gebhart/patrepeval huggingface dataset:
3′UTR shortening and EGF signaling: implications for breast cancer (2015)

Alternative polyadenylation (APA) plays a role in gene expression regulation generally by shortening of 3'UTRs (untranslated regions) upon proliferative signals and relieving microRNA-mediated repression. Owing to high proliferative indices of triple negative breast cancers (TNBCs), we hypothesized APA to cause 3'UTR length changes in this aggressive subgroup of breast cancers. Our probe-based meta-analysis approach identified 3'UTR length alterations where the significant majority was shortening events (∼70%, 113 of 165) of mostly proliferation-related transcripts in 520 TNBC patients compared with controls. Representative shortening events were further investigated for their microRNA binding potentials by computational predictions and dual-luciferase assay. In silico-predicted 3'UTR shortening events were experimentally confirmed in patient and cell line samples. To begin addressing the underlying mechanisms, we found CSTF2 (cleavage stimulation factor 2), a major regulator of 3'UTR shortening to be up-regulated in response to epidermal growth factor (EGF). EGF treatment also resulted with further shortening of the 3'UTRs. To investigate the contribution of CSTF2 and 3'UTR length alterations to the proliferative phenotype, we showed pharmacological inhibition of the EGF pathway to lead to a reduction in CSTF2 levels. Accordingly, RNAi-induced silencing of CSTF2 decreased the proliferative rate of cancer cells. Therefore, our computational and experimental approach revealed a pattern of 3'UTR length changes in TNBC patients and a potential link between APA and EGF signaling. Overall, detection of 3'UTR length alterations of various genes may help the discovery of new cancer-related genes, which may have been overlooked in conventional microarray gene expression analyses.
Methylation analysis of histone H4K12ac-associated promoters in sperm of healthy donors and subfertile patients (2015)

We suggest that aberrant histone acetylation within developmentally important gene promoters in subfertile men, but not DNA methylation, may reflect insufficient sperm chromatin compaction affecting the transfer of epigenetic marks to the oocyte.
Effect of hypothyreosis on the content of ceramides in rat tissues. (2003)

Ceramide is the second messenger in the sphingomyelin signalling pathway. A number of extracellular stimuli increase the content of ceramide in the cell. There are some data indicating that the content of ceramide may also be regulated by hormones. The aim of the present study was to examine the effect of hypothyreosis on the content and composition of ceramide in rat tissues. The rats were thyroidectomized and thereafter they received propylthiouracyl in drinking water. The control rats were sham operated. 30 days after thyroidectomy or sham operation the rats were anaesthetized and samples of the liver, white and red vastus lateralis and left ventricle were taken. One set of samples was frozen in liquid nitrogen for analysis of ceramide. Another set of samples was freshly homogenized in chloroform/methanol for further determination of the content of sphingomyelin phosphorous. The content and composition of ceramide-fatty acids was determined by means of gas-liquid chromatography. Twelve ceramides containing different fatty acid residues were identified in both groups. Hypothyreosis reduced the total content of ceramide in each tissue studied: in the heart by 50.9%, in the red vastus by 28.6%, in the white vastus by 29.4% and in the liver by 22%. Concomitantly, the content of individual ceramides was either reduced, stable or even elevated, depending on the tissue. The content of sphingomyelin was elevated in both sections of the vastus lateralis and remained stable in the heart and the liver. The ratio: total content of sphingomyelin to total content of ceramide was elevated in the muscles and remained stable in the liver. This indicates that the reduction in the content of ceramide in the tissues of hypothyroid rats may be a consequence either of a reduction in the formation of ceramide from sphingomyelin, its increased hydrolysis or both. It is concluded that normal thyroid function is needed to maintain the content and composition of ceramide in the tissues.
INFLUENCE OF COMPOSITE MATERIALS AND PROPORTION ON THEIR FRESH PROPERTIES AND MECHANICAL ONES OF HYBRID FIBER REINFORCED CEMENTITIOUS COMPOSITES (2011)

In this study, influence of composite materials and mix proportions on the fresh properties and the mechanical ones of Hybrid Fiber Reinforced Cementitious Composites ( HFRCC ) was experimentally investigated. Then, the influence was analyzed by applying the excess paste thickness theory proposed by Kennedy in 1940 and formulated as functions of dominant factors. Results of the experiment and the analysis revealed the following matters:1. The relative yield value and the relative plastic viscosity of HFRCC (yield value and plastic viscosity of HFRCC normalized by those of paste) decreased as the fiber volume content increased, and influenced by the geometry of contained steel fiber. Though it could not be quantified only by the excess paste thickness, the influence of sand-binder ratio, admixtures, volume content of each fiber and the geometry of the steel fiber on fresh properties and mechanical ones of HFRCC could be quantified by introducing modified excess paste thickness. However, it was not possible to apply it to express the influence of different water binder ratio.2. The value of ductility index obtained by three point bending test increased as the fiber volume content and the aspect ratio of the steel fiber increased. By introducing modified excess paste thickness, the influence of sand binder ratio, water binder ratio, fiber volume content and aspect ratio of the steel fiber on the value of ductility index of HFRCC could be quantified. However, it was not possible to apply it to express the influence of different admixtures.
New 9- or 10-Dentate Luminescent Lanthanide Chelates (2008)

Polyaminocarboxylate-based luminescent lanthanide complexes have unusual emission properties, including millisecond excited-state lifetimes and sharply spiked spectra compared to common organic fluorophores. There are three distinct sections in the structure of the luminescent lanthanide chelates: a polyaminocarboxylate backbone to bind the lanthanide ions tightly, an antenna molecule to sensitize the emission of lanthanide ions, and a reactive group to attach to biomolecules. We have previously reported the modifications on the chelates, on the antenna molecules (commonly cs124), and on the reactive sites. In searching for stronger binding chelates and better protection from solvent hydration, here we report the modification of the coordination number of the chelates. A series of 9- and 10-dentate chelates were synthesized. Among them, the 1-oxa-4,7-diazacyclononane (N2O)-containing chelate provides the best protection to the lanthanide ions from solvent molecule attack, and forms the most stable lanthanide coordination compounds. The TTHA-based chelate provides moderately good protection to the lanthanide ions.
The role of scatter factor receptor Met in mobilizing antigen presenting dendritic cells in vivo (2011)

Dendritic cells (DCs) are the major sentinels of immune surveillance system and a key link between innate and adaptive immunity by triggering T-cell specific immune responses. Thereby, the migratory properties of DCs are crucial for their immune function. Met is a receptor tyrosine kinase and the receptor for scatter factor (SF), also known as hepatocyte growth factor (HGF). Met signalling exhibits mitogenic, morphogenic and motogenic activity of various cells e.g. during embryonic development and wound healing. The functional expression of SF receptor/Met in skin DCs has been already shown. In this thesis, a detailed analysis of Met function in two major DC subpopulations in skin, dermal DCs (dDCs) and Langerhans cells (LCs), under steady-state and inflammatory conditions is presented by employing a conditional Met KO mouse model (Mx-Cre/Met fl/fl). In vivo, a distinct pattern of Met surface expression was found in different DC subpopulations, including dDCs and LCs in peripheral and lymphoid organs in steady-state. Activation of dDCs/LCs upon inflammation efficiently induced expression of Met both in vitro and in vivo. Dermal DC showed higher Met expression than LC and faster migration kinetics towards draining lymph nodes (LNs). Finally, genetic and pharmacological deficiency of Met severely impaired motility of dDCs/LCs resulting in failed mobilization of dDCs/LCs from skin and thus in disability of dDCs/LCs to mount an immune response in contact hypersensitivity reactions. Here, the regulation of matrix metalloproteinase activity by Met signalling was identified as one potential mechanism. Taken together, the data of this work demonstrate an essential function of Met for DC mobilization contributing to skin immunity and suggest new ways of treating autoimmune skin diseases.
Earlier the better: convalescent plasma (2020)

to eradicate inhibitors and how emicizumab may help to reduce the required FVIII dose, which is associated with enormous cost. The observation that FVIII provides additional prohemostatic effects in the presence of emicizumab in the mouse model is therefore noteworthy. 1 Key for any prohemostatic therapy in hemophilia is how the development of hemophilic arthropathy is affected. Early experimental data in monkeys indicate that emicizumab prevents joint bleeds, 8 but clinical trial data indicate that emicizumab does not reduce joint bleeds to 0 in all patients (and neither does FVIII) 2,5-7 ; thus, a better understanding of the effect of emicizumab on the progression and management of hemophilic arthropathy is urgently needed. The emicizumab-adapted hemophilia A mouse model will encompass an important tool to obtain such insights. However, it should be noted that additional modifications are needed, as indicated, before this model is suited for longer-term hemophilic arthropathy studies. 1 Finally, while it is typical to address bleeding in hemophilia from a clottingcentric perspective, it is equally important not to overlook that bleeding, and especially joint bleeding, has its own contributing mechanisms that in addition to coagulation may include endogenous anticoagulant pathways, fibrinolysis, vascular and bone remodeling pathways, and others. Joint bleeding is the cumulative disbalance of these pathways, and the mouse is arguable the best model to test how the contributions of these pathways are affected by emicizumab. The emicizumab-adapted hemophilia A mouse bleeding model developed by Ferri re et al enables such studies and is likely to stimulate new areas of hemophilia A research focused on emicizumab.
Right and left ventricular stroke volume measurements with velocity-encoded cine MR imaging: in vitro and in vivo validation. (1991)

The accuracy of measurements of flow velocity determined by using cine MR phase velocity mapping--velocity-encoded cine (VEC) MR--was assessed by comparing VEC MR data with independent measurements in a flow phantom and in human subjects. Constant flow velocities generated in a phantom (range, 20-408 cm/sec) were determined correctly by VEC MR (r = .997, standard error of the estimate [SEE] = 7.9 cm/sec). Peak systolic velocities in the main pulmonary artery determined by VEC MR correlated well with the measurements obtained by using continuous-wave Doppler echocardiography (r = .91). Stroke volumes measured at the aorta by VEC MR and continuous-wave Doppler imaging also correlated well with each other (r = .80). VEC MR measurements of aortic and pulmonary flow provided left and right ventricular stroke volumes that correlated well with left ventricular stroke volumes determined by short-axis cine MR images (r = .98, SEE = 3.7 ml, and r = .95, SEE = 4.8 ml, respectively). Intra- and interobserver variabilities were small for both left and right ventricular stroke volumes as measured with VEC MR. These results indicate that VEC MR accurately and reproducibly measures aortic and pulmonary flow velocities and volumes in the physiologic range of humans, and can be used to measure right and left ventricular stroke volumes under normal flow conditions.
The Internet: a global telecommunications solution? (2000)

The provision and support of new distributed multimedia services are of prime concern for telecommunications operators and suppliers. Clearly, the potential of the latest Internet protocols to contribute communications components is of considerable interest to them. In this article we first review some of the new types of application and their requirements, and identify the need to support applications that have strict QoS requirements, the so-called critical applications. We review two proposals for enhancing the Internet service architecture. In addition to the integrated services work of the IETF, we look at the proposals for differentiated services in the Internet. We then individually review protocol developments proposed to improve the Internet, and to support real-time and multimedia communications. These are IPv6 (the new version of the Internet Protocol), Resource reSerVation Protocol, and Multiprotocol Label Switching, respectively. In each case, we attempt to provide critical reviews in order to assess their suitability for this purpose. Finally, we indicate what the basis of the future infrastructure might be in order to support the full variety of application requirements.
Thyroid function disorders and secondary cancer following haematopoietic stem cell transplantation in pediatrics: State of the art and practical recommendations for a risk-based follow-up (2022)

Thyroid disorders (TD) represent a remarkable share of all the late morbidities experienced following pediatric haematopoietic stem cell transplantation (HSCT), with long-term reported occurrence often exceeding 70%. In addition, the data collected on wide cohorts of survivors assessed longitudinally outlined a progressive increase in the cumulative incidence of TD as far as 30 years following transplantation. Accordingly, a life-long monitoring of thyroid health is warranted among patients exposed to HSCT in childhood, in order to early detect TD and undertake a prompt dedicated treatment. Although several national and international <i>consortia</i> have provided recommendations for the early detection of thyroid disorders among childhood cancer survivors exposed to radiotherapy and alkylating agents, no guidelines specifically and thoroughly focused on HSCT-related TD have been published to date. As stem cell transplantation has become the standard-of-care in a growing body of non-oncological conditions, this urge has become pivotal. To highlight the challenging issues specifically involving this cohort of patients and to provide clinicians with the proposal of a practical follow-up protocol, we reviewed published literature in the light of the shared experience of a multidisciplinary team of pediatric oncologists, transplantologists, pathologists and endocrinologists involved in the long-term care of HSCT survivors. As a final result, we hereby present the proposals of a practical and customized risk-based approach to tailor thyroid health follow-up based on HSCT-related detrimental factors.
Asymmetric Intermolecular Boron Heck-Type Reactions via Oxidative Palladium(II) Catalysis with Chiral Tridentate NHC-Amidate-Alkoxide Ligands (2009)

Chiral dimeric tridentate NHC-amidate-alkoxide palladium(II) complexes, 3a and 3b, effected oxidative boron Heck-type reactions of aryl boronic acids with both acyclic and cyclic alkenes at room temperature to afford the corresponding coupling products with high enantioselectivities. The high degree of enantioselection, far superior to existing methods, stems from differences in the nonbonding interactions in the proposed transition states, due to the influence from bulky substituents of the alkene substrates and the "counter axial groups" of the palladium(II) catalysts.
5‐HT4 receptor‐mediated modulation of 5‐HT release in the rat hippocampus in vivo (1996)

1. In the present study, the ability of the 5-hydroxytryptamine, receptor (5-HT4 receptor) to modulate the release of 5-HT in the hippocampus of freely-moving rats was investigated by the in vivo microdialysis technique. 2. The 5-HT4 receptor agonist, renzapride (1.0-100 microM, administered via the microdialysis probe) increased extracellular hippocampal levels of 5-HT in concentration-dependent manner (approximately 200% maximal increase). The ability of renzapride (100 microM, administered via the microdialysis probe) to elevate extracellular levels of 5-HT remained in the presence of the selective 5-HT reuptake blocker, paroxetine (1.0 microM, administered via the microdialysis probe). Furthermore, another 5-HT4 receptor agonist 5-methoxytryptamine (5-MeOT; 10 microM, administered via the microdialysis probe, in the presence of the non-5-HT4 5-HT receptor antagonists pindolol (10 microM) and methysergide (10 microM)) maximally elevated extracellular levels of 5-HT by approximately 450% in the rat hippocampus. The elevation of extracellular 5-HT levels induced by either renzapride (100 microM) or 5-MeOT (10 microM) was completely prevented by combined administration of the selective 5-HT4 receptor antagonist, GR113808 (100 nM, administered via the microdialysis probe). GR113808 (100 nM, administered via the microdialysis probe) administered alone, however, reduced extracellular hippocampal 5-HT levels by some 60%. 3. Systemic administration of the 5-HT1A receptor agonist, 8-OH-DPAT (0.1 mg kg-1, s.c.) reduced extracellular levels of 5-HT in the rat hippocampus by approximately 40%. Prior administration of 8-OH-DPAT (0.1 mg kg-1, s.c.), with an associated reduction of extracellular hippocampal 5-HT levels by approximately 40-50%, however, failed to prevent a subsequent elevation of extracellular levels of 5-HT induced by renzapride (100 microM, administered via the microdialysis probe). 4. Systemic administration of the 5-HT4 receptor agonist, renzapride (0.25 and 1.0 mg kg-1, i.p.) increased extracellular levels of 5-HT in the hippocampus in a dose-dependent manner. The higher dose of renzapride increasing extracellular 5-HT levels by some 200%. The selective 5-HT4 receptor antagonist, GR125487D (1.0-100 micrograms kg-1, i.p.) caused a dose-dependent reduction in extracellular levels of 5-HT in the hippocampus (maximally approximately 80% reduction). Prior administration of GR125487D (10 micrograms kg-1, i.p.) prevented the elevation of extracellular levels of 5-HT induced by renzapride (1.0 mg kg-1, i.p.). 5. In conclusion, the present study provides evidence that activation of the 5-HT4 receptor facilitates 5-HT release in the rat hippocampus in vivo.
Supplementary Figure 4 from Combined Depletion of Cell Cycle and Transcriptional Cyclin-Dependent Kinase Activities Induces Apoptosis in Cancer Cells (2023)

Supplementary Figure 4 from Combined Depletion of Cell Cycle and Transcriptional Cyclin-Dependent Kinase Activities Induces Apoptosis in Cancer Cells
Biochemical Studies of Bacterial Viruses (1952)

Journal Article Biochemical Studies of Bacterial Viruses Get access Biochemical Studies of Bacterial Viruses . Evans E. A.Jr. , 68 pages. The University of Chicago Press , 5750 Ellis Avenue, Chicago 27, Illinois . ( 1952 ). $2.75 . AIBS Bulletin, Volume 2, Issue 5, October 1952, Pages 12–13, https://doi.org/10.1093/aibsbulletin/2.5.12-d Published: 01 October 1952
Metabolism of H2-CO2, methanol, and glucose by Butyribacterium methylotrophicum (1983)

The fermentative metabolism of Butyribacterium methylotrophicum grown on either H2-CO2, methanol, glucose, or CO is described. The following reaction stoichiometries were obtained: 1.00 H2 + 0.52 CO2 leads to 0.22 acetate + 0.06 cell C; 1 methanol + 0.18 CO2 + 0.01 acetate leads to 0.24 butyrate + 0.29 cell C; and 1.00 glucose leads to 0.31 CO2 + 1.59 acetate + 0.21 butyrate + 0.13 H2 + 1.58 cell C. Cell yields of 1.7 g (dry weight) per mol of H2, 8.2 g (dry weight) per mol of methanol, 42.7 g (dry weight) per mol of glucose, and 3.0 g (dry weight) per mol of CO were obtained from linear plots of cell synthesis and substrate consumption. Doubling times of 9.0, 9.0, and 3 to 4 h were observed during batch growth on H2-CO2, methanol, and glucose, respectively. Indicative of a growth factor limitation, glucose fermentation in defined medium displayed a lower cell synthesis efficiency than when yeast extract (0.05%) was present. B. methylotrophicum fermentation displayed atypically high substrate/cell carbon synthesis conversion ratios for an anaerobe, as greater than 24% of the carbon was assimilated into cells during growth on methanol or glucose. The data indicate that B. methylotrophicum conserves carbon-bound electrons during growth on single-carbon or multicarbon substrates.
Effects of light color and intensity on discrimination of red objects in broilers (2022)

Poultry are sensitive to red objects, such as comb and blood on the body surface, likely inducing injurious pecking in flocks. Light is an important factor that affects the pecking behavior of poultry. A wooden box was built to investigate the effects of Light Emitting Diode (LED) light color (warm white and cold white) and intensity (5 and 50 lux) of background light on the discrimination of red objects in broilers. A piece of red photographic paper (Paper 1) was used to simulate a red object and paired with another piece of paper (Paper 2 to 8) with a different color. Bigger number of the paired paper indicated greater color difference. The experiment consisted of three phases: adaptation, training, and test. In the adaptation phase, birds were selected for the adaptation to reduce the stress from the box. In the training phase, birds were trained to discriminate and peck at Paper 1 when paired with Paper 8 under one type of background light. Twenty-three birds were tested when the paired paper was changed from Paper 7 to 2. Each pair of paper included 12 trials for every bird, and response time to peck and proportion of choices of Paper 1 in the last 10 trials were collected. The results showed that broilers tested under 5 lux light had longer response times than broilers tested under 50 lux light (P < 0.05). When Paper 1 was paired with paper 7, broilers tested under warm white light had lower proportion of choices of Paper 1 than those tested under cold white light (P < 0.05). Color difference had a significant effect on response time of broilers (P < 0.05). Moreover, the proportion of choices of Paper 1 decreased to 50% (chance-level performance) when color of the paired paper was gradually similar to Paper 1. Conclusively, rearing broilers in warm white rather than cold white light with appropriate light intensity should be recommended to reduce damaging pecking behavior in broiler production.