gebhart/patrepeval huggingface dataset:
hilA is a novel ompR/toxR family member that activates the expression of Salmonella typhimurium invasion genes (1995)

During infection of its hosts, Salmonella enters intestinal epithelial cells. Many Salmonella typhimurium genes required for bacterial entry into host cells are encoded on a 40 kb 'pathogenicity island'. We report here the identification of hilA, a gene within the 'island' that appears to encode an activator of invasion gene expression. By using a set of lacZY transcriptional fusions to S. typhimurium invasion genes, we found that hilA activates the expression of invasion genes located on the 'pathogenicity island'. hilA is required for efficient entry into HEp-2 cells in vitro. The predicted amino acid sequence of hilA shares significant homology with the DNA-binding domains of the OmpR-ToxR family of transcriptional activators. However, unlike OmpR and ToxR, HilA contains neither a phosphoryl acceptor nor a membrane-spanning domain, and, therefore, its activity may be modulated by a novel mechanism. Many environmental conditions modulate the ability of Salmonella to enter non-phagocytic mammalian cells. It has been proposed that induction of Salmonella invasion proteins in response to a combination of environmental cues ensures that bacterial entry is limited to specific sites and times during infection. Our results are consistent with the hypothesis that hilA plays a key role in the regulation of Salmonella invasion during infection.
Merchant groups in the 17th-century Brazilian sugar trade: Reappraising old topics with new research insights (2004)

This paper examines the role of the New Christians within Portuguese mercantile organizations during the early modern period. It stems from the case of the General Brazil Company, because the foundation of this enterprise provides an example of how the 17th-century Portuguese authorities dealt with New Christian issues, allowing for a survey of Portuguese historiography on the subject.
HDAC2 overexpression confers oncogenic potential to human lung cancer cells by deregulating expression of apoptosis and cell cycle proteins (2012)

Histone deacetylase 2 (HDAC2) is crucial for embryonic development, affects cytokine signaling relevant for immune responses, and is often significantly overexpressed in solid tumors, but little is known of its role in human lung cancer. In this study, we demonstrated the aberrant expression of HDAC2 in lung cancer tissues and investigated oncogenic properties of HDAC2 in human lung cancer cell lines. HDAC2 inactivation resulted in regression of tumor cell growth and activation of cellular apoptosis via p53 and Bax activation and Bcl2 suppression. In cell cycle regulation, HDAC2 inactivation caused induction of p21WAF1/CIP1 expression, and simultaneously suppressed the expressions of cyclin E2, cyclin D1, and CDK2, respectively. Consequently, this led to the hypophosphorylation of pRb protein in G1/S transition and thereby inactivated E2F/DP1 target gene transcriptions of A549 cells. In addition, we demonstrated that HDAC2 directly regulated p21WAF1/CIP1 expression in a p53-independent manner. However, HDAC1 was not related to p21WAF1/CIP1 expression and tumorigenesis of lung cancer. Lastly, we observed that sustained-suppression of HDAC2 in A549 lung cancer cells attenuated in vitro tumorigenic properties and in vivo tumor growth of the mouse xenograft model. Taken together, we suggest that the aberrant regulation of HDAC2 and its epigenetic regulation of gene transcription in apoptosis and cell cycle components play an important role in the development of lung cancer.
The first constant domain (CH1 and CL) of an antibody used as heterodimerization domain for bispecific miniantibodies (1998)

Bispecific miniantibodies were constructed by genetically fusing the C(H)1 domain of an IgG1 to the C-terminus of a single-chain Fv fragment (scFv-425), specific for the EGF receptor, and fusing the C(L) domain of a kappa light chain to the C-terminus of a scFv specific for CD2 (scFv-M1). An efficient dicistronic gene arrangement for functional expression in Escherichia coli was constructed. Immunoblots demonstrated correct domain assembly and the formation of the natural C(H)1-C(L) disulfide bridge. Gel filtration confirmed the correct size, sandwich ELISAs demonstrated bispecific functionality, and SPR biosensor measurements determined binding to EGF-R in comparison to bivalent constructs. Bispecific anti-EGF-R/anti-CD2 miniantibodies are candidates for the immunotherapy of cancer.
Immune Complexes and the Evolution of Lyme Arthritis (1979)

In a prospective study of 78 patients with Lyme arthritis, abnormal serum C1q binding activity was present at the initial onset of erythema chronicum migrans in nearly all cases. The abnormal binding persisted in patients with subsequent nerve or heart involvement. In contrast, among those with only subsequent arthritis, it usually disappeared within three months (P = 0.018). However, in the synovial fluid of affected joints, abnormal binding was uniformly present, and always to a greater extent than in the circulation. The abnormally reactive material behaved like antigen-antibody complexes. It had a density of 19S or greater, dissociated below pH 4.2, and lacked antiglobulin activity. Cryoprecipitates containing immunoglobulin were good but insensitive predictors of its presence, but immune complexes themselves did not seem primarily responsible for cryoprecipitability. Thus, as judged by C1q binding, immune complexes remain disseminated in certain patients with Lyme arthritis but localize to joints in others. (N Engl J Med 301:1358–1363, 1979)
Observation on the Plasma Amino Acids of Patients with Colorectal Cancer. (1991)

大腸癌患者10名に対し,術前早朝空腹時採血を施行し,必須アミノ酸8種類,非必須アミノ酸12種類,計20種類の血漿遊離アミノ酸をアミノ酸自動分析器(日立835-50)で測定した.コントロール群として健常成人50名に対し,早朝空腹時採血を施行し,同様に20種類のアミノ酸を測定した.その結果,大腸癌患者においては,コントロール群に比し,有意の差をもって,Arg, Thr, Asp, Ser, Pro, Glnが減少し,Orn, Pheが増加していた.大腸癌患者がアミノ酸アンバランスの状態にあることは,制癌アミノ酸輪液製剤の開発に有用な知見であるものと考える.
Self‐Assembly of Thermally Responsive Nanoparticles of a Genetically Encoded Peptide Polymer by Drug Conjugation (2012)

Nanoparticles on demand: Upon the site-specific covalent attachment of hydrophobic molecules to one end of the biopolymer backbone, chimeric polypeptides (derived from elastin-like polypeptides) can self-assemble to form thermoresponsive nanoparticles suitable for drug delivery. Molecules with a distribution coefficient greater than 1.5 imparted sufficient amphiphilicity to drive self-assembly into sub-100 nm nanoparticles (see picture). As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Animal Applications of Research in Mammalian Development (1991)

On cellular and molecular approaches to gametogenesis, embryogenesis, and maternal-fetal interactions in animals important to agriculture. Notes new approaches to oocyte culture, egg and embryo cryopreservation, and genetic alteration of productivity and herd quality. Annotation copyright Book News,
Cereblon is expressed in the retina and binds to voltage‐gated chloride channels (2009)

The function of the central nervous system depends on the correct regulation of ion channels by interacting proteins. Here, we identified cereblon as a new interactor of the voltage-gated chloride channel ClC-2. A distal region of the ClC-2 C-terminus interacts with the Lon domain of cereblon. Cereblon is expressed in several brain regions including the retina. There, we detected cereblon in nuclear and synaptic layers and localized the protein in the same subcellular region of bipolar cell bodies previously reported to express ClC-2. Our data suggest that cereblon might be associated with voltage-gated chloride channels in the central nervous system.
Virtual radio: a framework for configurable radio networks (2008)

Network virtualization has recently been proposed for the development of large scale experimental networks, but also as design principle for a Future Internet. In this paper we describe the background to network virtualization and extend this concept into the wireless domain, which we denote as radio virtualization. With radio virtualization different virtual radio networks can operate on top of a common shared infrastructure and share the same radio resources. We present how this radio resource sharing can be performed efficiently without interference between the different virtual radio networks. Further we discuss how radio transmission functionality can be configured. Radio virtualization provides flexibility in the design and deployment of new wireless networking concepts. It allows customization of radio networks for dedicated networking services at reduced deployment costs.
Generating Videos with Scene Dynamics (2016)

We capitalize on large amounts of unlabeled video in order to learn a model of scene dynamics for both video recognition tasks (e.g. action classification) and video generation tasks (e.g. future prediction). We propose a generative adversarial network for video with a spatio-temporal convolutional architecture that untangles the scene’s foreground from the background. Experiments suggest this model can generate tiny videos up to a second at full frame rate better than simple baselines, and we show its utility at predicting plausible futures of static images. Moreover, experiments and visualizations show the model internally learns useful features for recognizing actions with minimal supervision, suggesting scene dynamics are a promising signal for representation learning. We believe generative video models can impact many applications in video understanding and simulation.
Efficacy of a dopamine-somatostatin chimeric molecule, BIM-23A760, in the control of cell growth from primary cultures of human non-functioning pituitary adenomas: a multi-center study (2008)

Dopamine D2 and somatostatin receptors (sstrs) were reported to affect non-functioning pituitary adenoma (NFPA) proliferation in vitro. However, the reported results differ according to the experimental conditions used. We established an experimental protocol allowing reproducible evaluation of NFPA cell proliferation in vitro, to test and compare the antiproliferative effects of dopamine and somatostatin analogs (alone or in combination) with the activity of the dopamine-somatostatin chimeric molecule BIM-23A760. The protocol was utilized by four independent laboratories, studying 38 fibroblast-deprived NFPA cell cultures. Cells were characterized for GH, POMC, sstr1-sstr5, total dopamine D2 receptor (D2R) (in all cases), and D2 receptor long and short isoforms (in 15 out of 38 cases) mRNA expression and for alpha-subunit, LH, and FSH release. D2R, sstr3, and sstr2 mRNAs were consistently observed, with the dominant expression of D2R (2.9+/-2.6 copy/copy beta-glucuronidase; mean+/-s.e.m.), when compared with sstr3 and sstr2 (0.6+/-1.0 and 0.3+/-0.6 respectively). BIM-23A760, a molecule with high affinity for D2R and sstr2, significantly inhibited [3H]thymidine incorporation in 23 out of 38 (60%) NFPA cultures (EC50=1.2 pM and Emax=-33.6+/-3.7%). BIM-23A760 effects were similar to those induced by the selective D2R agonist cabergoline that showed a statistically significant inhibition in 18 out of 27 tumors (compared with a significant inhibition obtained in 17 out of 27 tumors using BIM-23A760, in the same subgroup of adenomas analyzed), while octreotide was effective in 13 out of 27 cases. In conclusion, superimposable data generated in four independent laboratories using a standardized protocol demonstrate that, in vitro, chimeric dopamine/sstr agonists are effective in inhibiting cell proliferation in two-thirds of NFPAs.
Adenovirus‐mediated cytosine deaminase/5‐fluorocytosine suicide gene therapy of human hepatoblastoma in vitro (2009)

Assuming employment of fully active promoters, the SuperCD/5-FC approach may serve as a potentially useful anti-tumor strategy against advanced HB.
Solid-Phase Synthesis of O-Linked Glycopeptide Analogues of Enkephalin (2001)

The synthesis of 18 N-alpha-FMOC-amino acid glycosides for solid-phase glycopeptide assembly is reported. The glycosides were synthesized either from the corresponding O'Donnell Schiff bases or from N-alpha-FMOC-amino protected serine or threonine and the appropriate glycosyl bromide using Hanessian's modification of the Koenigs-Knorr reaction. Reaction rates of D-glycosyl bromides (e.g., acetobromoglucose) with the L- and D-forms of serine and threonine are distinctly different and can be rationalized in terms of the steric interactions within the two types of diastereomeric transition states for the D/L and D/D reactant pairs. The N-alpha-FMOC-protected glycosides [monosaccharides Xyl, Glc, Gal, Man, GlcNAc, and GalNAc; disaccharides Gal-beta(1-4)-Glc (lactose), Glc-beta(1-4)-Glc (cellobiose), and Gal-alpha(1-6)-Glc (melibiose)] were incorporated into 22 enkephalin glycopeptide analogues. These peptide opiates bearing the pharmacophore H-Tyr-c[DCys-Gly-Phe-DCys]- were designed to probe the significance of the glycoside moiety and the carbohydrate-peptide linkage region in blood-brain barrier (BBB) transport, opiate receptor binding, and analgesia.
Role of the Autonomic Nervous System in Atrial Fibrillation (2014)

Autonomic nervous system activation can induce significant and heterogeneous changes of atrial electrophysiology and induce atrial tachyarrhythmias, including atrial tachycardia and atrial fibrillation (AF). The importance of the autonomic nervous system in atrial arrhythmogenesis is also supported by circadian variation in the incidence of symptomatic AF in humans. Methods that reduce autonomic innervation or outflow have been shown to reduce the incidence of spontaneous or induced atrial arrhythmias, suggesting that neuromodulation may be helpful in controlling AF. In this review, we focus on the relationship between the autonomic nervous system and the pathophysiology of AF and the potential benefit and limitations of neuromodulation in the management of this arrhythmia. We conclude that autonomic nerve activity plays an important role in the initiation and maintenance of AF, and modulating autonomic nerve function may contribute to AF control. Potential therapeutic applications include ganglionated plexus ablation, renal sympathetic denervation, cervical vagal nerve stimulation, baroreflex stimulation, cutaneous stimulation, novel drug approaches, and biological therapies. Although the role of the autonomic nervous system has long been recognized, new science and new technologies promise exciting prospects for the future.
Wrestling with Native Chemical Ligation (2009)

An improved method for the semisynthesis of a potassium channel involving native chemical ligation allows the introduction of short sequences containing non-canonical amino acids at any position within the polypeptide chain. The work enhances the technology available for a range of fundamental investigations of membrane proteins and for applications of membrane channels and pores in biotechnology.
Platelet-activating factor acetylhydrolase activity in maternal, fetal, and newborn rabbit plasma during pregnancy and lactation. (1988)

The inactivation of the biologically active ether-containing glycerophospholipid platelet-activating factor (PAF) is catalyzed by the enzyme PAF acetylhydrolase (1-alkyl-2-acetyl-sn-glycero-3-phosphocholine acetylhydrolase, EC 3.1.1.48). The specific activity of acetylhydrolase has been assayed in maternal rabbit plasma prior to and throughout pregnancy and after parturition. The specific activity of acetylhydrolase was 131 +/- 8 nmol.min-1.ml-1 of plasma (mean +/- SEM) in the nonpregnant rabbit. Similar specific activities were found throughout the first half of pregnancy; however, on day 15 the acetylhydrolase activity began to decrease and reached a minimum around day 27. Within 24-48 hr following delivery, the specific activity of the enzyme increased to the levels found in the nonpregnant animals. The specific activity of acetylhydrolase in fetuses (gestational ages of 21-30 days) and neonates increased from 22 nmol.min-1.ml-1 of plasma (21-day-old) to 328 nmol.min-1.ml-1 of plasma (35-day-old rabbits). The decrease in enzymatic activity of the pregnant rabbit plasma cannot be accounted for by the presence of an inhibitor as determined by plasma-mixing experiments with nonpregnant and pregnant (27-day) plasma. The properties of this enzyme in the rabbit were consistent with those reported by others, i.e., substrate specificity, inactivation by heat and various inhibitors, and Ca2+ independency. The activity of PAF acetylhydrolase was associated primarily with the high density lipoprotein fraction in rabbit plasma. The decrease of this enzymatic activity during pregnancy may serve to remove the protective effect on myometrium to allow an increased amount of PAF to come in contact with this tissue.
RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models (2006)

icwww.epfl.ch/~stamatak
PCCA: A new approach for distance learning from sparse pairwise constraints (2012)

This paper introduces Pairwise Constrained Component Analysis (PCCA), a new algorithm for learning distance metrics from sparse pairwise similarity/dissimilarity constraints in high dimensional input space, problem for which most existing distance metric learning approaches are not adapted. PCCA learns a projection into a low-dimensional space where the distance between pairs of data points respects the desired constraints, exhibiting good generalization properties in presence of high dimensional data. The paper also shows how to efficiently kernelize the approach. PCCA is experimentally validated on two challenging vision tasks, face verification and person re-identification, for which we obtain state-of-the-art results.
Restoring Natural Sensory Feedback in Real-Time Bidirectional Hand Prostheses (2014)

Hand loss is a highly disabling event that markedly affects the quality of life. To achieve a close to natural replacement for the lost hand, the user should be provided with the rich sensations that we naturally perceive when grasping or manipulating an object. Ideal bidirectional hand prostheses should involve both a reliable decoding of the user's intentions and the delivery of nearly "natural" sensory feedback through remnant afferent pathways, simultaneously and in real time. However, current hand prostheses fail to achieve these requirements, particularly because they lack any sensory feedback. We show that by stimulating the median and ulnar nerve fascicles using transversal multichannel intrafascicular electrodes, according to the information provided by the artificial sensors from a hand prosthesis, physiologically appropriate (near-natural) sensory information can be provided to an amputee during the real-time decoding of different grasping tasks to control a dexterous hand prosthesis. This feedback enabled the participant to effectively modulate the grasping force of the prosthesis with no visual or auditory feedback. Three different force levels were distinguished and consistently used by the subject. The results also demonstrate that a high complexity of perception can be obtained, allowing the subject to identify the stiffness and shape of three different objects by exploiting different characteristics of the elicited sensations. This approach could improve the efficacy and "life-like" quality of hand prostheses, resulting in a keystone strategy for the near-natural replacement of missing hands.
In vivo gene transfection with heat shock protein 70 enhances myocardial tolerance to ischemia-reperfusion injury in rat. (1997)

Heat shock protein 70 (HSP70) has been reported to be involved in the myocardial self-preservation system. To obtain the evidence that HSP70 plays a direct role in the protection from myocardial ischemia-reperfusion injury, rat hearts were transfected with human HSP70 gene by intracoronary infusion of hemagglutinating virus of Japan (HVJ)-liposome containing human HSP70 gene. The control hearts were infused with HVJ-liposome without the HSP70 gene. The hearts from whole-body heat-stressed or nontreated rats were also examined. Western blot and immunohistochemical analysis showed that apparent overexpression of HSP70 occurred in the gene transfected hearts and that gene transfection might be more effective for HSP70 induction than heat stress. In Langendorff perfusion, better functional recovery as well as less creatine phosphokinase leakage after ischemia were obtained in the gene transfected hearts with HSP70 than in the control or nontreated hearts. Furthermore, the gene transfected hearts showed better functional recovery than the heat-stressed hearts. These results indicated that overexpressed HSP70 plays a protective role in myocardial injury, suggesting the possibility that gene transfection with HSP70 may become a novel method for myocardial protection through enforcing the self-preservation systems.
Aimless Excursions: Wandering in the Elderly (2006)

One in five people with dementia wander. Long-term care facilities must deal with wandering while simultaneously protecting residents, complying with life-safety codes, maintaining a home-like environment, and respecting resident rights. Wanderers tend to be physically healthier than those who do not wander, but more behaviorally disturbed. Experts indicate that 72% of patients who elope will attempt to elope again. Strategies like using commercial security systems, landscaping to direct wanderers' attention back to the facility, keeping resident albums with recent pictures and facts about the resident, and having a research-based policy help prevent serious outcomes.
Laser speckle contrast imaging for measuring blood flow (2007)

When a diffuse object is illuminated with laser light, a random interference effect known as a speckle pattern is produced. If there is movement in the object, the speckles fluctuate in intensity. These fluctuations can be used to provide information about the movement. A simple way of accessing this information is to image the speckle pattern-the fluctuations cause a blurring of the speckle, leading to a reduction in the local speckle contrast. Thus velocity distributions are coded as speckle contrast variations. The same information can be obtained by using the Doppler effect, but producing a two-dimensional Doppler map requires scanning: speckle imaging provides the same information without the need to scan. This paper reviews the development of laser speckle imaging, starting with the connection established between speckle fluctuations and movement in the nineteen-seventies. In the eighties, a photographic technique for monitoring retinal blood flow was developed, and ten years later a digital version was used to monitor capillary blood flow in the skin. Today, many groups around the world are either using or researching the technique, and the paper will close by presenting some of their recent results.