice generate high levels of CD8+ MHC class I-restricted, virus-specific CTL. These CTL are specific for the LCMV nucleoprotein epitope (residues 118 to 126) in association with the Ld class I molecule, analogous to the CTL response in wild-type mice. KOD mice are also susceptible to lethal LCM disease, with 75 to 80% of the mice dying 7 to 9 days following i.c. infection with virus. Similar to results with normal mice, lethal LCM disease in KOD mice is prevented by in vivo depletion of CD8+ T cells prior to i.c. infection. In contrast to wild-type mice, however, KOD mice cannot control LCMV and become persistently infected. Overall, these results demonstrate that beta2m is not an absolute requirement for presentation of endogenous antigen on Ld or for induction of virus-specific Ld-restricted CTL in vivo.
Encyclopedia of food science and technology (2000)

Now in a thoroughly-updated and expanded second edition, Wiley Encyclopedia of Food Science and Technology covers fundamental concepts and practical requirements in food science, as well as cutting-edge technological and industry information. The encyclopedia features A-to-Z coverage of all aspects of food science, including: the properties, analysis, and processing of foods; genetic engineering of new food products; and nutrition. In addition, nontechnical information is included, such as descriptions of selected scientific institutions, and research and development in government agencies. Like the first edition, this Second Edition will become the standard reference for food scientists, bioengineers, and biotechnologists. From reviews of the first edition: ...fills a definite need in the food science and technology literature...I have little doubt that this encyclopedia will become one of the classic works in this ever-growing subject.-Food and Chemistry
Impaired ABCA1-dependent Lipid Efflux and Hypoalphalipoproteinemia in Human Niemann-Pick type C Disease (2003)

The cholesterol trafficking defect in Niemann-Pick type C (NPC) disease leads to impaired regulation of cholesterol esterification, cholesterol synthesis, and low density lipoprotein receptor activity. The ATP-binding cassette transporter A1 (ABCA1), which mediates the rate-limiting step in high density lipoprotein (HDL) particle formation, is also regulated by cell cholesterol content. To determine whether the Niemann-Pick C1 protein alters the expression and activity of ABCA1, we determined the ability of apolipoprotein A-I (apoA-I) to deplete pools of cellular cholesterol and phospholipids in human fibroblasts derived from NPC1+/+, NPC1+/-, and NPC1-/- subjects. Efflux of low density lipoprotein-derived, non-lipoprotein, plasma membrane, and newly synthesized pools of cell cholesterol by apoA-I was diminished in NPC1-/- cells, as was efflux of phosphatidylcholine and sphingomyelin. NPC1+/- cells showed intermediate levels of lipid efflux compared with NPC1+/+ and NPC1-/- cells. Binding of apoA-I to cholesterol-loaded and non-cholesterol-loaded cells was highest for NPC1+/- cells, with NPC1+/+ and NPC1-/- cells showing similar levels of binding. ABCA1 mRNA and protein levels increased in response to cholesterol loading in NPC1+/+ and NPC1+/- cells but showed low levels at base line and in response to cholesterol loading in NPC1-/- cells. Consistent with impaired ABCA1-dependent lipid mobilization to apoA-I for HDL particle formation, we demonstrate for the first time decreased plasma HDL-cholesterol levels in 17 of 21 (81%) NPC1-/- subjects studied. These results indicate that the cholesterol trafficking defect in NPC disease results in reduced activity of ABCA1, which we suggest is responsible for the low HDL-cholesterol in the majority of NPC subjects and partially responsible for the overaccumulation of cellular lipids in this disorder.