gebhart/patrepeval huggingface dataset:
HIV Vaccine Development: Lessons from the Past and Promise for the Future (2003)

The global HIV epidemic continues to expand, exceeding previous predictions and causing tremendous suffering. An effective vaccine represents the best hope to curtail the HIV epidemic. The past fifteen years of HIV vaccine clinical trials have not identified an ideal HIV vaccine, but have provided many valuable lessons that contribute to the current generation of promising HIV vaccine regimens. An enhanced understanding of HIV and SIV immunopathogenesis has facilitated the design of vaccination regimens that elicit specific immune responses and effector mechanisms. Intensive investigation of recombinant gp120 subunit vaccines has revealed a previously unexpected complexity in eliciting neutralizing antibodies that are active against primary isolate viruses. The importance of CD8+ CTL responses in controlling HIV and SIV viremia has led to a series of vaccine candidates that effectively induce these responses. Proof that vaccination can prevent SIV/HIV disease has now been obtained in simian models of AIDS. A number of promising HIV vaccine regimens are currently being evaluated in human trials, and the pipeline of new vaccine vectors and combination regimens appears robust. Although challenges to the development of a safe and effective global HIV vaccine remain, the outlook for HIV vaccines in the future is bright.
Methods for separation of contributions from two radionuclides in autoradiography with a silicon strip detector (2000)

Two methods have been developed for the separation of contributions from two different nuclides in an autoradiography picture. Both approaches, a modified least squares (LS) and a maximum likelihood (ML) algorithm, are based on the position and energy information available from a digital detector. Tests and comparisons, using artificially as well as measured data, demonstrate that the ML approach performs slightly better, but is much more computationally demanding than the LS method.
Aortic Coarctation: A Comprehensive Analysis of Shape, Size, and Contractility of the Fetal Heart (2019)

The results demonstrate previously unappreciated differences in the shape, size, and function of the heart in fetuses with CoA. These differences may assist examiners in identifying fetuses with CoA.
Ultrastructural localization of cellular prion protein (PrPc) at the neuromuscular junction (1999)

We examined the localization of the normal cellular isoform of prion protein (PrPc) in mammalian skeletal muscle. Using two anti-PrP antibodies, the neuromuscular junction (NMJ) was preferentially stained after immunohistofluorescence. The mouse, hamster, and human NMJ displayed a fluorescent signal specific for PrPc. Postembedding immunoelectron microscopy analysis performed in the mouse muscle showed that the PrPc-specific colloidal gold immunolabelling was concentrated over the sarcoplasmic cytoplasm. The membrane of the postsynaptic domain was devoid of gold particles, while a weak signal was occasionally observed close to the presynaptic vesicles of the terminal axons. These results indicate that the PrP gene is expressed in mammalian muscle at the NMJ. The subsynaptic sarcoplasm of the NMJ appears to be the privileged site where PrPc presumably associated with endosome membrane may play a role in either physiological activity or maintenance of the morphological integrity of the synapse.
Capacity of Discrete Molecular Diffusion Channels (2011)

In diffusion-based molecular communications, messages can be conveyed via the variation in the concentration of molecules in the medium. In this paper, we intend to analyze the achievable capacity in transmission of information from one node to another in a diffusion channel. We observe that because of the molecular diffusion in the medium, the channel possesses memory. We then model the memory of the channel by a two-step Markov chain and obtain the equations describing the capacity of the diffusion channel. By performing a numerical analysis, we obtain the maximum achievable rate for different levels of the transmitter power, i.e., the molecule production rate.
Synthesis of poly(3-hydroxyalkanoate) (PHA) conjugates: PHA-carbohydrate and PHA-synthetic polymer conjugates (1991)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis of poly(3-hydroxyalkanoate) (PHA) conjugates: PHA-carbohydrate and PHA-synthetic polymer conjugatesManssur Yalpani, Robert H. Marchessault, Frederick G. Morin, and Clevys J. MonasteriosCite this: Macromolecules 1991, 24, 22, 6046–6049Publication Date (Print):October 1, 1991Publication History Published online1 May 2002Published inissue 1 October 1991https://pubs.acs.org/doi/10.1021/ma00022a024https://doi.org/10.1021/ma00022a024research-articleACS PublicationsRequest reuse permissionsArticle Views823Altmetric-Citations85LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
HGF/SF Activates Glycolysis and Oxidative Phosphorylation in DA3 Murine Mammary Cancer Cells (2000)

Hepatocyte growth factor/scatter factor (HGF/SF) is a paracrine growth factor which increases cellular motility and has also been implicated in tumor development and progression and in angiogenesis. Little is known about the metabolic alteration induced in cells following Met-HGF/SF signal transduction. The hypothesis that HGF/SF alters the energy metabolism of cancer cells was investigated in perfused DA3 murine mammary cancer cells by nuclear magnetic resonance (NMR) spectroscopy, oxygen and glucose consumption assays and confocal laser scanning microscopy (CLSM). 31P NMR demonstrated that HGF/SF induced remarkable alterations in phospholipid metabolites, and enhanced the rate of glucose phosphorylation (P < .05). 13C NMR measurements, using [13C1]-glucose-enriched medium, showed that HGS/SF reduced the steady state levels of glucose and elevated those of lactate (P < .05). In addition, HGF/SF treatment increased oxygen consumption from 0.58+/-0.02 to 0.71+/-0.03 micromol/hour per milligram protein (P < .05). However, it decreased CO2 levels, and attenuated pH decrease. The mechanisms of these unexpected effects were delineated by CLSM, using NAD(P)H fluorescence measurements, which showed that HGF/SF increased the oxidation of the mitochondrial NAD system. We propose that concomitant with induction of ruffling, HGF/SF enhances both the glycolytic and oxidative phosphorylation pathways of energy production.
Abstract 3002: Genome engineering approaches to generate models of chromosome arm-level cancer aneuploidy (2018)

Abstract Aneuploidy, whole chromosome or chromosome arm copy number imbalance, is a near-universal characteristic of human cancers. Although yeast and mammalian models of whole chromosome aneuploidies have been extensively investigated, chromosome arm-level aneuploidies have rarely been modeled. Cancer subtypes are often characterized by tumor-specific patterns of these arm-level copy number alterations; for example, squamous cell carcinomas (SCCs) from different tissues of origin (including lung, esophagus, and bladder) have a pattern of chromosome 3p loss and chromosome 3q gain. Our analysis of 495 lung SCCs found chromosome 3p deletion to be the most frequent genomic alteration, occurring in almost 80% of the tumors and covering the entire length of the chromosome arm. Over two-thirds of chromosome 3p genes showed significantly decreased expression in these samples. Without models of chromosome arm-level alterations, the phenotypic effects of specific aneuploidies in cancer, such as 3p deletion, remain unknown. However, recent advances in genome engineering and targeting of endonucleases allow new approaches to generate chromosomal alterations. Here, we used the CRISPR-Cas9 system to delete one copy of chromosome 3p in vitro. We successfully isolated almost 90 clones of immortalized lung epithelial cells with deletion of the 3p arm, with 8 validated by whole-genome sequencing. Consistent with patient data, expression of 3p genes was also decreased upon deletion. Phenotypic characterization revealed that cells with chromosome 3p deletion initially proliferated more slowly than their siblings. These chromosome 3p-deleted cells had increased G1 arrest, but did not undergo increased apoptosis or cell death. Interestingly, after several passages in culture, the proliferation defect was rescued in chromosome 3p-deleted cells; genome sequencing and karyotype analyses suggested that this was the result of chromosome 3 duplication. With our cellular model of chromosome arm-level aneuploidy, we uncovered a possible selection mechanism that allows aneuploidy tolerance in vitro. We used genome engineering to model chromosome arm-level deletions, providing a robust model that will address a gap in our understanding of aneuploidy in cancer. Citation Format: Alison Marie Taylor, Xiaoyang Zhang, Juliann Shih, Gavin Ha, Galen F. Gao, Ashton C. Berger, Andrew D. Cherniack, Rameen Beroukhim, Matthew Meyerson. Genome engineering approaches to generate models of chromosome arm-level cancer aneuploidy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3002.
The Intelligent Cache Controller of a Massively Parallel Processor JUMP-1 (1997)

This paper describes the intelligent cache controller of JUMP-1, a distributed shared memory type MPP. JUMP-1 adopts an off-the-shelf superscalar as the element processor to meet the requirement of peak performance, but such a processor lacks the ability to hide inter-processor communication latency, which may easily become too long on MPPs. Therefore JUMP-1 provides an intelligent memory system to remedy the week point. The cache controller is one of the main components of the memory system, and provides many cache-level supports for inter-processor communication; explicit cache control, high-bandwidth cache prefetching, and a few types of synchronization structures for fine-grained message communication.
Antibacterial Metabolites from the Sri Lankan Demosponge-Derived Fungus, <i>Aspergillus flavipes</i> (2016)

Sri Lankan sponge-derived fungi are an unexploited resource awaiting exploration for drug leads. Three fungi from the internal tissues of a demosponge collected on the west coast of Sri Lanka were isolated and antimicrobial activities of their crude extracts were evaluated. Aspochalasin B, D, M, asperphenamate and 4-OMe asperphenamate were isolated from the crude ethyl acetate extract of the fungus Aspergillus flavipes . Aspochalasin B and D showed antibacterial activities against Bacillus subtilis (MIC, 16 and 32 μg ml -1 respectively), Staphylococcus aureus and MRSA (MIC, 32 μg ml -1 ). The results highlight the potential of isolating bioactive secondary metabolites from Sri Lankan sponge-derived fungi.
Assessment of Arterial Compliance by Carotid Midwall Strain-Stress Relation in Normotensive Adults (1999)

Examining left ventricular midwall as opposed to endocardial mechanics enhances understanding of left ventricular function in individuals with abnormal cardiac geometry. Accordingly, we used carotid ultrasound and applanation tonometry of arterial pressure to derive carotid midwall strain and its relation to carotid peak-systolic and end-diastolic stresses in 82 apparently normal, employed subjects (56 men, 26 women; median age, 47 years; 70% white; 21% overweight) with no evidence of coronary or valvular heart disease. Regression equations relating carotid luminal and midwall strain to the increment in carotid stress during systole (Deltacarotid stress) were used to predict strain for the observed Deltastress. Observed/predicted carotid luminal or midwall strain was calculated as a measure of carotid luminal or midwall strain for imposed stress, termed stress-corrected strain. Midwall carotid strain was similar in women and men but was negatively related to older age (r=-0.35, P=0.001) and higher body mass index (r=-0.31, P=0.005) and brachial and carotid blood pressure (r=-0.30 to -0.45, all P<0.01). The pulsatile change in arterial load, measured by Deltacarotid stress, was positively related to midwall strain (r=0. 44, P<0.001) more closely than was carotid luminal strain. Regression analyses revealed that carotid midwall strain was positively related to Deltastress, with additional negative relations to age and carotid diastolic diameter (all P<0.001). Stress-corrected carotid midwall strain was strongly and negatively correlated with midwall elastic modulus and Young's modulus (both r=-0.77, P<0.001), followed by elastic modulus (r=-0.74, P<0.001), midwall Young's modulus (r=-0.73, P<0.001), midwall stiffness index (r=-0.70, P<0.001), and stiffness index (r=-0.66, P<0.001). Thus, in normal adults, carotid midwall strain is unrelated to gender, is positively related to pulsatile carotid load as measured by Deltacarotid stress, and is negatively related to age, overweight, and standard measures of arterial stiffness.
Epstein Barr virus induced lymphoma in a child with IPEX syndrome (2007)

IPEX syndrome (immune deficiency, polyendocrinopathy, enteropathy, X-linked) is a disorder or regulatory T cell (Treg) function which can result in early death due to infection or complications related to autoimmunity. Therapeutic options for these patients can include allogeneic stem cell transplantation (SCT) or the use of immunosuppressive regimens to control the manifestations of autoimmunity. We report a patient with IPEX syndrome who was managed with rapamycin and subsequently developed EBV induced lymphoma.
Immunization and challenge of mice with insect‐derived metacyclic trypomastigotes of <i>Trypanosoma cruzi</i> (1990)

Summary Infection with Trypanosoma cruzi was established in the reduviid vector, Dipetalogaster maximus , by repeated feedings on mice with high parasitaemias, and metacyclic trypomastigotes (IMT) were collected in insect urine after blood meals. The infectivity of IMT in mice was assessed by placing varying numbers of organisms, ranging from 5 to 5000, on to the conjunctivae or oral mucosa of anaesthetized animals. Half of the mice exposed to as few as 20 IMT by either route became parasitized, and the minimum inoculum size that resulted in all mice becoming infected was 640 IMT by the ocular route and 1250 IMT in the mice given parasites by mouth. Mice were immunized by tail vein infusion of irradiated IMT. Animals in the immunized group and in two control groups were then challenged by deposition of IMT on to the oral mucosa. Two of five immunized mice and nine of 10 comparison animals developed acute T. cruzi infection after challenge. These results indicate that IMT produced in this system are highly infective and that inocula containing 500–1000 IMT applied to the conjunctivae or oral mucosa constitute a gentle contaminative challenge. Moreover, our findings suggest that sterile protection against a contaminative challenge may be inducible by immunization with IMT, but experiments involving larger numbers of animals must be performed to resolve this question.
Where has the Urban Crisis Gone? (1985)

Two national phenomena, economic transformation and the baby boom's young households, have brought new life to the Boston economy and that of other cities. The transformation has been largely downtown-oriented, however, and few of the benefits have spilled over into the poorer neighborhoods where most of the city's population lives. Substantial public infrastructure investment and the urban renewal write-down of land costs helped stake the private investment boom evident since the mid-1970s. Property values have skyrocketed. The rise in one-and two-person households and nonfamily households also has been accelerating since the mid-1970s and ushering in a return to the cities. The expanding concentration of minority and other poor populations in the cities have lagged behind, real income has eroded, poverty has increased, housing has become scarce, and gentrification holds a threat of displacement. The beneficence of the economic boom has not flowed into the public coffers; Boston, New York, and other large cities have been held on a tight fiscal leash by cutbacks in federal aid, state parsimony, and tax limitation legislation. City public services have been reduced. Boston is attempting to cope with new populist directions. New city legislation and zoning regulations (patterned, in part, on San Francisco's pioneering effort) are designed to induce developers to fund and become involved in neighborhood housing and development. With the shift from throw-away housing to scarcity, investment and fix-up have become more attractive, and there is new interest in the neighborhood potential.
Waveguide Mixer Sum frequency Termination Considerations in an FM Communication System (1968)

In a 6-GHz FM communications system using a mixer with its diode mounted in waveguide, group delay and linearity anomalies were observed which resulted in serious degradation of intermodulation signal-to-noise performance. This paper describes the problem, presents the reasoning and the laboratory tests by which improper termination of the mixergenerated sum frequency was isolated as its source, and describes a waveguide sum frequency absorber located at the mixer to solve the problem. The necessity of giving attention to all the signals generated in a nonlinear device in waveguide is discussed in this paper and has application to all such components in FM systems.
The Utilization of 'Eucalyptus' Foliage by the Greater Glider ('Petauroides volans') and the Brushtail Possum ('Trichosurus vulpecula') (1985)

The utilization of 'Eucalyptus' foliage as a food source by Greater Gliders ('Petauroides volans') and Brushtail Possums ('Trichosurus vulpecula') was studied in captive animals fed diets of 'E. radiata' and 'E. melliodora' respectively. The rate of passage of solute (51Cr-EDTA) and particulate (103Ru-Phenanthroline) digesta markers was slow in both species. The mean retention time (MRT) of the two markers was 50h and 46h in the Greater Gliders and 51h and 46h in the Brushtail Possums. The lack of separation between these two markers was consistent with the lack of selective retention of fine particles in the hindgut of the Brushtail Possum. However, fine particles occurred in greater quantities in caecal digesta of the Greater Glider (48% DM) than in the stomach (30% DM) or faeces (16% DM). The rate of passage of an alternative particle marker (51Cr-mordanted large particles (0.5mm)) in the Greater Gliders, was less than half that of 103Ru-P. From this it was concluded that 103Ru-P excretion reflected the excretion of fine digesta particles which were selectively retained in the caecum along with solute digesta. ... Efficient mastication and a relatively large hindgut, together with the selective retention of fine particles in the case of the Greater Glider, were important adaptations for utilizing 'Eucalyptus' foliage diets. However, it seemed unlikely that either marsupial species could survive solely on these single species diets in the wild unless they were able to substantially increase their intake of easily digestible nutrients.
Copolymerization Theory of the Vulcanization of Rubber. VI. Hydrogen Sulfide Effects and Some Self-Limiting Features (1953)

Abstract Vulcanization with sulfur is ascribed to the formation of sulfur radicals, which are believed to copolymerize with the double bonds of the rubber molecule. Hydrogen sulfide is proposed as necessary for chain initiation, but, when formed in sufficient amounts, it serves as a chain terminator. This is believed to lead to numerous self-limiting features, including ceiling temperatures, postvulcanization, and delayed-action effects. Initiation may result from the oxidation of H 2 S to sulfur radicals, and termination to the formation of HS radicals.
Pooled association genome scanning for alcohol dependence using 104,268 SNPs: Validation and use to identify alcoholism vulnerability loci in unrelated individuals from the collaborative study on the genetics of alcoholism (2006)

Association genome scanning can identify markers for the allelic variants that contribute to vulnerability to complex disorders, including alcohol dependence. To improve the power and feasibility of this approach, we report validation of "100k" microarray-based allelic frequency assessments in pooled DNA samples. We then use this approach with unrelated alcohol-dependent versus control individuals sampled from pedigrees collected by the Collaborative Study on the Genetics of Alcoholism (COGA). Allele frequency differences between alcohol-dependent and control individuals are assessed in quadruplicate at 104,268 autosomal SNPs in pooled samples. One hundred eighty-eight SNPs provide (1) the largest allele frequency differences between dependent versus control individuals; (2) t values >or= 3 for these differences; and (3) clustering, so that 51 relatively small chromosomal regions contain at least three SNPs that satisfy criteria 1 and 2 above (Monte Carlo P = 0.00034). These positive SNP clusters nominate interesting genes whose products are implicated in cellular signaling, gene regulation, development, "cell adhesion," and Mendelian disorders. The results converge with linkage and association results for alcohol and other addictive phenotypes. The data support polygenic contributions to vulnerability to alcohol dependence. These SNPs provide new tools to aid the understanding, prevention, and treatment of alcohol abuse and dependence.
Effect of isomaltodextrin on dough rheology and bread quality (2021)

Summary Isomaltodextrin (IMD) is a novel highly branched α‐glucan ingredient that has potential applications in foods as a promising source of dietary fibre. In this study, we assessed the incorporation of IMD in baked products and its effect on dough rheology and physico‐textural characteristics of wheat breads. IMD was added to wheat flour to reach the US FDA level of ‘good’ source of fibre (10% IMD). Use of the straight‐dough method with IMD and regular dough mixing time (8 min) resulted in less elastic doughs and resulting breads displayed lower cohesiveness, springiness and chewiness compared to the control bread. A modified straight‐dough method, with longer mixing time (36 min) and adjusted water level (70%), and a sponge‐and‐dough method were used to allow gluten structure to more fully hydrate and develop. With IMD addition, the modified straight‐dough (36 min dough mixing time) and sponge‐and‐dough methods yielded enhanced dough elasticity compared to the original straight‐dough method. Breadmaking methods were identified (improved straight‐dough and sponge‐and‐dough) whereby IMD could be added at a 'good source' of fibre level with loaf appearance and texture similar to breads without IMD.