gebhart/patrepeval huggingface dataset:
Preparation of a cDNA Library and Preliminary Assessment of 1400 Genes from Mouse Growth Cartilage (1999)

Cartilage is an inconvenient tissue for the isolation of mRNA, and this has hampered studies of its component mRNAs conducted to date. Here, we describe the preparation of a good quality cDNA library from mouse growth cartilage (mGC). A total of 1.7 microg of poly(A)+ RNA was obtained from about 1200 pieces of the mGC zone of 60 young mice (BALB/c, 4 weeks old). Using this poly(A)+ RNA, we constructed a cDNA library using the pAP3neo vector by the linker-primer method. The complexity of the cDNA library was 2.6 x 106 colony-forming units (cfu), which signified that almost all of the mRNA components in the mGC were present in this cDNA library. From this library, 1401 clones were randomly selected and their insert sizes were examined. Of these clones, 166 (12%) had no inserts, 466 (33%) had inserts ranging in size from 0-0.9 kbp, 480 (34%) had inserts of 1. 0-1.9 kbp, 162 (12%) had inserts of 2.0-2.9 kbp, and 127 (9%) had sizes greater than 3.0 kbp. The average insert size was 1.45 kbp. The number of cfu and the insert size data qualified this library as of reasonably good quality. Clones with an insert size greater than 1 kbp (769 clones) were sequenced from their 5' ends. Among the 769 clones examined, 608 gave sequence data. Among these, 196 (32%) were unknown, 2 were only poly A, and 410 (67%) coded for known proteins. Of these, 55 clones coded for type II (pro)collagen, 54 for osteonectin, and 22 for other cartilage collagens (type IX, type X, and type XI). The rest included cartilage extracellular matrix genes, general cellular genes, and others. To judge further the quality of the library, 45 species coding for type II collagen chain were aligned based on their 5' end sequences. Three species (7%) contained almost the full-length insert, and the shortest one was 1. 5 kbp in length (full-length 5.6 kbp). These data show that this cDNA library is of reasonably good quality, making it likely that the large number of unknown inserts (32%) will provide a suitable pool for the identification and functional determination of new GC genes.
ElderFriends: Relieving Loneliness Among Elders (2006)

Educational Objectives 1. To discuss social isolation among older adults. 2. To promote awareness of the ElderFriends program, an intervention newly established in greater Richmond 3. To seek friendly visitors for the ElderFriends program.
Nitric Oxide-Releasing Amphiphilic Poly(amidoamine) (PAMAM) Dendrimers as Antibacterial Agents (2013)

A series of amphiphilic nitric oxide (NO)-releasing poly(amidoamine) (PAMAM) dendrimers with different exterior functionalities were synthesized by a ring-opening reaction between primary amines on the dendrimer and propylene oxide (PO), 1,2-epoxy-9-decene (ED), or a ratio of the two, followed by reaction with NO at 10 atm to produce N-diazeniumdiolate-modified scaffolds with a total storage of ~1 μmol/mg. The hydrophobicity of the exterior functionality was tuned by varying the ratio of PO and ED grafted onto the dendrimers. The bactericidal efficacy of these NO-releasing vehicles against established Gram-negative Pseudomonas aeruginosa biofilms was then evaluated as a function of dendrimer exterior hydrophobicity (i.e., ratio of PO/ED), size (i.e., generation), and NO release. Both the size and exterior functionalization of dendrimer proved important to a number of parameters including dendrimer-bacteria association, NO delivery efficiency, bacteria membrane disruption, migration within the biofilm, and toxicity to mammalian cells. Although enhanced bactericidal efficacy was observed for the hydrophobic chains (e.g., ED), toxicity to L929 mouse fibroblast cells was also noted at concentrations necessary to reduce bacterial viability by 5-logs (99.999% killing). The optimal PO to ED ratios for biofilm eradication with minimal toxicity against L929 mouse fibroblast cells were 7:3 and 5:5. The study presented herein demonstrated the importance of both dendrimer size and exterior properties in determining efficacy against established biofilms without compromising biocompatibility to mammalian cells.
Prefilter and Postfilter Cysteine/Cystine and Copper Concentrations in Pediatric Parenteral Nutrition Solutions (1992)

Pediatric amino acid products contain lower concentrations of methionine and require the addition of L-cysteine HCl just before infusion. Reports of a potential interaction between cysteine and copper, a routine addition to parenteral nutrition solutions, have appeared in the literature. This study serially evaluated cysteine/cystine and copper concentrations pre- and postfilter (0.22 microns) in two parenteral nutrition formulations prescribed for normal fluid (NF) or fluid-restricted (FR) pediatric patients. Solutions were infused via a peristaltic pump in vitro for 24 hours. Pre- and postfilter samples were obtained immediately after the infusion began (time 0) and at 1, 2, 3, 4, 8, 12, 16, 20, and 24 hours during the infusion. At 24 hours pre- and postfilter, cysteine/cystine were quantitated at 87.3% and 85% of the initial concentrations, respectively, for the NF solution and 92% and 91.5% for the FR solution. Pre- and postfilter copper was quantitated at 87.5% and 92.5% of the initial concentrations, respectively, for the NF solution and 88.2% and 95.2% for the FR solution. The 24 hour area under the curve for cysteine/cystine was 88.4% for the NF solution and 96.4% for the FR solution. For copper, the area under the curve for the NF solution was 99% and 96.7% for the FR solution. There was no visual evidence of incompatibility or precipitation. We conclude that copper-containing parenteral nutrition solutions with L-cysteine HCl added immediately before infusion are relatively stable after compounding and infusion over 24 hours.
Early Treatment of Obese (ob/ob) Mice with Triiodothyronine Increases Oxidative Metabolism in Muscle but not in Brown Adipose Tissue or Liver (1995)

We explored the possibility that early replacement of low triiodothyronine (T3) may improve the low oxidative metabolism in metabolically important tissues of ob/ob mice. Triiodothyronine doses (2.5 to 25.0 micrograms/100 g body wt) were injected intraperitoneally into ob/ob and non-ob/ob mice daily from 3 wk until 6 wk of age. Untreated ob/ob and non-ob/ob mice were injected with saline (pH 9.1). Food intake was equalized across all groups. At 6 wk of age, the O2 consumption of muscle, white and brown adipose tissues, and hepatocytes was measured. The saline-treated ob/ob mice showed lower muscle weights, higher fat pad and liver weights, and larger fat cell sizes than saline-treated non-ob/ob mice. In ob/ob mice, tissue O2 consumption was the same in muscle, lower in brown and white adipose tissues, but higher in liver compared with values in non-ob/ob mice. Triiodothyronine treatment in ob/ob mice resulted in lower values for body weight, liver weight, hepatocyte number, liver protein, epididymal fat pad weight, and white adipocyte number and size than in saline-treated ob/ob mice. Triiodothyronine treatment increased soleus muscle, liver and brown adipose tissue O2 consumption in non-ob/ob mice. In ob/ob mice, triiodothyronine increased only soleus muscle O2 consumption and required higher doses than in non-ob/ob mice to achieve an effect. These data are consistent with the concept of tissue triiodothyronine resistance in ob/ob mice. Low triiodothyronine levels and tissue resistance to triiodothyronine might be important early defects in this obesity syndrome.
A description of the amygdaloid complex in the rat and cat with observations on intra‐amygdaloid axonal connections (1978)

Abstract The cytoarchitectonic structure and divisions of the amygdaloid complex are described in the rat and cat, with special reference to the axonal connections of each of the amygdaloid nuclei, and to interspecies variations and similarities. Several intra‐amygdaloid connections are also described, based on autoradiographic experiments with small injections of 3 H‐amino acids into the individual nuclei. Although it has probably not been possible to determine all of the intra‐amygdaloid projections from these experiments, the connections which have been shown are very specific. The lateral nucleus projects to the basomedial nucleus, the lateral part of the central nucleus, and the periamygdaloid cortex, while the basolateral nucleus projects only to itself, the medial part of the central nucleus, and the nucleus of the lateral olfactory tract. The basomedial nucleus projects to the cellular layer of the medial nucleus and the amygdalo‐hippocampal area, while the molecular layer of these structures and of the posterior cortical nucleus, receives projections from the periamygdaloid cortex or from the endopiriform cortex. There are also interconnections between the medial and posterior cortical nuclei, and commissural connections between the posterior cortical nuclei of the two sides.
Sensing protein molecules using nanofabricated pores (2006)

We report the detection of protein molecules with nanofabricated pores using the resistive pulse sensing method. A 20-nm-thick silicon nitride membrane with a nanofabricated pore measuring about 55nm in diameter separated an electrolyte cell into two compartments. Current spike trains were observed when bovine serum albumin (BSA) was added to the negatively biased compartment. The magnitude of the spikes corresponded to particles 7–9nm in diameter (the size of a BSA molecule) passing through the pore. This suggests that the current spikes were current blockages caused by single BSA molecules. The presented nano-Coulter counting method could be applied to detect single protein molecules in free solution, and to study the translocation of proteins through a pore.
Complement Inhibitor Eculizumab in Atypical Hemolytic Uremic Syndrome (2009)

In this patient, complement inhibition by eculizumab temporarily terminated the microangiopathic hemolytic activity. Nevertheless, renal damage as a result of preceding and subsequent aHUS activity resulted in end-stage renal failure; therefore, therapeutic success may depend on early administration of eculizumab. The optimal duration of treatment may be variable and remains to be determined.
Confocal pattern period in multiple-aperture confocal imaging systems with coherent illumination (1997)

We have built a programmable multiple-aperture confocal imaging system that uses a spatial light modulator (a Texas Instruments digital micromirror device). Excellent axial resolution and confocal imaging quality have been experimentally demonstrated with this system, even when the distance between adjacent ON pixels is four times the size of the pixel aperture. By contrast, typical pinhole-based systems (e.g., a Nipkow disk) employ an adjacent aperture distance-to-size ratio of 10x . We have achieved improvement over such systems by 6.25x in both light-utilization efficiency and confocal image rate without adding more components and extra processing time.
New agents for the medical treatment of interstitial cystitis (2001)

Interstitial cystitis (IC) is a painful, sterile, disorder of the urinary bladder characterised by urgency, frequency, nocturia and pain. IC occurs primarily in women but also in men with recent findings indicating that chronic, abacterial prostatitis may be a variant of this condition. The prevalence of IC has ranged from about 8 - 60 cases/100,000 female patients depending on the population evaluated. About 10% of patients have severe symptoms that are associated with Hunner's ulcers on bladder biopsy; the rest could be grouped in those with or without bladder inflammation. Symptoms of IC are exacerbated by stress, certain foods and ovulatory hormones. Many patients also experience allergies, irritable bowel syndrome (IBS) and migraines. There have been various reports indicating dysfunction of the bladder glycosaminoglycan (GAG) protective layer and many publications showing a high number of activated bladder mast cells. Increasing evidence suggests that neurogenic inflammation and/or neuropathic pain is a major component of IC pathophysiology. Approved treatments so far include intravesical administration of dimethylsulphoxide (DMSO) or oral pentosanpolysulphate (PPS). New treatments focus on the combined use of drugs that modulate bladder sensory nerve stimulation (neurolytic agents), inhibit neurogenic activation of mast cells, or provide urothelial cytoprotection, together with new drugs with anti-inflammatory activity.
State-of-Charge Estimation of the Lithium-Ion Battery Using an Adaptive Extended Kalman Filter Based on an Improved Thevenin Model (2011)

An adaptive Kalman filter algorithm is adopted to estimate the state of charge (SOC) of a lithium-ion battery for application in electric vehicles (EVs). Generally, the Kalman filter algorithm is selected to dynamically estimate the SOC. However, it easily causes divergence due to the uncertainty of the battery model and system noise. To obtain a better convergent and robust result, an adaptive Kalman filter algorithm that can greatly improve the dependence of the traditional filter algorithm on the battery model is employed. In this paper, the typical characteristics of the lithium-ion battery are analyzed by experiment, such as hysteresis, polarization, Coulomb efficiency, etc. In addition, an improved Thevenin battery model is achieved by adding an extra <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">RC</i> branch to the Thevenin model, and model parameters are identified by using the extended Kalman filter (EKF) algorithm. Further, an adaptive EKF (AEKF) algorithm is adopted to the SOC estimation of the lithium-ion battery. Finally, the proposed method is evaluated by experiments with federal urban driving schedules. The proposed SOC estimation using AEKF is more accurate and reliable than that using EKF. The comparison shows that the maximum SOC estimation error decreases from 14.96% to 2.54% and that the mean SOC estimation error reduces from 3.19% to 1.06%.
Autologous dendritic cells transfected with prostate-specific antigen RNA stimulate CTL responses against metastatic prostate tumors (2002)

Autologous dendritic cells (DCs) transfected with mRNA encoding prostate-specific antigen (PSA) are able to stimulate potent, T cell–mediated antitumor immune responses in vitro. A phase I trial was performed to evaluate this strategy for safety, feasibility, and efficacy to induce T cell responses against the self-protein PSA in patients with metastatic prostate cancer. In 13 study subjects, escalating doses of PSA mRNA–transfected DCs were administered with no evidence of dose-limiting toxicity or adverse effects, including autoimmunity. Induction of PSA-specific T cell responses was consistently detected in all patients, suggesting in vivo bioactivity of the vaccine. Vaccination was further associated with a significant decrease in the log slope PSA in six of seven subjects; three patients that could be analyzed exhibited a transient molecular clearance of circulating tumor cells. The demonstration of vaccine safety, successful in vivo induction of PSA-specific immunity, and impact on surrogate clinical endpoints provides a scientific rationale for further clinical investigation of RNA-transfected DCs in the treatment of human cancer.
Removal of residual koh from palm oil based biodiesel using deep eutectic solvents (2011)

The Produced biodiesel through the alkali-catalyzed transesterification must be treated before utilization as an alternative fuel. Low content of catalyst is one of the important pointers needed for passing the EN 14214 and ASTM D6751 international biodiesel standards. In this work, potassium hydroxide (KOH) was selected as catalyst for the transesterification reaction. Two different salts namely; methyl triphenyl phosphunium bromide (MTPB) and choline chloride (ChCl) in combination with four different hydrogen bond donors namely; glycerol, ethylene glycol, 2,2,2-trifluoroacetamide and triethylen glycol were selected to synthesis eighteen deep eutectic solvents (DESs). These DESs were employed as solvents for the removal of residual KOH from palm oil based biodiesel. The results revealed that all tested DESs were able to reduce the content of KOH. The [ChCl:glycerol] DESs and [MTPB:glycerol] DESs proved to be capable of high KOH removal from palm oil-based biodiesel with an average removal efficiency of 98.59% and 97.57% respectively.
Statistical significance for genomewide studies (2003)

With the increase in genomewide experiments and the sequencing of multiple genomes, the analysis of large data sets has become commonplace in biology. It is often the case that thousands of features in a genomewide data set are tested against some null hypothesis, where a number of features are expected to be significant. Here we propose an approach to measuring statistical significance in these genomewide studies based on the concept of the false discovery rate. This approach offers a sensible balance between the number of true and false positives that is automatically calibrated and easily interpreted. In doing so, a measure of statistical significance called the q value is associated with each tested feature. The q value is similar to the well known p value, except it is a measure of significance in terms of the false discovery rate rather than the false positive rate. Our approach avoids a flood of false positive results, while offering a more liberal criterion than what has been used in genome scans for linkage.
Arylamine N-acetyltransferase (NAT2) mutations and their allelic linkage in unrelated Caucasian individuals: correlation with phenotypic activity. (1995)

The polymorphic arylamine N-acetyltransferase (NAT2; EC 2.3.1.5) is supposed to be a susceptibility factor for several drug side effects and certain malignancies. A group of 844 unrelated German subjects was genotyped for their acetylation type, and 563 of them were also phenotyped. Seven mutations of the NAT2 gene were evaluated by allele-specific PCR (mutation 341C to T) and PCR-RFLP for mutations at nt positions 191, 282, 481, 590, 803, and 857. From the mutation pattern eight different alleles, including the wild type coding for rapid acetylation and seven alleles coding for slow phenotype, were determined. Four hundred ninety-seven subjects had a genotype of slow acetylation (58.9%; 95% confidence limits 55.5%-62.2%). Phenotypic acetylation capacity was expressed as the ratio of 5-acetylamino-6-formylamino-3-methyluracil and 1-methylxanthine in urine after caffeine intake. Some 6.7% of the cases deviated in genotype and phenotype, but sequencing DNA of these probands revealed no new mutations. Furthermore, linkage pattern of the mutations was always confirmed, as tested in 533 subjects. In vivo acetylation capacity of homozygous wild-type subjects (NAT2*4/*4) was significantly higher than in heterozygous genotypes (P = .001). All mutant alleles showed low in vivo acetylation capacities, including the previously not-yet-defined alleles *5A, *5C, and *13. Moreover, distinct slow genotypes differed significantly among each other, as reflected in lower acetylation capacity of *6A, *7B, and *13 alleles than the group of *5 alleles. The study demonstrated differential phenotypic activity of various NAT2 genes and gives a solid basis for clinical and molecular-epidemiological investigations.
Impending extinction crisis of the world’s primates: Why primates matter (2017)

Nonhuman primates, our closest biological relatives, play important roles in the livelihoods, cultures, and religions of many societies and offer unique insights into human evolution, biology, behavior, and the threat of emerging diseases. They are an essential component of tropical biodiversity, contributing to forest regeneration and ecosystem health. Current information shows the existence of 504 species in 79 genera distributed in the Neotropics, mainland Africa, Madagascar, and Asia. Alarmingly, ~60% of primate species are now threatened with extinction and ~75% have declining populations. This situation is the result of escalating anthropogenic pressures on primates and their habitats-mainly global and local market demands, leading to extensive habitat loss through the expansion of industrial agriculture, large-scale cattle ranching, logging, oil and gas drilling, mining, dam building, and the construction of new road networks in primate range regions. Other important drivers are increased bushmeat hunting and the illegal trade of primates as pets and primate body parts, along with emerging threats, such as climate change and anthroponotic diseases. Often, these pressures act in synergy, exacerbating primate population declines. Given that primate range regions overlap extensively with a large, and rapidly growing, human population characterized by high levels of poverty, global attention is needed immediately to reverse the looming risk of primate extinctions and to attend to local human needs in sustainable ways. Raising global scientific and public awareness of the plight of the world's primates and the costs of their loss to ecosystem health and human society is imperative.
Distribution of cocaine recognition sites in monkey brain: I. In vitro autoradiography with [3H]CFT (1991)

The cocaine analog [3H]CFT ([3H]WIN 35,428) was used to map and characterize cocaine recognition sites in the squirrel monkey brain by quantitative autoradiography. Coronal tissue sections were incubated with 5 nM [3H]CFT to measure total binding or with [3H]CFT in the presence of 30 microM (-)-cocaine to measure nonspecific binding. High densities of [3H]CFT binding sites were present in dopamine-rich brain regions, including the caudate nucleus, putamen, nucleus accumbens, and olfactory tubercle. In each of these regions specific binding was greater than 90% of total binding. Several additional brain regions exhibited intermediate densities of [3H]CFT binding, including the substantia nigra, the zona incerta, the amygdala, and the hypothalamus. Low, though measurable levels of binding were observed in the bed nucleus of the stria terminalis, the ventral tegmental area, the medial preoptic area, the pineal, the hippocampus, and thalamic central nuclei. Near-background levels of binding were found in white matter, cortical regions, globus pallidus, and cerebellum. The pharmacological specificity of [3H]CFT binding in various brain regions was determined in competition studies using [3H]CFT and a range of concentrations of selected monoamine uptake inhibitors. In all brain regions examined, stereoselective inhibition of [3H]CFT binding was observed for the (-) over the (+) isomer of cocaine. For other drugs tested, competition experiments indicated a rank order of potency of GBR 12909 greater than or equal to CFT greater than bupropion, suggestive of binding of [3H]CFT to elements of the dopamine transport system. The results demonstrate that although densities of [3H]CFT binding sites are highest in the caudate nucleus, putamen, and nucleus accumbens/olfactory tubercle, significant levels of binding can be detected in other brain regions that may contribute to the behavioral and physiological effects of cocaine.
Cerebrospinal fluid inhibits Alzheimer β‐amyloid fibril formation in vitro (1993)

Alzheimer's disease is characterized by the deposition of beta-protein (A beta) as amyloid. Recently, it was found that A beta is a normal component of serum and cerebrospinal fluid. Synthetic peptides homologous to A beta form amyloid-like fibrils spontaneously in water or physiological solutions. Using a peptide homologous to A beta 1-40, we find that fibril formation is inhibited by the presence of cerebrospinal fluid.