gebhart/patrepeval huggingface dataset:
Reduced Bone Mineral Content in Totally Thyroidectomized Patients: Possible Effect of Calcitonin Deficiency* (1983)

To further investigate the relationship between calcitonin deficiency and osteoporosis, we have measured bone mineral content (BMC) by single photon absorptiometry in patients made iatrogenically calcitonin deficient by prior total thyroidectomy for thyroid cancer. Compared to sex-, age-, height-, and weight-matched normal controls, male patients had a significantly lower mean BMC at the midradius (1.162 +/- 0.02 vs. 1.301 +/- 0.05 g/cm; P less than 0.02) and the distal radius (1.180 +/- 0.04 vs. 1.338 +/- 0.04 g/cm; P less than 0.01). Female patients also had a significantly lower BMC at the midradius compared to those of a similarly matched group of normal controls and a group of patients on L-T4 suppression for nodular goiters (0.791 +/- 0.04 vs. 0.896 +/- 0.05 vs. 0.891 +/- 0.03 g/cm; P less than 0.025). We conclude that calcitonin deficiency from surgical thyroidectomy is associated with significant decreases in bone mineral content in both sexes. This lends further support to the concept that calcitonin deficiency may be an important causative factor in the development of osteoporosis.
Two mammalian helix-loop-helix factors structurally related to Drosophila hairy and Enhancer of split. (1992)

We report the molecular characterization of two novel rat helix-loop-helix (HLH) proteins, designated HES-1 and HES-3, that show structural homology to the Drosophila hairy and Enhancer of split [E(spl)] proteins, both of which are required for normal neurogenesis. HES-1 mRNA, expressed in various tissues of both embryos and adults, is present at a high level in the epithelial cells, including the embryonal neuroepithelial cells, as well as in the mesoderm-derived tissues such as the embryonal muscle. In contrast, HES-3 mRNA is produced exclusively in cerebellar Purkinje cells. HES-1 represses transcription by binding to the N box, which is a recognition sequence of E(spl) proteins. Interestingly, neither HES-1 nor HES-3 alone interacts efficiently with the E box, but each protein decreases the transcription induced by E-box-binding HLH activators such as E47. Furthermore, HES-1 also inhibits the functions of MyoD and MASH1 and effectively diminishes the myogenic conversion of C3H10T1/2 cells induced by MyoD. These results suggest that HES-1 may play an important role in mammalian development by negatively acting on the two different sequences while HES-3 acts as a repressor in a specific type of neurons.
Expression of GABA transporter subtypes (GAT1, GAT3) in the adult rabbit retina (1999)

GAT3 is probably involved in both neuronal and glial GABA uptake whereas GAT1 is involved in predominantly neuronal uptake, and possibly also into non-GABA-ergic amacrine cells. Further, there may be at least two populations of GABA containing neurons.
PSFM-DBT: Identifying DNA-Binding Proteins by Combing Position Specific Frequency Matrix and Distance-Bigram Transformation (2017)

DNA-binding proteins play crucial roles in various biological processes, such as DNA replication and repair, transcriptional regulation and many other biological activities associated with DNA. Experimental recognition techniques for DNA-binding proteins identification are both time consuming and expensive. Effective methods for identifying these proteins only based on protein sequences are highly required. The key for sequence-based methods is to effectively represent protein sequences. It has been reported by various previous studies that evolutionary information is crucial for DNA-binding protein identification. In this study, we employed four methods to extract the evolutionary information from Position Specific Frequency Matrix (PSFM), including Residue Probing Transformation (RPT), Evolutionary Difference Transformation (EDT), Distance-Bigram Transformation (DBT), and Trigram Transformation (TT). The PSFMs were converted into fixed length feature vectors by these four methods, and then respectively combined with Support Vector Machines (SVMs); four predictors for identifying these proteins were constructed, including PSFM-RPT, PSFM-EDT, PSFM-DBT, and PSFM-TT. Experimental results on a widely used benchmark dataset PDB1075 and an independent dataset PDB186 showed that these four methods achieved state-of-the-art-performance, and PSFM-DBT outperformed other existing methods in this field. For practical applications, a user-friendly webserver of PSFM-DBT was established, which is available at http://bioinformatics.hitsz.edu.cn/PSFM-DBT/.
Ouabain binding sites and (Na+,K+)-ATPase activity in rat cardiac hypertrophy. Expression of the neonatal forms. (1986)

The adaptation of the myocardium to mechanical overload which results in cardiac hypertrophy involves several membrane functions. The digitalis receptor in sarcolemma vesicles from hypertrophied rat hearts is characterized by binding of [3H]ouabain and ouabain-induced inhibition of (Na+,K+)-ATPase. The results show the existence of two families of ouabain binding sites with apparent dissociation constants (Kd) of 1.8-3.2 X 10(-8) M and 1-8 X 10(-6) M, respectively, which are similar to those found in normal hearts. The presence of the high affinity receptor in hypertrophied rat heart is correlated to a detectable inhibition of the (Na+,K+)-ATPase (IC50 = 1-3 X 10(-8) M). However, the high and low affinity sites in hypertrophied hearts bind and release ouabain at 4-5-fold slower rates than the corresponding sites in normal hearts. These properties are similar to that we observed in newborn rat cardiac preparations. Taken together with the expression of myosin isoforms (Schwartz, K., Lompre, A.M., Bouveret, P., Wisnewsky, C., and Whalen, R.G. (1982) J. Biol. Chem. 23, 14412-14418), our data show that the physiological adaptation of the heart also involves the resurgence of the neonatal forms of the digitalis receptor.
Comparative efficacy and safety of intravenous ferric carboxymaltose in the treatment of postpartum iron deficiency anemia (2008)

Parenteral iron carboxymaltose is a safe and effective treatment option for postpartum anemia, with advantages of a shorter treatment period, better compliance, rapid normalization of iron storages, and lower incidence of gastrointestinal side effects.
Determinants in the 5' noncoding region of poliovirus Sabin 1 RNA that influence the attenuation phenotype (1989)

A number of recombinants between the virulent Mahoney and attenuated Sabin strains of type 1 poliovirus were constructed by using infectious cDNA clones of the two strains. To identify a strong neurovirulence determinant(s) residing in the genome region upstream of nucleotide position 1122, these recombinant viruses were subjected to biological tests, including monkey neurovirulence tests. The results of the monkey neurovirulence tests suggested the important contribution of an adenine residue (Mahoney type) at position 480 to the expression of the neurovirulence phenotype of type 1 poliovirus. This nucleotide, however, had only a minor effect, if any, on viral temperature sensitivity. Monkey neurovirulence tests on the recombinant virus whose genome had a guanine residue (Sabin type) at position 480 and variants generated from this recombinant virus in the central nervous system of monkeys strongly suggested that only one nucleotide change, from adenine to guanine, was not sufficient for full expression of the attenuation phenotype encoded by this genome region. These results suggest that the expression of the attenuation phenotype depends on the highly ordered structure formed in the 5' noncoding sequence and that the formation of such a structure is possibly influenced by the nucleotide at position 480. Furthermore, in vitro biological tests performed on viruses recovered from the central nervous system of monkeys injected with a temperature-sensitive recombinant virus showing the small-plaque and d phenotypes revealed that most of the recovered viruses had even higher temperature sensitivities and that all of the recovered viruses that had acquired the large-plaque phenotype had lost the d phenotype to some extent. These results indicate that there may be an unknown selection pressure(s) in the central nervous system and that common determinants might be involved in the expression of the small-plaque and d phenotypes.
Does Simian Virus 5 Infect Humans? (1984)

Simian virus 5 (SV5) isolates derived after co-cultivation of human bone marrow aspirates of multiple sclerosis (MS) patients were shown by immunoprecipitation, cross-neutralization and haemagglutination inhibition techniques to be similar antigenically but not identical to the prototype strain. Analyses of human sera (MS and control) showed that about 20% contained neutralizing antibodies to SV5 and immunoprecipitated the specific SV5 HN polypeptide. A competition assay using a specific SV5 monoclonal antibody confirmed that a human serum containing such neutralizing activity also blocked a specific SV5 epitope whereas another human serum with demonstrable antibodies to the related human parainfluenza virus type 2 did not block this epitope. These tests therefore suggested that SV5 can infect humans. However, there was no indication, on the basis of these tests, of any aetiological relationship of the SV5 infection to the induction of MS.
Aw Foh Du? a Rhetorical Question (1985)

Almost every afternoon of the dry season the pulse of Bo- town slows to a lull and Bo assumes a dream-like presence allowing the alchemy of sun and heat to cast its spell of quiescence.Brief, but necessary, it lends one resilience to confront another day in the glare of tropical West Africa.The concrete-block buildings stand stark naked in blinding pink, white, and green, unprotected by the clothing of shade trees.If you half-close your eyes you can visualize Bo as it once thrivedat the beginning of the centuryin colorful tribal array, the center of trade in this Southern province of Sierra Leone.The clatter of calls in Krio, Mende, Timne, and Englishreplete with seventeen other languagescrowd the air with greetings and laughter.The smells of produce, fufu, tobacco, poio, and the fish, fresh from Freetown, all blend in a potion of excitement and promise.There is a bustle among the vividly colored figures, promising growth and abundance as the business of trade occupies young and old in happy collusion.
Potential serum biomarkers for glioblastoma diagnostic assessed by proteomic approaches (2014)

Proteomic technologies have been used to investigate the protein profile of glioblastoma patients and established several potential diagnostic biomarkers. While it is unlikely for a single biomarker to be highly effective for glioblastoma diagnostic, our data proposed an alternative and efficient approach by using a novel combination of multiple biomarkers.
Developmental consequences of abnormal folate transport during murine heart morphogenesis (2004)

Our findings demonstrate for the first time a prominent role of the Folbp1 gene in mediating susceptibility to heart defects.
Cytokinins in Plant Pathogenic Bacteria and Developing Cereal Grains (1993)

Cytokinin analysis by immunoaffinity chromatography (IAC), high-performance liquid chromatography (HPLC) and radioimmunoassay (RIA) or enzyme-linked immunosorption assay (ELISA) has been used to study two separate topics: the role of tRNA in bacterial cytokinin biosynthesis and the changes in cytokinin concentration which occur during cereal grain development. Transfer RNA isopentenylation in the gall-forming plant pathogen Agrobacterium tumefaciens is encoded by the chromosomal miaA locus. Mutation of miaA reduces tRNA isopentenylation significantly and preliminary data suggest that turnover of isopentenylated tRNA is responsible for low level secretion of free N6-isopentenyladenine (iP) by the bacteria. However, the major route of cytokinin biosynthesis by gall-forming plant patho- genic bacteria is not via tRNA turnover but by direct biosynthesis mediated by dimethylallylpyro- phosphate: 5'-AMP transferase (DMAPP :AMP transferase) encoded by such genes as ipt, tzs (from A, tumefaciens) or ptz (from Pseudomonas savastanoi). Analysis of cytokinin levels in developing wheat and rice grains in the period immediately following pollination showed large transient increases in zeatin (Z) and zeatin riboside (ZR) which coincided with the period of maximum endosperm cell division reported by others. Detailed analyses of maize kernels, where development can be staged readily, showed that Z and ZR concentrations peaked 9 days after pollination (DAP). During the period 8-10 DAP, cytokinin oxidase underwent a significant increase in specific activity, indicating that cytokinin catabolism was enhanced as endosperm cell division ended.
Superresolution with Plenoptic 2.0 Cameras (2009)

We demonstrate working superresolution with Plenoptic 2.0 camera without need for traditional image registration in software. This paper describes our method, based only on the camera geometry and microlens parameters.
Two-directional cascade molecules: synthesis and characterization of [9]-n-[9] arborols (1986)

A series of two-directional cascade molecules (arborols) has been synthesized by a two-step nucleophilic substitution–amidation procedure; the [9]-10-[9] arborol forms a thermally reversible aqueous gel, which has been investigated via microscopy and light scattering techniques.
Stimuli-responsive microgel-based etalons for optical sensing (2015)

Responsive polymers have found numerous applications over the years. This review highlights their use as components of photonic materials, with emphasis on responsive polymer-based etalons. The use of these materials for sensing and biosensing is detailed.
Genotypic identification of rickettsiae and estimation of intraspecies sequence divergence for portions of two rickettsial genes (1991)

DNA sequences from specific genes, amplified by the polymerase chain reaction technique, were used as substrata for nonisotopic restriction endonuclease fragment length polymorphism differentiation of rickettsial species and genotypes. The products amplified using a single pair of oligonucleotide primers (derived from a rickettsial citrate synthase gene sequence) and cleaved with restriction endonucleases were used to differentiate almost all recognized species of rickettsiae. A second set of primers was used for differentiation of all recognized species of closely related spotted fever group rickettsiae. The procedure circumvents many technical obstacles previously associated with identification of rickettsial species. Multiple amplified DNA digest patterns were used to estimate the intraspecies nucleotide sequence divergence for the genes coding for rickettsial citrate synthase and a large antigen-coding gene of the spotted fever group rickettsiae. The estimated relationships deduced from these genotypic data correlate reasonably well with established rickettsial taxonomic schemes.
Amino acid synthetic media for fungal pathogens based on aminopeptidase specificities:Histoplasma capsulatum, Blastomyces dermititidis, Paracoccidioides brasiliensis and Cryptococcus neoformans. (1975)

The development of simple and chemically defined liquid media for Histoplasma capsulatum, Blastomyces dermatitidis, Paracoccidioides brasiliensis and Crypto-occus neoformans according to their aminopeptidases profiles as amino acid requirement was described. When 1.5% purified agar was added, these media also supported excellent mycelial growth and sporulation of the deep mycoses. H. capsulatum was converted to and maintained in yeast phase when 0.1% L-cystine was added to the solid medium incubated at 37 degrees C.
Decalcified bone as a substrate for osteogenesis. An appraisal of the interrelation of bone and marrow in combined grafts (1977)

This paper examines the fate of decalcified allografts (homografts) of iliac cancellous bone impregnated with autologous red marrow and implanted intermuscularly into the anterior abdominal wall of rabbits. In contrast to the findings of Urist and other workers that cortical bone decalcified with hydrochloric acid (HCl) and then freeze-dried is inductive to new bone formation in various heterotopic sites, evidence is presented that iliac bone decalcified by HCl and grafted alone to a muscular site is itself very weakly inductive to bone formation. However, when combined with autologous bone marrow the HCl-decalcified bone provides a better substrate for bone formation by marrow cells than does either undecalcified iliac bone, or iliac bone decalcified with ethylene-diamine-tetra-acetic acid. The freezing or freeze-drying of decalcified bone does not affect new bone formation when implanted alone or with autologous marrow. The differences between the cortical and cancellous bone as inductive substrates for osteogenesis are discussed and the interrelationship of bone and marrow in combined bone grafts are re-evaluated.
Strategic Cognitive Sequencing: A Computational Cognitive Neuroscience Approach (2013)

We address strategic cognitive sequencing, the "outer loop" of human cognition: how the brain decides what cognitive process to apply at a given moment to solve complex, multistep cognitive tasks. We argue that this topic has been neglected relative to its importance for systematic reasons but that recent work on how individual brain systems accomplish their computations has set the stage for productively addressing how brain regions coordinate over time to accomplish our most impressive thinking. We present four preliminary neural network models. The first addresses how the prefrontal cortex (PFC) and basal ganglia (BG) cooperate to perform trial-and-error learning of short sequences; the next, how several areas of PFC learn to make predictions of likely reward, and how this contributes to the BG making decisions at the level of strategies. The third models address how PFC, BG, parietal cortex, and hippocampus can work together to memorize sequences of cognitive actions from instruction (or "self-instruction"). The last shows how a constraint satisfaction process can find useful plans. The PFC maintains current and goal states and associates from both of these to find a "bridging" state, an abstract plan. We discuss how these processes could work together to produce strategic cognitive sequencing and discuss future directions in this area.
Acetate metabolism by Escherichia coli in high-cell-density fermentation (1994)

Little is known about the cellular physiology of Escherichia coli at high cell densities (e.g., greater than 50 g [dry cell weight] per liter), particularly in relation to the cellular response to different growth conditions. E. coli W3100 cultures were grown under identical physical and nutritional conditions, by using a computer-controlled fermentation system which maintains the glucose concentration at 0.5 g/liter, to high cell densities at pH values of 6.0, 6.5, 7.0, and 7.5. The data suggest a relationship between the pH of the environment and the amount of acetate excreted by the organism during growth. At pH values of 6.0 and 6.5, the acetate reached a concentration of 6 g/liter, whereas at pH 7.5, the acetate reached a concentration of 12 g/liter. Furthermore, at pH values of 6.0 to 7.0, the E. coli culture undergoes a dramatic metabolic switch in which oxygen and glucose consumption and CO2 evolution all temporarily decreased by 50 to 80%, with a concomitant initiation of acetate utilization. After a 30-min pause in which approximately 50% of the available acetate is consumed, the culture recovers and resumes consuming glucose and oxygen and producing acetate and CO2 at preswitch levels. During the switch period, the specific activity of isocitrate lyase typically increases approximately fourfold.
Growth Characteristics of Cytomegalovirus in Human Fibroblasts with Demonstration of Protein Synthesis Early in Viral Replication (1973)

In high-multiplicity infection of human fibroblasts, human cytomegalovirus of WI-38 human diploid cells produced early cell rounding 6 to 24 h after inoculation. This early cell rounding was caused only by inoculation with infectious virions. Inhibitors of protein synthesis, but not DNA inhibitors, prevented this cytopathic effect. Apparently, a new protein is synthesized in infected fibroblasts from about 2 h postinoculation. Infectivity of cell-associated and supernatant infectious virus reached maximal levels at 5 to 7 and 10 days postinoculation, respectively. Synthesis of DNA, infectious virus, complement-fixing antigen, and precipitin antigen all began between 24 and 48 h, with the bulk of synthesis occurring 48 to 96 h postinoculation.
The Low-Density Lipoprotein Receptor-Related Protein Is a Pro-Survival Receptor in Schwann Cells: Possible Implications in Peripheral Nerve Injury (2006)

Schwann cells undergo phenotypic modulation in peripheral nerve injury. In the adult rodent, Schwann cells are resistant to death-promoting challenges. The responsible receptors and signaling pathways are incompletely understood. In this study, we demonstrate that low-density lipoprotein receptor-related protein-1 (LRP-1) is expressed in adult sciatic nerve. After crush injury, LRP-1 is lost from the axoplasm and substantially upregulated in Schwann cells. Increased LRP-1 mRNA expression was observed locally at the injury site in multiple forms of sciatic nerve injury, including crush injury, chronic constriction injury, and axotomy. Endogenously produced tumor necrosis factor-alpha (TNF-alpha) was mostly responsible for the increase in LRP-1 expression; this activity was reproduced by direct injection of TNF-alpha into injured nerves in the TNF-alpha gene knock-out mouse. TNF receptor II was primarily involved. TNF-alpha also increased LRP-1 mRNA in Schwann cells in primary culture. Silencing of Schwann cell LRP-1 with siRNA decreased phosphorylated Akt and increased activated caspase-3. Equivalent changes in cell signaling were observed in LRP-1-deficient murine embryonic fibroblasts. Schwann cell death was induced in vitro by serum withdrawal or TNF-alpha, to a greater extent when LRP-1 was silenced. Schwann cell death was induced in vivo by injecting the LRP-1 antagonist, receptor-associated protein, into axotomy sites in adult rats. These results support a model in which LRP-1 functions as a pro-survival receptor in Schwann cells.
A photocatalyzed aliphatic fluorination (2014)

We disclose a new approach to the catalysis of alkane fluorination employing ultraviolet light and a photosensitizer, 1,2,4,5-tetracyanobenzene (TCB).
Subtilisin Amylosacchariticus (1972)

The denatured diisopropylphosphoryl derivative of subtilisin Amylosacchariticus was digested with chymotrypsin and the peptides resolved by ion exchange chromatography on Dowex 50-X2. The 44 peptides obtained in pure form accounted for 259 of the 275 residues in the protein. Sequence studies were performed on some of these peptides. This information combined with that previously obtained from tryptic and cyanogen bromide peptides and, in some cases, from comparisons of the sequence to that in subtilisin BPN′ has provided enough evidence for the complete amino acid sequence of subtilisin Amylosacchariticus. There are 35 differences in sequence between subtilisins Amylosacchariticus and BPN′ with most of these being conservative in nature.