gebhart/patrepeval huggingface dataset:
Estradiol and Selective Estrogen Receptor Modulators Differentially Regulate Target Genes with Estrogen Receptors α and β (2003)

Estrogens and selective estrogen receptor modulators (SERMs) interact with estrogen receptor (ER) alpha and beta to activate or repress gene transcription. To understand how estrogens and SERMs exert tissue-specific effects, we performed microarray analysis to determine whether ERalpha or ERbeta regulate different target genes in response to estrogens and SERMs. We prepared human U2OS osteosarcoma cells that are stably transfected with a tetracycline-inducible vector to express ERalpha or ERbeta. Western blotting, immunohistochemistry, and immunoprecipitation studies confirmed that U2OS-ERalpha cells synthesized only ERalpha and that U2OS-ERbeta cells expressed exclusively ERbeta. U2OS-ERalpha and U2OS-ERbeta cells were treated either with 17beta-estradiol (E2), raloxifene, and tamoxifen for 18 h. Labeled cRNAs were hybridized with U95Av2 GeneChips (Affymetrix). A total of 228, 190, and 236 genes were significantly activated or repressed at least 1.74-fold in U2OS-ERalpha and U2OS-ERbeta cells by E2, raloxifene, and tamoxifen, respectively. Most genes regulated in ERalpha cells in response to E2, raloxifene, and tamoxifen were distinct from those regulated in ERbeta cells. Only 38 of the 228 (17%) genes were regulated by E2 in both U2OS-ERalpha and U2OS-ERbeta cells. Raloxifene and tamoxifen regulated only 27% of the same genes in both the ERalpha and ERbeta cells. A subset of genes involved in bone-related activities regulated by E2, raloxifene, and tamoxifen were also distinct. Our results demonstrate that most genes regulated by ERalpha are distinct from those regulated by ERbeta in response to E2 and SERMs. These results indicate that estrogens and SERMs exert tissue-specific effects by regulating unique sets of targets genes through ERalpha and ERbeta
Role of T Lymphocytes and Interferon-γ in Ischemic Stroke (2006)

These findings indicate that CD4+ and CD8+ T lymphocytes, but not B lymphocytes, contribute to the inflammatory and thrombogenic responses, brain injury, and neurological deficit associated with experimental stroke. Although IFN-gamma plays a pivotal role in stroke-induced inflammatory responses, T lymphocytes appear to be a minor source of this cytokine.
Absence of the RT-6 T cell subset in diabetes-prone BB/W rats. (1986)

Diabetes-prone Bio-breeding/Worcester (DP) rats exhibit a severe T cell lymphopenia and autoimmune pancreatic insulitis. The present results indicate that the T cell lymphopenia is due in large part, if not entirely, to the absence of the RT-6+ peripheral T cell subset, which includes members of both the helper/inducer (W3/25) and suppressor/cytotoxic (OX 8) antigenic phenotypes. Delineation of the causal mechanism(s) for the selective absence of RT-6+ T cells in DP rats may provide important insights into the cellular basis of the insulin-dependent diabetes mellitus syndrome in these animals.
Lack of a role of circulating bradykinin in the blood pressure response to acute angiotensin converting enzyme inhibition in rats. (1987)

The role of circulating bradykinin in blood pressure regulation was investigated in conscious normotensive rats using a competitive antagonist of bradykinin. The acute blood pressure effect of this antagonist was also evaluated after inhibition of angiotensin converting enzyme with captopril and during simultaneous infusion of exogenous angiotensin II. No evidence was found for a role of circulating bradykinin in rats studied under normal conditions. Endogenous bradykinin seemed however involved in blood pressure control during angiotensin II infusion. Acute angiotensin converting enzyme inhibition had no influence on the blood pressure response to the bradykinin antagonist.
Sox15 Is Required for Skeletal Muscle Regeneration (2004)

The Sox genes define a family of transcription factors that play a key role in the determination of cell fate during development. The preferential expression of the Sox15 in the myogenic precursor cells led us to suggest that the Sox15 is involved in the specification of myogenic cell lineages or in the regulation of the fusion of myoblasts to form myotubes during the development and regeneration of skeletal muscle. To identify the physiological function of Sox15 in mice, we disrupted the Sox15 by homologous recombination in mice. Sox15-deficient mice were born at expected ratios, were healthy and fertile, and displayed normal long-term survival rates. Histological analysis revealed the normal ultrastructure of myofibers and the presence of comparable amounts of satellite cells in the skeletal muscles of Sox15(-/-) animals compared to wild-type animals. These results exclude the role of Sox15 in the development of satellite cells. However, cultured Sox15(-/-) myoblasts displayed a marked delay in differentiation potential in vitro. Moreover, skeletal muscle regeneration in Sox15(-/-) mice was attenuated after application of a crush injury. These results suggest a requirement for Sox15 in the myogenic program. Expression analyses of the early myogenic regulated factors MyoD and Myf5 showed the downregulation of the MyoD and upregulation of the Myf5 in Sox15(-/-) myoblasts. These results show an increased proportion of the Myf5-positive cells and suggest a role for Sox15 in determining the early myogenic cell lineages during skeletal muscle development.
Characterization of Structural Determinants of Granzyme B Reveals Potent Mediators of Extended Substrate Specificity (2004)

Granzymes are trypsin-like serine proteases mediating apoptotic cell death that are composed of two genetically distinct subfamilies: granzyme A-like proteases resemble trypsin in their active site architecture, while granzyme B-like proteases are quite distinct. Granzyme B prefers substrates containing P4 to P1 amino acids Ile/Val, Glu/Met/Gln, Pro/Xaa, and aspartic acid N-terminal to the proteolytic cleavage. By investigating the narrow extended specificity of the granzyme B-like proteases the mediators of their unique specificity are being defined. The foci of this study were the structural determinants Ile99, Tyr174, Arg192, and Asn218. Even modest mutations of these residues resulted in unique extended specificity profiles as determined using combinatorial substrate libraries and individual fluorogenic substrates. As with other serine proteases, Ile99 completely defines and predicts P2 specificity, primarily through the binding constant Km. Asn218 variants have minor effects alone but in combination with mutations at Arg192 and Ile99 alter P2 through P4 extended specificity. For each variant, the activity on its cognate substrate was equal to that of granzyme B for the same substrate. Thus, mutations at these determinants change extended selectivity preferentially over catalytic power. Additionally Asn218 variants result in increased activity on the wild type substrate, while the N218A/I99A variant disrupts the additivity between P2 and P4 specificity. This defines Asn218 not only as a determinant of specificity but also as a structural component required for P2 and P4 independence. This study confirms four determinants of granzyme B extended substrate specificity that constitute a canon applicable to the study of the remaining family members.
Transplantation of Mesenchymal Stem Cells Is an Optimal Approach for Plastic Surgery (2006)

Mesenchymal stem cells (MSCs) are able to differentiate into a variety of cell types, offering promising approaches for stem cell-mediated tissue regeneration. Here, we explored the potential of utilizing MSCs to reconstruct orofacial tissue, thereby altering the orofacial appearance. We demonstrated that bone marrow MSCs were capable of generating bone structures and bone-associated marrow elements on the surfaces of the orofacial bone. This resulted in significant recontouring of the facial appearance in mouse and swine. Notably, the newly formed bone and associated marrow tissues integrated with the surfaces of the recipient bones and re-established a functional bone marrow organ-like system. These data suggested that MSC-mediated tissue regeneration led to a body structure extension, with the re-establishment of all functional components necessary for maintaining the bone and associated marrow organ. In addition, we found that the subcutaneous transplantation of another population of MSCs, the human periodontal ligament stem cells (PDLSCs), could form substantial amounts of collagen fibers and improve facial wrinkles in mouse. By contrast, bone marrow MSCs failed to survive at 8 weeks post-transplantation under the conditions used for the PDLSC transplantation. This study suggested that the mutual interactions between donor MSCs and recipient microenvironment determine long-term outcome of the functional tissue regeneration. Disclosure of potential conflicts of interest is found at the end of this article.
Main effects screening: a distributed continuous quality assurance process for monitoring performance degradation in evolving software systems (2005)

Developers of highly configurable performance-intensive software systems often use a type of in-house performance-oriented "regression testing" to ensure that their modifications have not adversely affected their software's performance across its large configuration space. Unfortunately, time and resource constraints often limit developers to in-house testing of a small number of configurations and unreliable extrapolation from these results to the entire configuration space, which allows many performance bottlenecks and sources of QoS degradation to escape detection until systems are fielded. To improve performance assessment of evolving systems across large configuration spaces, we have developed a distributed continuous quality assurance (DCQA) process called main effects screening that uses in-the-field resources to execute formally designed experiments to help reduce the configuration space, thereby allowing developers to perform more targeted in-house QA. We have evaluated this process via several feasibility studies on several large, widely-used performance-intensive software systems. Our results indicate that main effects screening can detect key sources of performance degradation in large-scale systems with significantly less effort than conventional techniques.
No benefit derived from repetitive transcranial magnetic stimulation in depression: a prospective, single centre, randomised, double blind, sham controlled "add on" trial. (2004)

Repetitive transcranial magnetic stimulation (rTMS) has been reported to demonstrate slight effects in the treatment of depression. Hence, a novel bilateral versus unilateral and sham stimulation design was applied to further assess rTMS' antidepressant effects. Forty one medication free patients with major depression, admitted to a psychiatric unit specialising in affective disorders, were consecutively randomised into 3 groups. Group A1 (n = 12) received unilateral active stimulation consisting of high frequency (hf) rTMS over the left dorsolateral prefrontal cortex (LDLPC) and subsequent sham low frequency (lf) rTMS over the right dorsolateral prefrontal cortex (RDLPC). Group A2 (n = 13) received simultaneous bilateral active stimulation consisting of hf-rTMS over the LDLPC and lf-rTMS over the RDLPC. Group C (n = 13) received bilateral sham stimulation. Stimulation was performed on 10 consecutive workdays. All patients received antidepressant medication on the first day of stimulation, which was continued during and after the stimulation period. As no significant difference in antidepressant outcome between group A1 and A2 was found, the two groups were pooled. The time course of the outcome variables Hamilton depression rating scale (HDRS(21)) and Beck depression inventory (days 0, 7, 14, 28) by repeated measures analysis of variance revealed no significant group differences (in terms of a group by time interaction), whereas there was a significant effect of time on all three outcome variables in all groups. The results suggest that rTMS as an "add on" strategy, applied in a unilateral and a bilateral stimulation paradigm, does not exert an additional antidepressant effect.
Bidirectional Transcription Directs Both Transcriptional Gene Activation and Suppression in Human Cells (2008)

Small RNAs targeted to gene promoters in human cells have been shown to modulate both transcriptional gene suppression and activation. However, the mechanism involved in transcriptional activation has remained poorly defined, and an endogenous RNA trigger for transcriptional gene silencing has yet to be identified. Described here is an explanation for siRNA-directed transcriptional gene activation, as well as a role for non-coding antisense RNAs as effector molecules driving transcriptional gene silencing. Transcriptional activation of p21 gene expression was determined to be the result of Argonaute 2-dependent, post-transcriptional silencing of a p21-specific antisense transcript, which functions in Argonaute 1-mediated transcriptional control of p21 mRNA expression. The data presented here suggest that in human cells, bidirectional transcription is an endogenous gene regulatory mechanism whereby an antisense RNA directs epigenetic regulatory complexes to a sense promoter, resulting in RNA-directed epigenetic gene regulation. The observations presented here support the notion that epigenetic silencing of tumor suppressor genes, such as p21, may be the result of an imbalance in bidirectional transcription levels. This imbalance allows the unchecked antisense RNA to direct silent state epigenetic marks to the sense promoter, resulting in stable transcriptional gene silencing.
Mutations in sodium-channel gene SCN9A cause a spectrum of human genetic pain disorders (2007)

The voltage-gated sodium-channel type IX alpha subunit, known as Na(v)1.7 and encoded by the gene SCN9A, is located in peripheral neurons and plays an important role in action potential production in these cells. Recent genetic studies have identified Na(v)1.7 dysfunction in three different human pain disorders. Gain-of-function missense mutations in Na(v)1.7 have been shown to cause primary erythermalgia and paroxysmal extreme pain disorder, while nonsense mutations in Na(v)1.7 result in loss of Na(v)1.7 function and a condition known as channelopathy-associated insensitivity to pain, a rare disorder in which affected individuals are unable to feel physical pain. This review highlights these recent developments and discusses the critical role of Na(v)1.7 in pain sensation in humans.
Radiotherapy and the Tumor Stroma: The Importance of Dose and Fractionation (2014)

Ionizing radiation is a non-specific but highly effective way to kill malignant cells. However, tumor recurrence sustained by a minor fraction of surviving tumor cells is a commonplace phenomenon caused by the activation of both cancer cell intrinsic resistance mechanisms, and also extrinsic intermediaries of therapy resistance, represented by non-malignant cells and structural components of the tumor stroma. The improved accuracy offered by advanced radiotherapy (RT)-technology permits reduced volume of healthy tissue in the irradiated field, and has been triggering an increase in the prescription of high-dose oligo-fractionated regimens in the clinics. Given the remarkable clinical success of high-dose RT and the current therapeutic shift occurring in the field, in this review we revise the existing knowledge on the effects that different radiation regimens exert on the different compartments of the tumor microenvironment, and highlight the importance of anti-tumor immunity and other tumor cell extrinsic mechanisms influencing therapeutic responses to high-dose radiation.
Rapid and simple method of photobleaching to reduce background autofluorescence in lung tissue sections. (2015)

Autofluorescence exhibited by tissues often interferes with immunofluorescence. Using imaging and spectral analysis, we observed remarkable reduction of autofluorescence of formalin fixed paraffin embedded tissues irradiated with light prior to incubation with immunofluorescent dyes. The technique of photobleaching offers significant improvement in the quality and specificity of immunofluorescence. This has the potential for better techniques for disease diagnosis.
Finding the Linchpins of the Dark Web: a Study on Topologically Dedicated Hosts on Malicious Web Infrastructures (2013)

Malicious Web activities continue to be a major threat to the safety of online Web users. Despite the plethora forms of attacks and the diversity of their delivery channels, in the back end, they are all orchestrated through malicious Web infrastructures, which enable miscreants to do business with each other and utilize others' resources. Identifying the linchpins of the dark infrastructures and distinguishing those valuable to the adversaries from those disposable are critical for gaining an upper hand in the battle against them. In this paper, using nearly 4 million malicious URL paths crawled from different attack channels, we perform a large-scale study on the topological relations among hosts in the malicious Web infrastructure. Our study reveals the existence of a set of topologically dedicated malicious hosts that play orchestrating roles in malicious activities. They are well connected to other malicious hosts and do not receive traffic from legitimate sites. Motivated by their distinctive features in topology, we develop a graph-based approach that relies on a small set of known malicious hosts as seeds to detect dedicate malicious hosts in a large scale. Our method is general across the use of different types of seed data, and results in an expansion rate of over 12 times in detection with a low false detection rate of 2%. Many of the detected hosts operate as redirectors, in particular Traffic Distribution Systems (TDSes) that are long-lived and receive traffic from new attack campaigns over time. These TDSes play critical roles in managing malicious traffic flows. Detecting and taking down these dedicated malicious hosts can therefore have more impact on the malicious Web infrastructures than aiming at short-lived doorways or exploit sites.
The clinical implication and molecular mechanism of preferential IL-4 production by modified glycolipid-stimulated NKT cells (2004)

OCH, a sphingosine-truncated analog of α-galactosylceramide (αGC), is a potential therapeutic reagent for a variety of Th1-mediated autoimmune diseases through its selective induction of Th2 cytokines from natural killer T (NKT) cells. We demonstrate here that the NKT cell production of IFN-γ is more susceptible to the sphingosine length of glycolipid ligand than that of IL-4 and that the length of the sphingosine chain determines the duration of NKT cell stimulation by CD1d-associated glycolipids. Furthermore, IFN-γ production by NKT cells requires longer T cell receptor stimulation than is required for IL-4 production by NKT cells stimulated either with immobilized mAb to CD3 or with immobilized "αGC-loaded" CD1d molecules. Interestingly, transcription of IFN-γ but not that of IL-4 was sensitive to cycloheximide treatment, indicating the intrinsic involvement of de novo protein synthesis for IFN-γ production by NKT cells. Finally, we determined c-Rel was preferentially transcribed in αGC-stimulated but not in OCH-stimulated NKT cells and was essential for IFN-γ production by activated NKT cells. Given the dominant immune regulation by the remarkable cytokine production of ligand-stimulated NKT cells in vivo, in comparison with that of (antigen-specific) T cells or NK cells, the current study confirms OCH as a likely therapeutic reagent for use against Th1-mediated autoimmune diseases and provides a novel clue for the design of drugs targeting NKT cells.
Conditional transgenic expression of the ipt gene indicates a function for cytokinins in paracrine signaling in whole tobacco plants (1997)

This study investigated whether an increased production of the plant hormone cytokinin in roots, the main site of its synthesis and putative signaling organ, can influence developmental events, such as growth of axillary shoot meristems or leaf senescence, in the plant shoot. To this end, transgenic tobacco plants (Nicotiana tabacum L.) were generated that conditionally overproduce cytokinins. These plants harbour the ipt gene under the transcriptional control of a modified 35S promoter that is repressed in plants with high titers of tetracycline repressor protein. De-repression of transcription led to a rapid more than 50-fold increase of hormone concentration. The time course of changes in the steady-state levels of 16 different cytokinin metabolites, as a consequence of IPT enzyme activity, was monitored in different plant tissues. Zeatin riboside was the first and most dramatically increased product; zeatin, dihydrozeatin and glucosides accumulated later. The consequences of enhanced cytokinin synthesis remained mainly restricted to the site of hormone production. For example, de-repression of ipt gene transcription in lateral buds caused the growth of single buds only at the site of tetracycline application. In reciprocal grafts of transgenic plants with wild-type plants, no biological cytokinin effects, i.e. growth of lateral shoot meristems or sequential leaf senescence, were observed in the non-transgenic plant part. Also, the increase in steady-state levels of cytokinins remained restricted mainly to the transgenic part, despite a specific increase of the zeatin riboside concentration in the transpiration stream. These results question the role of cytokinins as a long-range root-to-shoot signal in correlative control of apical dominance and sequential leaf senescence of tobacco, and support the assumption that this hormone is relevant to paracrine signaling.
Estrogen and progesterone receptor status affect genome-wide DNA methylation profile in breast cancer (2010)

DNA methylation is the main epigenetic modification that occurs at the early stages of carcinogenesis. We performed a genome-wide DNA methylation profiling to evaluate whether the DNA methylation state is different in the estrogen receptor (ER) and progesterone receptor (PR) status of breast cancer. Twelve ER+/PR+ and 12 ER-/PR- breast cancer tissues were selected from the biorepository of the Seoul Breast Cancer Study for Infinium Methylation Assay. The difference of the DNA methylation state of 27 578 methylation sites in 14 000 genes between two groups was evaluated by Student's t-test. False discovery rate (FDR) was estimated to evaluate the probability of false positive associations. Of the 27 578 sites, 148 sites (0.54%) were significantly different between ER+/PR+ and ER-/PR- breast cancers (P < 0.001); 93 hypermethylated and 55 hypomethylated. Five genes, FAM124B (P = 7.26 × 10(-7)), MANEAL (P = 3.38 × 10(-7)), ST6GALNAC1 (P = 2.85 × 10(-6)), NAV1 (P = 5.94 × 10(-6)) and PER1 (P = 6.45 × 10(-6)) remained significant after correction for multiple tests (FDR < 0.05). In a subsequent replication study for five genes, four of the five genes were validated; FAM124B and ST6GALNAC1 were significantly hypermethylated, and NAV1 and PER1 were significantly hypomethylated in ER+/PR+ breast cancers (P < 0.05). In the first genome-wide DNA methylation profiling according to the receptor status of breast cancer, we found that ER/PR status affects the DNA methylation state of FAM124B, ST6GALNAC1, NAV1 and PER1 in breast cancer.
Temperature Dependence of “Elementary Processes” in Doping Semiconductor Nanocrystals (2009)

Controlled doping is a critical step toward various unique nanostructures. This report shall demonstrate that doping chemistry of colloidal nanocrystals is much more complex than what has been proposed in the existing experimental and theoretical reports. Four individual processes, namely "surface adsorption", "lattice incorporation", "lattice diffusion", and "lattice ejection", will be identified, each of which possesses its own critical temperature. A given type of host nanocrystals can be switched from being impossible to dope to becoming successfully doped. The key is to program the reaction temperature to accommodate all elementary processes.