gebhart/patrepeval huggingface dataset:
The Role of Hepatic Nuclear Factor 1α and PDX-1 in Transcriptional Regulation of the pdx-1 Gene (2001)

The PDX-1 homeodomain transcription factor regulates pancreatic development and adult islet beta cell function. Expression of the pdx-1 gene is almost exclusively localized to beta cells within the adult endocrine pancreas. Islet beta cell-selective transcription is controlled by evolutionarily conserved subdomain sequences (termed Areas I (-2839 to -2520 base pairs (bp)), II (-2252 to -2023 bp), and III (-1939 to -1664 bp)) found within the 5'-flanking region of the pdx-1 gene. Areas I and II are independently capable of directing beta cell-selective reporter gene activity in transfection assays, with Area I-mediated stimulation dependent upon binding of hepatic nuclear factor 3 beta (HNF3 beta), a key regulator of islet beta cell function. To identify other transactivators of Area I, highly conserved sequence segments within this subdomain were mutagenized, and their effect on activation was determined. Several of the sensitive sites were found by transcription factor data base analysis to potentially bind endodermally expressed transcription factors, including HNF1 alpha (-2758 to -2746 bp, Segment 2), HNF4 (-2742 to -2730 bp, Segment 4; -2683 to -2671 bp, Segment 7-8), and HNF6 (-2727 to -2715 bp, Segment 5). HNF1 alpha, but not HNF4 and HNF6, binds specifically to Area I sequences in vitro. HNF1 alpha was also shown to specifically activate Area I-driven transcription through Segment 2. In addition, PDX-1 itself was found to stimulate Area I activation. The chromatin immunoprecipitation assay performed with PDX-1 antisera also demonstrated that this factor bound to Area I within the endogenous pdx-1 gene in beta cells. Our results indicate that regulatory factors binding to Area I conserved sequences contribute to the selective transcription pattern of the pdx-1 gene and that control is mediated by endodermal regulators like HNF1 alpha, HNF3 beta, and PDX-1.
Identification of Sequential Events and Factors Associated with Microglial Activation, Migration, and Cytotoxicity in Retinal Degeneration inrdMice (2005)

Activation of microglia, as well as expression of their signaling molecules (chemokines) and microglia-derived toxic factor (TNF-alpha), coincides with or precedes the occurrence of photoreceptor apoptosis, suggesting activated microglia play a major role in retinal degeneration in rd mice. The chemokines MCP-1, MCP-3, MIP-1alpha, MIP-1beta, and RANTES are involved in activation and recruitment of the microglia to the degenerating photoreceptor cell layer. TNF-alpha, produced by the activated microglia, may accentuate the photoreceptor cell death.
A WNTer wonderland in Snowbird (2006)

The Keystone Symposium on ;Wnt and beta-catenin signaling in development and disease' was held recently in Snowbird, UT, USA. Organized by Mariann Bienz and Hans Clevers, this meeting covered a wide range of topics, including Wnt protein biogenesis, Wnt receptors and signaling pathways, beta-catenin/Tcf complexes and gene expression, Wnt signaling in development, cancer, stem cell biology and regeneration, and therapeutics that target the Wnt/beta-catenin pathway.
Hematopoietic cytokines inhibit apoptosis induced by transforming growth factor beta 1 and cancer chemotherapy compounds in myeloid leukemic cells (1992)

Transforming growth factor-beta 1 (TGF-beta 1) induces cell death in myeloid leukemia by apoptosis. In the M1 myeloid leukemia, this induction of apoptosis was inhibited by granulocyte colony-stimulating factor (G-CSF) or interleukin-6 (IL-6) and to a lesser extent by IL-1 alpha. IL-3 and stem cell factor/mast cell growth factor (SCF) showed only a marginal effect, and granulocyte-macrophage and macrophage CSFs (GM-CSF and M-CSF, respectively) were inactive. The induction of apoptosis by TGF-beta 1 in a different myeloid leukemia (7-M12) was inhibited by GM-CSF and IL-3 but not by the other cytokines. In the absence of TGF-beta 1, both M1 and 7-M12 leukemic cells were independent of hematopoietic cytokines for cell viability and growth. The cytotoxic compounds vincristine, vinblastine, adriamycin, cytosine arabinoside, cycloheximide, and sodium azide, some of which are used in cancer chemotherapy, induced cell death by apoptosis in both leukemias. As with TGF-beta 1, apoptosis induced by these cytotoxic compounds was inhibited by GM-CSF (7-M12 leukemia) and by G-CSF or IL-6 (M1 leukemia). Cyclosporine A decreased cell multiplication in M1 cells without inducing apoptosis, and G-CSF and IL-6 inhibited the cytostatic effect of cyclosporine A. It is suggested that the clinical use of cytokines to correct therapy-associated myelosuppression should be carefully timed to avoid protection of malignant cells from the cytotoxic action of the therapeutic compounds.
Haplotyping as Perfect Phylogeny: A Direct Approach (2003)

A full haplotype map of the human genome will prove extremely valuable as it will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A haplotype map project has been announced by NIH. The biological key to that project is the surprising fact that some human genomic DNA can be partitioned into long blocks where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected (Helmuth, 2001; Daly et al., 2001; Stephens et al., 2001; Friss et al., 2001). In this paper we explore the algorithmic implications of the no-recombination in long blocks observation, for the problem of inferring haplotypes in populations. This assumption, together with the standard population-genetic assumption of infinite sites, motivates a model of haplotype evolution where the haplotypes in a population are assumed to evolve along a coalescent, which as a rooted tree is a perfect phylogeny. We consider the following algorithmic problem, called the perfect phylogeny haplotyping problem (PPH), which was introduced by Gusfield (2002) - given n genotypes of length m each, does there exist a set of at most 2n haplotypes such that each genotype is generated by a pair of haplotypes from this set, and such that this set can be derived on a perfect phylogeny? The approach taken by Gusfield (2002) to solve this problem reduces it to established, deep results and algorithms from matroid and graph theory. Although that reduction is quite simple and the resulting algorithm nearly optimal in speed, taken as a whole that approach is quite involved, and in particular, challenging to program. Moreover, anyone wishing to fully establish, by reading existing literature, the correctness of the entire algorithm would need to read several deep and difficult papers in graph and matroid theory. However, as stated by Gusfield (2002), many simplifications are possible and the list of "future work" in Gusfield (2002) began with the task of developing a simpler, more direct, yet still efficient algorithm. This paper accomplishes that goal, for both the rooted and unrooted PPH problems. It establishes a simple, easy-to-program, O(nm(2))-time algorithm that determines whether there is a PPH solution for input genotypes and produces a linear-space data structure to represent all of the solutions. The approach allows complete, self-contained proofs. In addition to algorithmic simplicity, the approach here makes the representation of all solutions more intuitive than in Gusfield (2002), and solves another goal from that paper, namely, to prove a nontrivial upper bound on the number of PPH solutions, showing that that number is vastly smaller than the number of haplotype solutions (each solution being a set of n pairs of haplotypes that can generate the genotypes) when the perfect phylogeny requirement is not imposed.
Sequencing and Chromosomal Localization of the RA138 Gene Encoding a Rice Allergenic Protein (1998)

A cDNA clone (RA138) encoding a rice allergenic (RA) protein has been isolated during a large-scale random sequencing of a cDNA library prepared from developing seeds. The nucleotide sequence of the RA138 gene contained an open reading frame (ORF, 477 bp) encoding a 17 kDa protein. The amino acid sequence deduced from the ORF was composed of 159 amino acid residues and was highly homologous to those from RA genes previously isolated, such as RA5 (92% identity), RA14 (73%), and RA17 (68%). The protein contained 10 cysteine residues that were conserved in the alpha-amylase/trypsin inhibitor family including RA proteins. Excluding a putative signal peptide consisting of 26 amino acid residues, the mature protein would be 14.4 kDa in size and have a pI of 7.0. DNA gel blot analysis under high stringency conditions indicated that multiple copies of the RA138 gene were present in the rice genome. The chromosomal location of the RA138 gene has been identified on chromosome 7 in a segregation analysis using a population of 164 recombinant inbred lines derived from a cross between Milyang 23 and Gihobyeo. The locus that may contain multiple copies of the RA138 was located between RFLP markers RG477A and C492 with genetic distances of 10.7 cM and 6.7 cM, respectively.
Cooling, Heating, Generating Power, and Recovering Waste Heat with Thermoelectric Systems (2008)

Thermoelectric materials are solid-state energy converters whose combination of thermal, electrical, and semiconducting properties allows them to be used to convert waste heat into electricity or electrical power directly into cooling and heating. These materials can be competitive with fluid-based systems, such as two-phase air-conditioning compressors or heat pumps, or used in smaller-scale applications such as in automobile seats, night-vision systems, and electrical-enclosure cooling. More widespread use of thermoelectrics requires not only improving the intrinsic energy-conversion efficiency of the materials but also implementing recent advancements in system architecture. These principles are illustrated with several proven and potential applications of thermoelectrics.
Rituximab maintenance therapy: a step forward in follicular lymphoma (2007)

Whilst recent advances in the treatment of follicular lymphoma (FL) have improved the outlook for many patients, relapses still occur and the search continues for strategies to extend the duration of remission without significantly increasing toxicity. One such strategy is the use of rituximab maintenance therapy for patients responding to initial induction. There is now a large body of evidence demonstrating clear benefits of rituximab maintenance versus observation following induction with either rituximab plus chemotherapy (R chemo), chemotherapy alone, or rituximab monotherapy, in both first-line and relapsed/refractory settings. A very important finding is that rituximab maintenance can significantly improve overall survival in FL patients responding to induction with either R-chemo or chemotherapy alone. Also, compared with rituximab retreatment at disease progression, the maintenance approach produces much better complete remission rates and significantly longer continuous remissions and progression-free survival. Various maintenance schedules have been explored, all of which demonstrate clear benefits. However, the optimal dose, schedule, and duration of maintenance therapy still need to be established. Current data indicate that rituximab maintenance can be safely administered for up to 2 years, although assessment of long-term safety requires longer follow-up. From the patient's perspective, rituximab maintenance also prolongs the period in which patients are symptom-free and able to lead a relatively normal daily life. Also, rituximab maintenance may help patients feel they can control their disease, rather than passively waiting for relapse.
The mesenchymal stem cells in multiple sclerosis (MSCIMS) trial protocol and baseline cohort characteristics: an open-label pre-test: post-test study with blinded outcome assessments (2011)

ClinicalTrials.gov (NCT00395200).
The formalin test: A quantitative study of the analgesic effects of morphine, meperidine, and brain stem stimulation in rats and cats (1977)

A method for assessing pain and analgesia in rats and cats is described. The procedure involves subcutaneous injection of dilute formalin into the forepaw, after which the animal's responses are rated according to objective behavioral criteria. The formalin test is a statistically valid technique which has two advantages over other pain tests: (1) little or no restraint is necessary, permitting unhindered observation of the complete range of behavioral responses; and (2) the pain stimulus is continuous rather than transient, thus bearing greater resemblance to most clinical pain. The analgesic effects of morphine, meperidine, and stimulation of the periaqueductal grey matter are evaluated using this test.
On the Mode of Action of Lipid-lowering Agents (1971)

Rat liver acetyl coenzyme A carboxylase was purified about 200-fold and the inhibition of this enzyme by certain hypolipidemic drugs was studied.The inhibition was more pronounced if the drugs were added before rather than after the citrate activation of the enzyme.Kinetic analysis revealed noncompetitive inhibition of the drugs with respect to the substrates acetyl-CoA, ATP, and HCO,-, and competitive inhibition with respect to the activator, citrate.Sucrose density gradient centrifugations showed that the drugs reverse the aggregating effect of citrate to form the active polymeric forms of the enzyme from the inactive monomers.Arrhenius plots and heat-inactivation studies suggest gross conformational changes of the enzyme protein in the presence of the drugs.Relative aflinities of acetyl coenzyme A carboxylase for citrate and the drugs are expressed by the calculated dissociation constant for citrate and the inhibition constants of the drugs.Derangement of fatty acid synthesis in vivo is conceivable by competition of the drugs with the activation of acetyl-CoA carboxylase at low and physiologically possible concentrations of the drugs and citrate.
A 43-kDa Protein Related to c-Erb A α1 Is Located in the Mitochondrial Matrix of Rat Liver (1995)

In order to characterize Sterling's triiodothyronine (T3) mitochondrial receptor using photoaffinity labeling, we observed two specific T3-binding proteins in the inner membrane (28 kDa) and in the matrix (43 kDa) of rat liver mitochondria. Western blots and immunoprecipitation using antibodies raised against the T3-binding domain of the T3 nuclear receptor c-Erb A alpha 1 indicated that at least the 43-kDa protein was c-Erb A alpha 1-related. In addition, gel mobility shift assays demonstrated the occurrence of a c-Erb A alpha 1-related mitochondrial protein that specifically binds to a natural or a palindromic thyroid-responsive element. Moreover, this protein specifically binds to a direct repeat 2 sequence located in the D-loop of the mitochondrial genome. Furthermore, electron microscopy studies allowed the direct observation of a c-Erb A-related protein in mitochondria. Lastly, the relative amounts of the 43-kDa protein related to c-Erb A alpha 1 were in good correlation with the known mitochondrial mass in three typical tissues. Interestingly, expression of a truncated form of the c-Erb A alpha 1 nuclear receptor in CV1 cells was associated with a mitochondrial localization and a stimulation of mitochondrial activity. These results supply evidence of the localization of a member of the nuclear receptor superfamily in the mitochondrial matrix involved in the regulation of mitochondrial activity that could act as a mitochondrial T3-dependent transcription factor.
[Treatments of the martial deficiencies: preparations available in France]. (2006)

The financial advantage of the oral treatments of iron is minimised by their low bioavailibility (10 to 20%) and the fact that instructions for oral treatments are often badly followed by the patient (eg: tablets taken too far away from meals inducing frequent digestive problems). In France, since Maltofer (hydroxic ferric polymaltose) has been discontinued, Venofer (complex hydroxide ferric saccharose) is the only alternative intraveinous treatment with a cost which is now ten times higher than it was before. In foreign countries, other specialised products for intraveinous treatments (notably with a base of dextran iron with low molecular weight) have shown similar efficiency and are as safe to use as the complex hydroxide ferric saccharose. The hypothesis of a better control of the oxydative stress in giving a prophylactic treatment of 20 to 50 mg of hydroxide ferric saccharose at each treatment (because of the presence of free plasmatic iron) must be validated and the conditioning by unit may have to be adjusted.
A Multi Targeting Conditionally Replicating Adenovirus Displays Enhanced Oncolysis while Maintaining Expression of Immunotherapeutic Agents (2015)

Studies have demonstrated that oncolytic adenoviruses based on a 24 base pair deletion in the viral E1A gene (D24) may be promising therapeutics for treating a number of cancer types. In order to increase the therapeutic potential of these oncolytic viruses, a novel conditionally replicating adenovirus targeting multiple receptors upregulated on tumors was generated by incorporating an Ad5/3 fiber with a carboxyl terminus RGD ligand. The virus displayed full cytopathic effect in all tumor lines assayed at low titers with improved cytotoxicity over Ad5-RGD D24, Ad5/3 D24 and an HSV oncolytic virus. The virus was then engineered to deliver immunotherapeutic agents such as GM-CSF while maintaining enhanced heterogenic oncolysis.
Molecular characterization of PadA, a phenylacetaldehyde dehydrogenase from Escherichia coli (1997)

The padA gene encoding the phenylacetaldehyde dehydrogenase involved in the catabolism of 2-phenylethylamine in Escherichia coli has been cloned, sequenced, and located at 31.0 min on the chromosome. The deduced PadA polypeptide contains 499 amino acid residues with a predicted molecular mass of 53.7 kDa, and its primary structure reveals significant similarity with that of members of the aldehyde dehydrogenase superfamily. By engineering optimal transcription and translation elements, a high expression of the padA gene has been achieved. The active PadA enzyme is a homodimer that prefers NAD+ over NADP+ as coenzyme. The enzyme efficiently oxidizes only phenylacetaldehyde-like aromatic aldehydes, and has a weak esterase activity with p-nitrophenol. The padA gene constitutes a new catabolic tool for designing DNA cassettes to expand the abilities of microorganisms to degrade toxic aromatic compounds.
Prospective randomised comparison of photocoagulation and rubber band ligation in treatment of haemorrhoids. (1983)

Two hundred and sixty eight patients with haemorrhoids were allocated at random to treatment by either photocoagulation (group 1, n=141) or rubber band ligation (group 2, n=127) and followed up for one year. There was no significant difference in the symptomatic outcome of treatment between the two groups at one, four, or 12 months, irrespective of whether first or second degree haemorrhoids were treated. Side effects of treatment (bleeding or severe pain) were significantly more common after rubber band ligation (n=11) than after photocoagulation (n=2; p less than 0.01). Further outpatient treatment, however, was required significantly more often after photocoagulation (n=23) than rubber band ligation (n=6) (p greater than 0.02), and 19 patients (14 in group 1 and five in group 2; NS) subsequently had a haemorrhoidectomy. At one year 26 of 103 patients were dissatisfied after photocoagulation compared with 20 of 88 after rubber band ligation. Photocoagulation is a safe and comfortable treatment which gives long term results that are as good as those of rubber band ligation. Complications are more common after rubber band ligation, but further treatment is required more commonly after photocoagulation.
Adaptive Dynamic Simulations for Distribution Systems Using Multistate Load Models (2018)

The deployment of new sensors and devices on electric distribution systems is increasing the awareness of phenomena characterized by intermittent periods of highly dynamic activity that occur within extended periods of relatively static behavior. The deployment of new devices has enabled the observation of these phenomena; however, the currently available simulation methods cannot accurately reproduce the entire system behavior. Existing simulation methods, and their associated models, are able to capture portions of these phenomena, but there is not a method for efficiently modeling the entire event in a single simulation. This paper presents a novel method of adaptive simulation that enables automated transitions between quasi-static time-series and electromechancial simulation modes, as necessary to capture relevant system dynamics. The transitions between the simulation modes are triggered automatically during the running simulation based on the evolution of the system variables, utilizing multistate modes for generators and motors. This method allows for a single simulation that spans the entire time-frame, has the ability to capture dynamic events, and includes all relevant power system controls. The method of adaptive simulation can support the direct analysis of dynamic power system events, co-simulation of transmission and distribution systems, the development of control systems, and the development of reduced-order models.
Appendage Regeneration in Adult Vertebrates and Implications for Regenerative Medicine (2005)

The regeneration of complex structures in adult salamanders depends on mechanisms that offer pointers for regenerative medicine. These include the plasticity of differentiated cells and the retention in regenerative cells of local cues such as positional identity. Limb regeneration proceeds by the local formation of a blastema, a growth zone of mesenchymal stem cells on the stump. The blastema can regenerate autonomously as a self-organizing system over variable linear dimensions. Here we consider the prospects for limb regeneration in mammals from this viewpoint.
Determination of volatile organic compounds in exhaled breath of patients with lung cancer using solid phase microextraction and gas chromatography mass spectrometry (2009)

SPME is a relatively insensitive method and compounds not observed in exhaled breath may be present at a concentration lower than LOD. The main achievement of the present work is the validated identification of compounds observed in exhaled breath of lung cancer patients. This identification is indispensible for future work on the biochemical sources of these compounds and their metabolic pathways.
Functional Hybrid Devices of Proteins and Inorganic Nanoparticles (2003)

The combination of inorganic nanoparticles with biological functionality, such as the ATP-triggered release of CdS nanoparticles from inclusion complexes with chaperonins (see schematic illustration), opens up innovative approaches to novel hybrid devices applicable in biomedical sensing and the fabrication of advanced functional materials.
Optical saturation of intersubband absorption in GaAs-AlxGa1−xAs quantum wells (1988)

We have investigated intersubband absorptions between the conduction ground state and the first excited state of two AlxGa1−xAs/GaAs/AlxGa1−xAs multiple quantum well structures with x=0.3 and 85 Å well width, and with x=0.57 and 96 Å well width. Small-signal measurements show absorption peaks at 10.45 and 10.15 μm, respectively. Under an intense resonant excitation from a pulsed CO2 laser, saturation of the intersubband absorption occurred. The saturation intensity is estimated to be 340±120 kW/cm2 for the first sample and 375±120 kW/cm2 for the second. From these values, we have deduced subband decay times of the order of 10.6±3.5 ps for the first sample and 15.5±5 ps for the second.