Miracle-dz/UniFAR-FTUs huggingface dataset:
EHD3-Dependent Endosome Pathway Regulates Cardiac Membrane Excitability and Physiology

Rationale: Cardiac function is dependent on the coordinate activities of membrane ion channels, transporters, pumps, and hormone receptors to tune the membrane electrochemical gradient dynamically in response to acute and chronic stress. Although our knowledge of membrane proteins has rapidly advanced during the past decade, our understanding of the subcellular pathways governing the trafficking and localization of integral membrane proteins is limited and essentially unstudied in vivo. In the heart, to our knowledge, there are no in vivo mechanistic studies that directly link endosome-based machinery with cardiac physiology. Objective: To define the in vivo roles of endosome-based cellular machinery for cardiac membrane protein trafficking, myocyte excitability, and cardiac physiology. Methods and Results: We identify the endosome-based Eps15 homology domain 3 (EHD3) pathway as essential for cardiac physiology. EHD3-deficient hearts display structural and functional defects including bradycardia and rate variability, conduction block, and blunted response to adrenergic stimulation. Mechanistically, EHD3 is critical for membrane protein trafficking, because EHD3-deficient myocytes display reduced expression/localization of Na/Ca exchanger and L-type Ca channel type 1.2 with a parallel reduction in Na/Ca exchanger–mediated membrane current and Cav1.2-mediated membrane current. Functionally, EHD3-deficient myocytes show increased sarcoplasmic reticulum [Ca], increased spark frequency, and reduced expression/localization of ankyrin-B, a binding partner for EHD3 and Na/Ca exchanger. Finally, we show that in vivo EHD3-deficient defects are attributable to cardiac-specific roles of EHD3 because mice with cardiac-selective EHD3 deficiency demonstrate both structural and electric phenotypes. Conclusions: These data provide new insight into the critical role of endosome-based pathways in membrane protein targeting and cardiac physiology. EHD3 is a critical component of protein trafficking in heart and is essential for the proper membrane targeting of select cellular proteins that maintain excitability.
Insulin and Glucagon Regulation of GlutathioneS-Transferase Expression in Primary Cultured Rat Hepatocytes

Diabetes is a major cause of morbidity and mortality, and complications resulting from diabetes have been attributed in part to increased oxidative stress. Glutathione S-transferases (GSTs) constitute a major protective mechanism against oxidative stress. Studies of the expression and activity of GSTs during diabetes are inconclusive, with both increased and decreased GST expression being reported in vivo. Insulin and glucagon effects on GST expression and the signaling pathway involved in the glucagon regulation of GST expression were examined in primary cultured rat hepatocytes. The addition of insulin resulted in the elevation of alpha-class GST protein levels, whereas alpha- and pi-class GST protein levels were markedly decreased in hepatocytes cultured with glucagon. In contrast, mu-class GST protein expression was unaffected by insulin or glucagon treatment. Insulin concentrations ≥1 nM resulted in increased GST activities and alpha-class GST protein levels, whereas glucagon concentrations ≥20 nM decreased alpha- and pi-class protein levels and activity. Treatment of cells with 8-bromo-cAMP or dibutyryl-cAMP also resulted in decreased alpha- and pi-class GST protein levels. Pretreatment withN-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline sulfonamide (H89), a selective inhibitor of protein kinase A, before glucagon addition markedly attenuated the glucagon effect. This study demonstrates that insulin and glucagon regulate, in an opposing manner, the expression of alpha-class GSTs and that glucagon completely inhibits pi-class GST expression in vitro, suggesting that hepatic GST expression may be decreased during diabetes. Furthermore, the present study implicates cAMP and protein kinase A in mediating the inhibitory effect of glucagon on GST expression.
TnIfast IRE enhancer: Multistep developmental regulation during skeletal muscle fiber type differentiation

To identify developmental steps leading to adult skeletal muscle fiber‐type–specific gene expression, we carried out transgenic mouse studies of the IRE enhancer of the quail TnIfast gene. Histochemical analysis of IRE/herpesvirus tk promoter/β‐galactosidase reporter transgene expression in adult muscle directly demonstrated IRE‐driven fast vs. slow fiber‐type specificity, and IIB>IIX>IIA differential expression among the fast fiber types: patterns similar to those of native‐promoter TnIfast constructs. These tissue‐ and cell‐type specificities are autonomous to the IRE and do not depend on interactions with a muscle gene promoter. Developmental studies showed that the adult pattern of IRE‐driven transgene expression emerges in three steps: (1) activation during the formation of primary embryonic (presumptive slow) muscle fibers; (2) activation, to markedly higher levels, during formation of secondary (presumptive fast) fibers, and (3) differential augmentation of expression during early postnatal maturation of the IIB, IIX, IIA fast fiber types. These results provide insight into the roles of gene activation and gene repression mechanisms in fiber‐type specificity and can account for apparently disparate results obtained in previous studies of TnI isoform expression in development. Each of the three IRE‐driven developmental steps is spatiotemporally associated with a different major regulatory event at the fast myosin heavy chain gene cluster, suggesting that diverse muscle gene families respond to common, or tightly integrated, regulatory signals during multiple steps of muscle fiber differentiation. © 2002 Wiley‐Liss, Inc.
A repertoire approach to cross-platform media use behavior

Media users receive an overwhelmingly large supply of media content from multiple media, yet much research on media use examines the use of a single medium. This study investigates patterns of media use across multiple media platforms by taking a media repertoire approach. Using single-source data that merge television peoplemeter data and a survey on other media use of the same respondents, this study identifies five distinctive media repertoires (TV-Oriented Entertainment, Internet Only, News on Traditional Media, Tabloid Newspapers, and Cable TV Only). This study finds significant differences in user background characteristics, total news media use, political interest, and political knowledge among representative users of each media repertoire. Regression analyses on factor scores reveal that media repertoires are explained by individual and structural factors of media choice discussed in previous research. The implications for future research on media repertoires as news, information, and entertainment sources are discussed.
Comparison of 99mTc-sestamibi and doxorubicin to monitor inhibition of P-glycoprotein function

P-glycoprotein (Pgp) overexpression is a well-recognized factor in resistance to chemotherapy. Doxorubicin flow cytometry is used to monitor Pgp function in haematological specimens and biopsies from other cancers, and radionuclide imaging with sestamibi has recently shown promise for non-invasive monitoring. In the present study the two methods were directly compared in single-cell suspensions of three variants of the human breast carcinoma cell line MCF7: sensitive MCF7/WT, doxorubicin-selected MCF7/AdrR, and MDR1 -gene-transfected MCF7/BC19 cells with doxorubicin resistance factors of 1, 192, and 14, respectively. Accumulation of sestamibi and mean fluorescence of doxorubicin (5.5 μM) were assessed over 60 min in the presence and absence of Pgp modulators GG918 (0.01 to 0.2 μM) and PSC833 (0.05 to 2.0 μM). Accumulation curves for sestamibi and doxorubicin differed among the cell variants under control conditions, with sestamibi showing a significantly greater difference between WT and resistant cells than doxorubicin. Both GG918 and PSC833 reversed uptake deficits to WT levels for sestamibi in MCF7/BC19 cells and doxorubicin in MCF7/BC19 and MCF7/AdrR cells, but failed to show the same effect for sestamibi in MCF7/AdrR cells (~30% of MCF7/WT level). Thus, both methods clearly distinguished sensitive from resistant MCF7 variants, with the radionuclide method showing greater sensitivity. © 2001 Cancer Research Campaign http://www.bjcancer. com
Intra-tumoral production of IL18, but not IL12, by TCR-engineered T cells is non-toxic and counteracts immune evasion of solid tumors

ABSTRACT Adoptive therapy with engineered T cells shows promising results in treating patients with malignant disease, but is challenged by incomplete responses and tumor recurrences. Here, we aimed to direct the tumor microenvironment in favor of a successful immune response by local secretion of interleukin (IL-) 12 and IL-18 by sadministered T cells. To this end, we engineered T cells with a melanoma-specific T cell receptor (TCR) and murine IL-12 and/or IL-18 under the control of a nuclear-factor of activated T-cell (NFAT)-sensitive promoter. These T cells produced IL-12 or IL-18, and consequently enhanced levels of IFNγ, following exposure to antigen-positive but not negative tumor cells. Adoptive transfer of T cells with a TCR and inducible (i)IL-12 to melanoma-bearing mice resulted in severe, edema-like toxicity that was accompanied by enhanced levels of IFNγ and TNFα in blood, and reduced numbers of peripheral TCR transgene-positive T cells. In contrast, transfer of T cells expressing a TCR and iIL-18 was without side effects, enhanced the presence of therapeutic CD8+ T cells within tumors, reduced tumor burden and prolonged survival. Notably, treatment with TCR+iIL-12 but not iIL-18 T cells resulted in enhanced intra-tumoral accumulation of macrophages, which was accompanied by a decreased frequency of therapeutic T cells, in particular of the CD8 subset. In addition, when administered to mice, iIL-18 but not iIL-12 demonstrated a favorable profile of T cell co-stimulatory and inhibitory receptors. In conclusion, we observed that treatment with T cells engineered with a TCR and iIL18 T cells is safe and able to skew the tumor microenvironment in favor of an improved anti-tumor T cell response.
External pH effects on the depolarization-activated K channels in guard cell protoplasts of Vicia faba

Previous studies reveal that the pH of the apoplastic solution in the guard cell walls may vary between 7.2 and 5.1 in closed and open stomata, respectively. During these aperture and pH changes, massive K+ fluxes cross the cellular plasma membrane driving the osmotic turgor and volume changes of guard cells. Therefore, we examined the effect of extracellular pH on the depolarization-activated K channels (KD channels), which constitute the K+ efflux pathway, in the plasma membrane of Vicia faba guard cell protoplasts. We used patch clamp, both in whole cells as well as in excised outside-out membrane patches. Approximately 500 KD channels, at least, could be activated by depolarization in one protoplast (density: approximately 0.6 micron-2). Acidification from ph 8.1 to 4.4 decreased markedly the whole-cell conductance, GK, of the KD channels, shifted its voltage dependence, GK- EM, to the right on the voltage axis, slowed the rate of activation and increased the rate of deactivation, whereas the single channel conductance was not affected significantly. Based on the GK-EM shifts, the estimated average negative surface charge spacing near the KD channel is 39 A. To quantify the effects of protons on the rates of transitions between the hypothesized conformational states of the channels, we fitted the experimental macroscopic steady state conductance-voltage relationship and the voltage dependence of time constants of activation and deactivation, simultaneously, with a sequential three-state model CCO. In terms of this model, protonation affects the voltage-dependent properties via a decrease in localized, rather than homogeneous, surface charge sensed by the gating moieties. In terms of either the CO or CCO model, the protonation of a site with a pKa of 4.8 decreases the voltage-independent number of channels, N, that are available for activation by depolarization.
Field Evaluation of Traditionally Used Plant-Based Insect Repellents and Fumigants Against the Malaria Vector Anopheles darlingi in Riberalta, Bolivian Amazon

Abstract Inexpensive insect repellents may be needed to supplement the use of impregnated bed-nets in the Amazon region, where the primary malaria vector, Anopheles darlingi (Root), is exophilic and feeds in the early evening. Three plants that are traditionally used to repel mosquitoes in Riberalta, Bolivian Amazon, were identified by focus group, and then they were tested against An. darlingi as well as Mansonia indubitans (Dyar & Shannon)/Mansonia titillans (Walker). Cymbopogon citratus (Staph), Guatemalan lemongrass, essential oil at 25% was used as a skin repellent, and it provided 74% protection for 2.5 h against predominantly An. darlingi and 95% protection for 2.5 h against Mansonia spp. Attalea princeps (name not verified) husks, burned on charcoal in the traditional way provided 35 and 51% protection against An. darlingi and Mansonia spp. , respectively. Kerosene lamps, often used to light rural homes, were used as a heat source to volatilize 100% Mentha arvensis (Malinv ex. Bailey) essential oil, and they reduced biting by 41% inside traditional homes against Mansonia spp. , although they were ineffective outdoors against An. darlingi. All three plant-based repellents provided significant protection compared with controls. Plant-based repellents, although less effective than synthetic alternatives, were shown by focus groups to be more culturally acceptable in this setting, in particular para-menthane-3, 8, idol derived from lemon eucalyptus, Corymbia citriodora (Hook). Plant-based repellents have the potential to be produced locally and therefore sold more cheaply than synthetic commercial repellents. Importantly, their low cost may encourage user compliance among indigenous and marginalized populations.
Lenalidomide plus cyclophosphamide, doxorubicin, vincristine, prednisone and rituximab is safe and effective in untreated, elderly patients with diffuse large B-cell lymphoma: a phase I study by the Fondazione Italiana Linfomi

Despite improvements in standard therapy with rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone for patients with untreated, diffuse large B-cell lymphoma, up to 40% of these patients relapse. Lenalidomide alone or in combination with rituximab has been shown to be active in relapsed/refractory aggressive lymphomas. In this phase I study we determined the maximum tolerated dose of lenalidomide plus rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone in untreated, elderly (median age 68 years) patients with diffuse large B-cell lymphoma. Four lenalidomide doses (5, 10, 15, and 20 mg/day on days 1–14) allocated using the continual reassessment method were planned to be administered for 14 days in combination with each course of rituximab, cyclophosphamide, doxorubicin, vincristine and prednisone for a total of six courses. Seven cohorts of patients (n=3 in each cohort) were treated (total n=21) at 10, 20, 15, 15, 15, 10, and 10 mg of lenalidomide. Dose-limiting toxicities occurred in seven patients during the first three courses of treatment. The third dose-level of lenalidomide (15 mg/day) was selected as the maximum tolerated dose, with an estimated probability of dose-limiting toxicities of 0.345 (95% credibility interval 0.164–0.553). Grade 3–4 hematologic adverse events were: neutropenia in 28% of the courses, thrombocytopenia in 9%, and anemia in 3%. Non-hematologic toxicities were moderate: grade 4 increase of creatinine phosphokinase (n=1), grade 3 cardiac (n=2), grade 3 neurological (n=3), and grade 3 gastrointestinal (n=1). In this phase I study, the overall response rate was 90%, with 81% achieving complete remission. This combination regimen appears safe in elderly patients with diffuse large B-cell lymphoma and its efficacy will be assessed in the ongoing phase II trial. This trial was registered at www.clinicaltrials. gov as NCT00907348.
Discrepancies between patient and physician estimates for the success of stem cell transplantation.

CONTEXT Stem cell transplantation is associated with considerable morbidity and mortality. The extent to which patients and their physicians correctly estimate these risks is unknown. OBJECTIVE To measure the expectations of patients and physicians prior to stem cell transplantation and correlate them with actual outcomes after transplantation. DESIGN Prospective cohort study with baseline questionnaire administered July 1996 through November 1999 and follow-up to May 2000. SETTING Tertiary care transplant center in the United States. PARTICIPANTS Of 458 surveys mailed, evaluable returned surveys were included for 313 autologous and allogeneic stem cell transplantation patients and their physicians. MAIN OUTCOME MEASURES Patient and physician expectations prior to transplantation (measured on 6-point Likert scales) of treatment-related mortality, cure with transplantation, and cure without transplantation; actual treatment-related mortality and disease-free survival among patients with at least 1 year of follow-up after transplantation (n = 263). RESULTS Both patients and physicians were fairly accurate in estimating treatment-related mortality when actual mortality was less than 30%. However, in situations in which mortality was higher than 30%, such as with allogeneic transplantation for intermediate or advanced disease, physician expectations were lower, while patients remained optimistic. Similarly, physicians provided lower estimates of disease-free survival in cases of intermediate or advanced disease while patient expectations remained high and constant regardless of disease stage. CONCLUSIONS Patients and their physicians have the most concordant and accurate expectations when the outcome of stem cell transplantation is likely to be favorable. However, patients with more advanced disease fail to recognize the higher risks associated with their situations.
Lack of Support for the Association between GAD2 Polymorphisms and Severe Human Obesity

The demonstration of association between common genetic variants and chronic human diseases such as obesity could have profound implications for the prediction, prevention, and treatment of these conditions. Unequivocal proof of such an association, however, requires independent replication of initial positive findings. Recently, three (−243 A>G, +61450 C>A, and +83897 T>A) single nucleotide polymorphisms (SNPs) within glutamate decarboxylase 2 (GAD2) were found to be associated with class III obesity (body mass index > 40 kg/m2). The association was observed among 188 families (612 individuals) segregating the condition, and a case-control study of 575 cases and 646 lean controls. Functional data supporting a pathophysiological role for one of the SNPs (−243 A>G) were also presented. The gene GAD2 encodes the 65-kDa subunit of glutamic acid decarboxylase—GAD65. In the present study, we attempted to replicate this association in larger groups of individuals, and to extend the functional studies of the −243 A>G SNP. Among 2,359 individuals comprising 693 German nuclear families with severe, early-onset obesity, we found no evidence for a relationship between the three GAD2 SNPs and obesity, whether SNPs were studied individually or as haplotypes. In two independent case-control studies (a total of 680 class III obesity cases and 1,186 lean controls), there was no significant relationship between the −243 A>G SNP and obesity (OR = 0.99, 95% CI 0.83–1.18, p = 0.89) in the pooled sample. These negative findings were recapitulated in a meta-analysis, incorporating all published data for the association between the −243G allele and class III obesity, which yielded an OR of 1.11 (95% CI 0.90–1.36, p = 0.28) in a total sample of 1,252 class III obese cases and 1,800 lean controls. Moreover, analysis of common haplotypes encompassing the GAD2 locus revealed no association with severe obesity in families with the condition. We also obtained functional data for the −243 A>G SNP that does not support a pathophysiological role for this variant in obesity. Potential confounding variables in association studies involving common variants and complex diseases (low power to detect modest genetic effects, overinterpretation of marginal data, population stratification, and biological plausibility) are also discussed in the context of GAD2 and severe obesity.
Communication costs of Strassen's matrix multiplication

Algorithms have historically been evaluated in terms of the number of arithmetic operations they performed. This analysis is no longer sufficient for predicting running times on today's machines. Moving data through memory hierarchies and among processors requires much more time (and energy) than performing computations. Hardware trends suggest that the relative costs of this communication will only increase. Proving lower bounds on the communication of algorithms and finding algorithms that attain these bounds are therefore fundamental goals. We show that the communication cost of an algorithm is closely related to the graph expansion properties of its corresponding computation graph. Matrix multiplication is one of the most fundamental problems in scientific computing and in parallel computing. Applying expansion analysis to Strassen's and other fast matrix multiplication algorithms, we obtain the first lower bounds on their communication costs. These bounds show that the current sequential algorithms are optimal but that previous parallel algorithms communicate more than necessary. Our new parallelization of Strassen's algorithm is communication-optimal and outperforms all previous matrix multiplication algorithms. <! -- END_PAGE_1 -->
JNK Inhibition Inhibits Lateral Line Neuromast Hair Cell Development

JNK signaling is known to play a role in regulating cell behaviors such as cell cycle progression, cell proliferation, and apoptosis, and recent studies have suggested important roles for JNK signaling in embryonic development. However, the precise function of JNK signaling in hair cell development remains poorly studied. In this study, we used the small molecule JNK inhibitor SP600125 to examine the effect of JNK signaling abrogation on the development of hair cells in the zebrafish lateral line neuromast. Our results showed that SP600125 reduced the numbers of both hair cells and supporting cells in neuromasts during larval development in a dose-dependent manner. Additionally, JNK inhibition strongly inhibited the proliferation of neuromast cells, which likely explains the decrease in the number of differentiated hair cells in inhibitor-treated larvae. Furthermore, western blot and in situ analysis showed that JNK inhibition induced cell cycle arrest through induction of p21 expression. We also showed that SP600125 induced cell death in developing neuromasts as measured by cleaved caspase-3 immunohistochemistry, and this was accompanied with an induction of p53 gene expression. Together these results indicate that JNK might be an important regulator in the development of hair cells in the lateral line in zebrafish by controlling both cell cycle progression and apoptosis.