gebhart/patrepeval huggingface dataset:
Influence of Age on Pulsatile Luteinizing Hormone Release and Responsiveness of the Gonadotrophs to Sex Hormone Feedback in Men (1987)

The influence of aging on serum LH and testosterone (T) pulse frequency and gonadotroph sensitivity to androgen and estrogen feedback was studied in young (less than 55 yr old) and elderly (greater than 65 yr) Trappist monks. LH pulse frequency (sampling interval, 20 min) was significantly lower [0.25 +/- 0.03 (+/- SEM) vs. 0.38 +/- 0.02 pulses/h; P less than 0.01] in elderly (n = 21) than in young monks (n = 27); the pulse amplitudes were similar. Similarly, T pulse frequency was lower in the elderly than in the young monks (0.13 +/- 0.04 vs. 0.23 +/- 0.02 pulses/h; P less than 0.01). In elderly men, the hypothalamo-pituitary complex was more sensitive to 5 alpha-androstan-17 beta-ol-3-one feedback, as determined by the decrease in serum LH and T levels. Moreover, during 5 alpha-androstan-17 beta-ol-3-one (125 mg/day, percutaneously, for 10 days) administration, the LH response to LHRH (100 micrograms, iv) was significantly higher in the elderly men compared to the pretreatment response. During estradiol (1.5 mg/day, percutaneously for 10 days) administration, the LH response to LHRH was decreased in the elderly men, but unchanged in the young men, suggesting greater responsiveness to estradiol in the elderly men. We conclude that in aged men, decreased testicular androgen secretion is not exclusively the consequence of a primary testicular alteration, but that important changes occur in hypothalamo-pituitary function, specifically decreased LH pulse frequency and increased LH responsiveness to sex hormone feedback.
One Hundred Years of Lung Cancer (2005)

A hundred years ago, lung cancer was a reportable disease, and it is now the commonest cause of death from cancer in both men and women in the developed world, and before long, will reach that level in the developing world as well. The disease has no particular symptoms or signs for its detection at an early stage. Most patients therefore present with advanced stage IIIB or IV disease. Screening tests began in the 1950s with annual chest x-ray films and sputum cytology but they resulted in no improvement in overall mortality compared with control subjects. The same question is now being asked of spiral low-dose computed tomographic scanning. There have been big refinements in the staging classification of lung cancer and advances in stage identification using minimally invasive technology. Postsurgical mortality has declined from the early days of the 1950s but 5-year cure rates have only barely improved. The addition of chemotherapy to radical radiotherapy, together with novel radiotherapy techniques, is gradually improving the outcome for locally advanced, inoperable non-small cell lung cancer. Chemotherapy offers modest survival improvement for patients with non-small cell lung cancer, the modern agents being better tolerated resulting in an improved quality of life. The management of small cell lung cancer, which appeared so promising at the beginning of the 1970s, has hit a plateau with very little advance in outcome over the last 15 years. The most important and cost-effective management for lung cancer is smoking cessation, but for those with the disease, novel agents and treatment approaches are urgently needed.
Noninvasive Prenatal Screening for Genetic Diseases Using Massively Parallel Sequencing of Maternal Plasma DNA (2015)

The identification of cell-free fetal DNA (cffDNA) in maternal plasma in 1997 heralded the most significant change in obstetric care for decades, with the advent of safer screening and diagnosis based on analysis of maternal blood. Here, we describe how the technological advances offered by next-generation sequencing have allowed for the development of a highly sensitive screening test for aneuploidies as well as definitive prenatal molecular diagnosis for some monogenic disorders.
Sequence analysis, expression, and conservation of Escherichia coli uracil DNA glycosylase and its gene (ung). (1988)

The complete nucleotide sequence of the Escherichia coli ung gene is described. Transcription initiation and termination sites were determined by S1 nuclease and RNase mapping. The common prokaryotic -35, -10, and the ribosome binding site sequences are represented by TGTTCTGTA, TAAGCTA, and AGGAGAG at their respective locations. A putative hairpin transcription terminator structure is present at the major transcription terminator sites. The open reading frame of the ung gene codes for a protein of 229 amino acids (25,664 daltons). The molecular weight, amino acid composition, and the N-terminal amino acid sequence of the uracil DNA glycosylase purified from E. coli cells match with the open reading frame of the ung gene. The protein sequence analysis shows that the N-terminal methionine is cleaved off in the mature protein. The in vitro transcription coupled translation of the ung gene directs the synthesis of a protein which comigrates with uracil DNA glycosylase. Also, the CNBr cleavage of the protein synthesized in vitro confirms the positions of the methionines deduced from the DNA sequence. The levels of ung gene expression remain constant up to the early stationary phase, but decline in the late stationary phase of the E. coli culture. The E. coli gene showed a strong sequence homology to Shigella, a weak sequence homology to Salmonella and Citrobacter, and a very weak sequence homology to Proteus genes. No sequence homologies were seen for Pseudomonas, Clostridium, Micrococcus, and several eukaryotic genomes.
Characterization of cis-Acting Elements Regulating Transcription from the Promoter of a Constitutively Active Rice Actin Gene (1992)

The promoter of the constitutively expressed rice (Oryza sativa) actin 1 gene (Act1) is highly active in transformed rice plants (W. Zhang, D. McElroy, and R. Wu, Plant Cell 3:1150-1160, 1991). A region 834 bp upstream of the Act1 transcription initiation site contains all the regulatory elements necessary for maximal gene expression in transformed rice protoplasts (D. McElroy, W. Zhang, J. Cao, and R. Wu, Plant Cell 2:163-171, 1990). We have constructed a series of Act1 promoter deletions fused to a bacterial beta-glucuronidase reporter sequence (Gus). Transient expression assays in transformed rice protoplasts, as well as transformed maize cells and tissues, identified two distinct cis-acting regulatory elements in the Act1 promoter. A 38-bp poly(dA-dT) region was found to be a positive regulator of Act1 promoter activity. Deletion of the poly(dA-dT) element lowered Gus expression by at least threefold compared with expression produced by the full-length Act1 promoter. By gel retardation and footprinting, we identified a ubiquitous rice protein which specifically recognizes this poly(dA-dT) element in the constitutively active Act1 promoter. A CCCAA pentamer repeat-containing region was found to be a negative regulator of the Act1 promoter in transformed rice protoplasts. Transient expression assays in different maize cells and tissues with use of the Act1 deletion constructs suggested that the CCCAA pentamer repeat region functions in a complex tissue-specific manner. A CCCAA-binding protein was detected only in root extracts.
Amino acid sequence of the alpha subunit of human leukocyte adhesion receptor Mo1 (complement receptor type 3). (1988)

Mo1 (complement receptor type 3, CR3; CD11b/CD18) is an adhesion-promoting human leukocyte surface membrane heterodimer (alpha subunit 155 kD [CD11b] noncovalently linked to a beta subunit of 95 kD [CD18]). The complete amino acid sequence deduced from cDNA of the human alpha subunit is reported. The protein consists of 1,136 amino acids with a long amino-terminal extracytoplasmic domain, a 26-amino acid hydrophobic transmembrane segment, and a 19-carboxyl-terminal cytoplasmic domain. The extracytoplasmic region has three putative Ca2+-binding domains with good homology and one with weak homology to the "lock washer" Ca2+-binding consensus sequence. These metal-binding domains explain the divalent cation-dependent functions mediated by Mo1. The alpha subunit is highly homologous to the alpha subunit of leukocyte p150,95 and to a lesser extent, to the alpha subunit of other "integrin" receptors such as fibronectin, vitronectin, and platelet IIb/IIIa receptors in humans and position-specific antigen-2 (PS2) in Drosophila. Mo1 alpha, like p150, contains a unique 187-amino acid stretch NH2-terminal to the metal-binding domains. This region could be involved in some of the specific functions mediated by these leukocyte glycoproteins.
Interleukin-13: Central Mediator of Allergic Asthma (1998)

The worldwide incidence, morbidity, and mortality of allergic asthma are increasing. The pathophysiological features of allergic asthma are thought to result from the aberrant expansion of CD4(+) T cells producing the type 2 cytokines interleukin-4 (IL-4) and IL-5, although a necessary role for these cytokines in allergic asthma has not been demonstrable. The type 2 cytokine IL-13, which shares a receptor component and signaling pathways with IL-4, was found to be necessary and sufficient for the expression of allergic asthma. IL-13 induces the pathophysiological features of asthma in a manner that is independent of immunoglobulin E and eosinophils. Thus, IL-13 is critical to allergen-induced asthma but operates through mechanisms other than those that are classically implicated in allergic responses.
Control of developmental timing by small temporal RNAs: a paradigm for RNA‐mediated regulation of gene expression (2002)

Heterochronic genes control the timing of developmental programs. In C. elegans, two key genes in the heterochronic pathway, lin-4 and let-7, encode small temporally expressed RNAs (stRNAs) that are not translated into protein. These stRNAs exert negative post-transcriptional regulation by binding to complementary sequences in the 3' untranslated regions of their target genes. stRNAs are transcribed as longer precursor RNAs that are processed by the RNase Dicer/DCR-1 and members of the RDE-1/AGO1 family of proteins, which are better known for their roles in RNA interference (RNAi). However, stRNA function appears unrelated to RNAi. Both sequence and temporal regulation of let-7 stRNA is conserved in other animal species suggesting that this is an evolutionarily ancient gene. Indeed, C. elegans, Drosophila and humans encode at least 86 other RNAs with similar structural features to lin-4 and let-7. We postulate that other small non-coding RNAs may function as stRNAs to control temporal identity during development in C. elegans and other organisms.
Stabilization of Organometallic Species Achieved by the Use of N‐Heterocyclic Carbene (NHC) Ligands (2005)

Abstract This review describes the stabilization of various coordinatively unsaturated metal centers through the incorporation of N‐heterocyclic carbene (NHC) ligands. Such species are more thermally stable compared to the more ubiquitous tertiary phosphane systems. Although NHCs can be considered as phosphane mimics it has become apparent that there are substantial differences between the two ligand families. In general, NHC ligands are much more electron‐donating and sterically demanding than bulky phosphane ligands. We also discuss the various thermochemical and infrared studies of metal carbene species that have provided insight into NHC ligands properties, and at last allowed meaningful comparison to tertiary phosphane ligands. While NHCs are generally viewed as strong binding low reactive ligands, in some instances they have been found to be not so innocent and can undergo facile intramolecular C–H activation as well as abnormal ligand binding [C‐5(4) vs. C‐2]. Here we highlight such reactions with late‐transition metal centers that have allowed the isolation of various unsaturated LTM species. These have so far eluded isolation in analogous phosphane‐based systems. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2005)
Mass spectometry/mass spectrometry : techniques and applications of tandem mass spectrometry (1988)

Introduction to mass spectrometry/mass spectrometry - history of mass spectrometry/mass spectrometry, concepts and principles, nomenclature MS/MS instrumentation - principles of charged-particle analysis, sector-based MS/MS instruments, quadrupole instruments, hybrid instruments, MS/MS with ion-trapping techniques, reaction regions reactions in MS/MS - unimolecular dissociation, activation reactions reactive collisions, charge permutation reactions applications of MS/MS to fundamental studies - ion structures, reaction meachanisms, thermochemistry characteristics of MS/MS for analytical applications - sample considertions, choice of ionization method, interpretation of MS/MS spectra analytical applications - environmental applications, natural products applications, industrial products applications, foods and flavours applications, forensic chemistry applications, petroleum and petroleum products applications, bioorganic applications, pharmaceutical applications, applications to continuos flow samples and processes conclusions and outlook - instrumentation in MS/MS, outlook for advanced applications, interpretation of MS/MS data, conclusions. Appendices: MS/MS scan modes on various instrument configurations frequently used symbols and acronyms.
Sodium and Chloride Concentrations, pH, and Depth of Airway Surface Liquid in Distal Airways (2003)

The composition and depth of the airway surface liquid (ASL) are key parameters in airway physiology that are thought to be important in the pathophysiology of cystic fibrosis and other diseases of the airways. We reported novel fluorescent indicator and microscopy methods to measure [Na+], [Cl-], pH, and depth of the ASL in large airways (Jayaraman, S., Y. Song, L. Vetrivel, L. Shankar, and A.S. Verkman. 2001. J. Clin. Invest. 107:317-324.). Here we report a stripped-lung preparation to measure ASL composition and depth in small distal airways. Distal ASL was stained with ion- or pH-sensitive fluorescent indicators by infusion into mouse trachea of a perfluorocarbon suspension of the indicator. After stripping the pleura and limited microdissection of the lung parenchyma, airways were exposed for measurement of ASL [Na+], [Cl-], and pH by ratio imaging microscopy, and depth by confocal microscopy. The stripped-lung preparation was validated in stability and tissue viability studies. ASL [Na+] was 122 +/- 2 mM, [Cl-] was 123 +/- 4 mM and pH was 7.28 +/- 0.07, and not dependent on airway size (<100- to >250-mum diameter), ENaC inhibition by amiloride, or CFTR inhibition by the thiazolidinone CFTRinh-172. ASL depth was 8-35 mum depending on airway size, substantially less than that in mouse trachea of approximately 55 mum, and not altered significantly by amiloride. These results establish a novel lung preparation and fluorescence approach to study distal airway physiology and provide the first data on the composition and depth of distal ASL.
The generation of human long-term marrow cultures from marrow depleted of Ia (HLA-DR) positive cells (1984)

Successful long-term cultures were generated from marrow buffy-coat cells incubated with either of two monoclonal anti-Ia antibodies, 7.2 and HBIOa, and complement. The mean CFU-GM toxicity for 7.2 and HBIOa was 81% and 94%, respectively, of the complement control. Cultures generated from marrows treated with 7.2 and complement produced between 30% and 163% of the CFU-GM (mean, 78.2 +/- 52.4%) and 33% of the BFU-E produced by the complement control cultures. Long-term cultures from marrows treated with the more cytotoxic HBIOa antibody yielded 261% of the CFU-GM present at culture initiation. Our data suggest that the progenitor cells necessary for generation of long-term cultures from human marrow are Ia-negative and may represent less mature stem cells than those measurable by semisolid colony assays. Furthermore, marrow treated with cytotoxic anti-Ia antibodies may be suitable for use in autologous transplantation.
Modulation of antigen processing by bound antibodies can boost or suppress class II major histocompatibility complex presentation of different T cell determinants. (1995)

Bound antibodies can modulate antigen processing but it is not clear to what extent this affects antigen presentation. Here we show that presentation of T cell determinants in tetanus toxin can be either enhanced or suppressed as a direct consequence of antibody modulation of antigen processing in human B lymphoblastoid cells. Remarkably, a single bound antibody or its Fab fragment can simultaneously enhance the presentation of one T cell determinant by more than 10-fold while strongly suppressing the presentation of a different T cell determinant. Biochemical analysis demonstrates that both the suppressed and boosted determinants fall within an extended domain of antigen stabilized or "footprinted" by this antibody during proteolysis. These results demonstrate that bound antibodies can modulate the capture of peptides by class II major histocompatibility complex (MHC), thus manipulating the T cell response towards or away from particular determinants. Altered processing of protein-protein complexes leading to enhanced loading of class II MHC and substantially lowered threshold for T cell activation suggests a novel mechanism that might reveal "cryptic" self determinants.
Pilot Design for Sparse Channel Estimation in OFDM-Based Cognitive Radio Systems (2014)

In this correspondence, sparse channel estimation is first introduced in orthogonal frequency-division multiplexing (OFDM)-based cognitive radio systems. Based on the results of spectrum sensing, the pilot design is studied by minimizing the coherence of the dictionary matrix used for sparse recovery. Then, it is formulated as an optimal column selection problem where a table is generated and the indexes of the selected columns of the table form a pilot pattern. A novel scheme using constrained cross-entropy optimization is proposed to obtain an optimized pilot pattern, where it is modeled as an independent Bernoulli random process. The updating rule for the probability of each active subcarrier selected as a pilot subcarrier is derived. A projection method is proposed so that the number of pilots during the optimization is fixed. Simulation results verify the effectiveness of the proposed scheme and show that it can achieve 11.5% improvement in spectrum efficiency with the same channel estimation performance compared with the least squares (LS) channel estimation.
Pushbroom stereo for high-speed navigation in cluttered environments (2015)

We present a novel stereo vision algorithm that is capable of obstacle detection on a mobile ARM processor at 120 frames per second. Our system performs a subset of standard block-matching stereo processing, searching only for obstacles at a single depth. By using an onboard IMU and state-estimator, we can recover the position of obstacles at all other depths, building and updating a local depth-map at framerate. Here, we describe both the algorithm and our implementation on a high-speed, small UAV, flying at over 20 MPH (9 m/s) close to obstacles. The system requires no external sensing or computation and is, to the best of our knowledge, the first high-framerate stereo detection system running onboard a small UAV.
Acute Myelogenous Leukemia: A Human Cell Line Responsive to Colony-Stimulating Activity (1978)

A permanent human cell line that maintains the granulocytic characteristics of acute myelogenous leukemia cells has been established. The cells of this line form myeloid colonies in soft gel culture in the presence of human colony-stimulating activity. The cell line may be useful for studying human acute myelogenous leukemia and the mechanism of response to colony-stimulating activity.
The role of cytokines in cancer-related fatigue (2001)

Fatigue is prominent in cancer patients and probably multifactorial in origin. Factors contributing to fatigue include anemia, weight loss, fever, pain, medication, and infection. In cancer patients, many of these factors are influenced by a frequently disrupted balance between endogenous cytokine levels and their natural antagonists. Indeed, cancer cells and the immune system appear to overexpress a range of cytokines in patients with malignancies. Some of these cytokines act as autocrine or paracrine growth factors for the neoplastic tissue while simultaneously causing secondary symptoms related to fatigue. For instance, cancer-associated anemia may be due to a blunted erythropoietin response and/or cytokines (interleukin-1 [IL-1], IL-6, tumor necrosis factor-alpha [TNF-alpha]), which suppress erythropoiesis. Cancerous cachexia, a wasting syndrome and a hallmark of cancer, can be attributed to loss of appetite or enhanced energy expenditure. Several different interleukins, as well as TNF, interferon-gamma, and leukemia inhibitory factor, act as cachectins in animal models. Similarly, fever and night sweats are influenced by pyrogenic cytokines. Recently, molecules that function as cytokine antagonists have been identified. These molecules may be exploitable in combating the components of cancer-related fatigue, and may inhibit tumor growth as well.
Characterization of a rat model of incisional pain (1996)

In this study, we developed a rat model of incisional pain. A 1-cm longitudinal incision was made through skin, fascia and muscle of the plantar aspect of the hindpaw in halothane-anesthetized rats. Withdrawal responses were measured using von Frey filaments at different areas around the wound before surgery and for the next 6 days. A cumulative pain score based on the weight bearing behavior of the animals was also utilized. The results of tests for withdrawal responses and scores based on weight bearing suggest that a surgical incision of the rat foot causes a reliable and quantifiable mechanical hyperalgesia lasting for several days after surgery. An incision that only included skin and fascia but not muscle in the foot caused less severe hyperalgesia during the initial postoperative period. Distinct areas around the wound had different withdrawal thresholds during the study period. Even remote sites as much as 10 mm from the wound showed persistent mechanical hyperalgesia. Selective denervations of the rat hindpaw prior to foot incision revealed both the sural and tibial nerves were responsible for transmitting input from the incision that produces hyperalgesia. This model should allow us to understand mechanisms of sensitization caused by surgery and investigate new therapies for postoperative pain in humans.
The role of αv integrins during angiogenesis: insights into potential mechanisms of action and clinical development (1999)

Angiogenesis depends on specific molecular interactions between vascular cells and components of the extracellular matrix (ECM). This Perspective focuses on the functional role of integrins in angiogenesis and neovascularization. Specifically, we discuss the mechanism by which antagonists of αv integrins disrupt angiogenesis in vivo and how they may impact patients with cancer and inflammatory disease. Role of ECM and integrins during angiogenesis and vasculogenesis. Angiogenesis depends not only on growth factors and their receptors but is also influenced by receptors for ECM proteins. In general, cell adhesion to the ECM is mediated by integrins, heterodimeric transmembrane proteins that comprise a diverse family of over 15 α and 8 β subunits. Integrin subunits can heterodimerize in over 20 combinations. Different integrin combinations may recognize a single ECM ligand, while others bind several different ECM proteins. Integrin-mediated adhesion leads to intracellular signaling events that regulate cell survival, proliferation, and migration (1). These signals include elevation in intracellular pH and calcium, inositol lipid synthesis, and the tyrosine phosphorylation of a wide range of nonreceptor tyrosine kinases such as focal adhesion kinase and Src kinases, as well as adaptor proteins such as Shc, p130 CAS, and Crk II. These signaling events trigger a number of downstream signals, including activation of the Ras/mitogen-activated protein (MAP) kinase pathway (1).