gebhart/patrepeval huggingface dataset:
TGF-β signaling alterations and susceptibility to colorectal cancer (2007)

In 2006, more than 55,000 patients died of colorectal cancer in the US, accounting for approximately 10% of all cancer deaths. Despite significant progress in screening combined with the development of novel effective therapies, colorectal cancer ranks second to lung cancer as a cause of cancer death. Twin studies indicate that 35% of all colorectal cancers are inherited, but high-penetrance tumor susceptibility genes only account for approximately 3-6% of all cases. The remainder of the unexplained familial risk is presumably due to other high-penetrance genes, but polygenic mechanisms and low-penetrance tumor susceptibility genes are likely to account for a greater proportion of familial colorectal cancers. In this regard, there is growing evidence that a common hypomorphic variant of the type I TGF-beta receptor, TGFBR1*6A, may account for approximately 3% of all colorectal cancer cases, a fraction higher than that attributable to mismatch repair genes MLH1, MSH2, MSH6 and PMS2. Furthermore, TGFBR1*6A is emerging as a potent modifier of colorectal cancer risk among individuals with a strong family of colorectal cancer. The TGF-beta signaling pathway plays a central but paradoxical role in the predisposition and progression of colorectal cancer. TGF-beta is a potent inhibitor of normal colonic epithelial cells acting as a tumor suppressor. However, TGF-beta promotes the survival, invasion and metastasis of colorectal cancer cells, thereby acting as an oncogene. Understanding how selective alterations of the TGF-beta signaling pathway contribute to colorectal cancer development and progression will likely permit the identification of an additional fraction of inherited colorectal cancer cases and provide novel opportunities for therapeutic intervention.
Enhancing the reactivity and strength of cotton fibers (1992)

Abstract Both sodium hydroxide solution of mercerizing strength and anhydrous methylamine are suitable pretreatments for enhancing the reactivity of cotton cellulose. Favorable results are achieved by maintaining the fiber material in the never‐dried state after the swelling treatment. Extraction by organic solvents is to be preferred over water‐washing in order to remove the swelling agent. When cotton is swollen with either aqueous sodium hydroxide or anhydrous methylamine and then washed and dried, its crystallinity, as determined by X‐ray diffraction is not lowered as much as it is if it is acetylated to an acetyl content of about 9% before drying. The greatest modifications of the crystal structure of cotton were found on methylamine treatment followed by chloroform and pyridine washing and acetylation in the never‐dried state (MeCP product), as well as by alcoholic mercerization followed by ethanol and pyridine washing and acetylation in the never‐dried state (AMEP). As determined by moisture regains, no significant differences are apparent between the accessibility of samples of low acetyl content (ca. 9%) prepared by either the AMEP or by the MeCP treatment. The DTA curves of methylamine‐treated cotton with an acetyl content close to that of commercial diacetate and the commercial product are dissimilar. It can be concluded from the DTA curve of the deacetylated product prepared from this MeCP sample that it has a highly disordered structure. The tensile properties of the acetylated products of low acetyl content are considerably improved if acetylation is preceded by mercerization with subsequent solvent exchange, and less so if it is preceded by methylamine followed by solvent exchange. Incorporation of acetyl groups significantly enhances the breaking strength and extensibility of mercerized solvent‐washed materials.
Population structure and particle swarm performance (2003)

The effects of various population topologies on the particle swarm algorithm were systematically investigated. Random graphs were generated to specifications, and their performance on several criteria was compared. What makes a good population structure? We discovered that previous assumptions may not have been correct.
From causal to z-linearizable transactional memory (2007)

The current generation of time-based transactional memories (TMs) has the advantage of being simple and efficient, and providing strong linearizability semantics. Linearizability matches well the goal of TM to simplify the design and implementation of concurrent applications. However, long transactions can have a much lower likelihood of committing than smaller transactions because of the strict ordering constraints imposed by linearizability. We investigate the use of weaker semantics for TM and introduce a new consistency criterion that we call z-linearizability. By combining properties of linearizability and serializability, z-linearizability provides a good trade-off between strong semantics and good practical performance even for long transactions.
System-level synthesis of low-power hard real-time systems (1997)

We present a system-level approach for power optimization undera set of user specified costs and timing constraints of hard real-timedesigns. The approach optimizes all three degrees of freedom forpower minimization, namely switching activity, effective capacityand voltage supply.We first define two key associated optimization problems, processorallocation and task assignment, and establish their computationalcomplexity. Efficient algorithms are developed for bothsystem design problems. The statistical analysis of comprehensiveexperimental results and their comparison with the developed conservativeand optimistic sharp lower bounds, clearly indicates thequality of the proposed optimization techniques.
Ballast curves for HPS lamps operating on high frequency (2003)

The author presents a simple method for designing ballast curves for high pressure sodium (HPS) lamps operating at a frequency >20 kHz. Since the HPS lamp is a complicated plasma device, an approximation can be useful. An approximate model based on a resistive substitution of HPS lamps operating at a high frequency is introduced and used to transform the problem of ballast design to a treatable electronic problem.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Heterocyclic Aromatics in Petroleum Coke, Snow, Lake Sediments, and Air Samples from the Athabasca Oil Sands Region (2017)

The aromatic fractions of snow, lake sediment, and air samples collected during 2011-2014 in the Athabasca oil sands region were analyzed using two-dimensional gas chromatography following a nontargeted approach. Commonly monitored aromatics (parent and alkylated-polycyclic aromatic hydrocarbons and dibenzothiophenes) were excluded from the analysis, focusing mainly on other heterocyclic aromatics. The unknowns detected were classified into isomeric groups and tentatively identified using mass spectral libraries. Relative concentrations of heterocyclic aromatics were estimated and were found to decrease with distance from a reference site near the center of the developments and with increasing depth of sediments. The same heterocyclic aromatics identified in snow, lake sediments, and air were observed in extracts of delayed petroleum coke, with similar distributions. This suggests that petroleum coke particles are a potential source of heterocyclic aromatics to the local environment, but other oil sands sources must also be considered. Although the signals of these heterocyclic aromatics diminished with distance, some were detected at large distances (>100 km) in snow and surface lake sediments, suggesting that the impact of industry can extend >50 km. The list of heterocyclic aromatics and the mass spectral library generated in this study can be used for future source apportionment studies.
Coccidial Immunity Studies in Chickens I (1951)

JOHNSON (1927) first demonstrated that immunity or resistance to coccidial infection in chickens was developed following coccidial infection. Tyzzer (1929, 1932) has shown there are several different species of coccidia that infect chickens and that the immunity produced is species specific and no cross-immunity is produced between species. Very little has been done to determine the possibility of a program of artificial immunization since this basic information was disclosed. This report deals with a trial on chicks to establish guides for dosages, age to inoculate, management, and the role coccidiostatic drugs may play in a program of artificial immunization. It also provides data on the effect of immunization on development of growing birds and their ability to withstand coccidial challenge. PROCEDURE The trial consisted of four pens of straight run New Hampshire chicks with 195 chicks to each pen. They were brooded under electric brooders with shavings as litter. For . . .
Synthesis of Molecularly Imprinted Polymer Nanoparticles for α-Casein Detection Using Surface Plasmon Resonance as a Milk Allergen Sensor (2018)

Food recalls due to undeclared allergens or contamination are costly to the food manufacturing industry worldwide. As the industry strives for better manufacturing efficiencies over a diverse range of food products, there is a need for the development of new analytical techniques to improve monitoring of the presence of unintended food allergens during the food manufacturing process. In particular, the monitoring of wash samples from cleaning in place systems (CIP), used in the cleaning of food processing equipment, would allow for the effective removal of allergen containing ingredients in between food batches. Casein proteins constitute the biggest group of proteins in milk and hence are the most common milk protein allergen in food ingredients. As such, these proteins could present an ideal analyte for cleaning validation. In this work, molecularly imprinted polymer nanoparticles (nanoMIPs) with high affinity toward bovine α-casein were synthesized using a solid-phase imprinting method. The nanoMIPs were then characterized and incorporated into label free surface plasmon resonance (SPR) based sensor. The nanoMIPs demonstrated good binding affinity and selectivity toward α-casein (K<sub>D</sub> ∼ 10 × 10<sup>-9</sup> M). This simple affinity sensor demonstrated the quantitative detection of α-casein achieving a detection limit of 127 ± 97.6 ng mL<sup>-1</sup> (0.127 ppm) which is far superior to existing commercially available ELISA kits. Recoveries from spiked CIP wastewater samples were within the acceptable range (87-120%). The reported sensor could allow food manufacturers to adequately monitor and manage food allergen risk in food processing environments while ensuring that the food produced is safe for the consumer.
Interferon-gamma deficiency prevents coronary arteriosclerosis but not myocardial rejection in transplanted mouse hearts. (1997)

We have hypothesized that T cell cytokines participate in the pathogenesis of graft arterial disease (GAD). This study tested the consequences of IFN-gamma deficiency on arterial and parenchymal pathology in murine cardiac allografts. Hearts from C-H-2(bm12)KhEg (bm12, H-2(bm12)) were transplanted into C57/B6 (B6, H-2(b)), wild-type, or B6 IFN-gamma-deficient (GKO) recipients after immunosuppression by treatment with anti-CD4 and anti-CD8 mAbs. In wild-type recipients, myocardial rejection peaked at 4 wk, (grade 2. 1+/-0.3 out of 4, mean+/-SEM, n = 9), and by 8-12 wk evolved coronary arteriopathy. At 12 wk, the GAD score was 1.4+/-0.3, and the parenchymal rejection grade was 1.2+/-0.3 (n = 8). In GKO recipients of bm12 allografts, myocardial rejection persisted at 12 wk (grade 2.5+/-0.3, n = 6), but no GAD developed (score: 0.0+/-0.0, n = 6, P < 0.01 vs. wild-type). Mice treated with anti-IFN-gamma mAbs showed similar results. Isografts generally showed no arterial changes. In wild-type recipients, arterial and parenchymal cells showed increased MHC class II molecules, intercellular adhesion molecule-1, and vascular cell adhesion molecule-1 compared to normal or isografted hearts. The allografts in GKO recipients showed attenuated expression of these molecules (n = 6). Thus, development of GAD, but not parenchymal rejection, requires IFN-gamma. Reduced expression of MHC antigens and leukocyte adhesion molecules may contribute to the lack of coronary arteriopathy in hearts allografted into GKO mice.
TechMatters: Get Animated: Online Tools for Creating Comics in the Classroom (2012)

Of course, these tools can also be used by students in the classroom and for course assignments. For example, rather than an oral report, allow students engaged with group work to ―present‖ their ideas back to the class in the form of a comic. In the case of a for-credit library course, you could have students create a comic to communicate their expectations or anxieties about the class as an introductory assignment or to summarize their learning experience at the end.
Cloning and Characterization of the Two Enzymes Responsible for Trypanothione Biosynthesis in Crithidia fasciculata (1998)

Protozoa of the order Kinetoplastida differ from other organisms in their ability to conjugate glutathione (gamma-Glu-Cys-Gly) and spermidine to form trypanothione (N1,N8-bis(glutathionyl)spermidine), which is involved in maintaining intracellular thiol redox and in defense against oxidants. In this study, the genes from Crithidia fasciculata, Cf-GSS and Cf-TRS, which encode, respectively, glutathionylspermidine synthetase (EC 6.3.1.8) and trypanothione synthetase (EC 6.3.1.9) have been cloned and expressed. The deduced amino acid sequence of both Cf-GSS and Cf-TRS share 50% sequence similarity with the Escherichia coli glutathionylspermidine synthetase/amidase. Both genes are present as single copies in the C. fasciculata genome. When expressed in E. coli and Saccharomyces cerevisiae, neither protein was present in an active soluble form. However, thiol analysis of S. cerevisiae demonstrated that cells transformed with the Cf-GSS gene contained substantial amounts of glutathionylspermidine, whereas cells expressing both the Cf-GSS and Cf-TRS genes contained glutathionylspermidine and trypanothione, confirming that these genes encode the functional glutathionylspermidine and trypanothione synthetases from C. fasciculata. The translation products of Cf-GSS and Cf-TRS show significant homology to the amidase domain present in E. coli glutathionylspermidine synthetase, which can catalyze both synthesis and degradation of glutathionylspermidine. Glutathionylspermidine synthetase isolated from C. fasciculata was found to possess a similar amidase activity.
The 3D Tractus: A Three-Dimensional Drawing Board (2006)

We present the 3D Tractus: a simple and inexpensive system for interaction and exploration of three-dimensional (3D) data. The device is based on a traditional drawing board-like mechanical structure that can be easily moved up and down while its surface height is being tracked using a simple sensor. Users interact with a tablet or tablet PC that rests on the surface while simultaneously changing its height. The result is direct mapping of virtual and physical spaces allowing intuitive 3D interaction and data exploration. The 3D Tractus allows us to investigate novel 3D interaction techniques based on sketching and drawing as well as intuitive visual indicators and GUI layouts. The 3D Tractus' simple design concept can be easily adapted to other tabletop systems and the simple nature of the physical interaction allows the design of various exciting applications. We detail here the design and development of the 3D Tractus hardware and software as well as preliminary evaluation of a 3D drawing and sketching application realized using the new tabletop interface.
Preliminary Design of a Loop Reactor for Bulk Propylene Polymerization (1990)

Abstract Some typical problems in the early design stages of a tubular loop reactor for bulk propylene polymerization are analyzed. Characteristic variables are identified, and a shortcut method for the preliminary estimation of the reactor dimensions is developed. the influences of process variables such as catalytic activity, suspended solid fraction, and average particle size are studied. In particular, a relationship between the average particle size in the reactor and the particle size at both the inlet and the outlet is obtained. the behavior of the reactor under different operating conditions is studied, and critical parameters are identified. Most relevant results are related to the importance of the particle size inside the reactor. the two goals of maximum yield and maximum productivity for a given loop reactor configuration cannot be achieved simultaneously: While catalyst yield increases with the third power of the average particle size in the reactor, the smaller the average particle size in the reactor, the greater the productivity. the steps to be followed for a preliminary design of a propylene polymerization, loop reactor are discussed. A priority list for the sequence of parameters to be adopted is proposed, according to the relative importance of the variables involved.
Green fluorescence induced by EF‐hand assembly in a split GFP system (2009)

The affinity between the 1-157 and 158-238 fragments of green fluorescent protein (GFP) is too low for spontaneous in vivo reassembly of the protein upon co-expression of the two fragments. This prevents chromophore maturation and the cells lack GFP fluorescence. We have utilized the very high affinity between the two EF-hands of calbindin D(9k) to facilitate GFP assembly from its fragments and to introduce a calcium dependent molecular switch. In GFPN-EF1, residues 1-157 of GFP are fused to residues 1-43 of calbindin, and in EF2-GFPC, residues 44-75 of calbindin are fused to residues 158-238 of GFP. When co-expressed, GFPN-EF1 and EF2-GFPC associate spontaneously and rapidly resulting in a folded reconstituted protein with bright GFP fluorescence. The high affinity of GFPN-EF1 for EF2-GFPC leads to brighter fluorescence of the cells compared to cells with a control constructs carrying leucine zippers (Wilson et al., Nature Methods 2004;3:255). The complex of GFPN-EF1 and EF2-GFPC was purified from cells using metal-ion chelate chromatography and the temperature dependence of GFP fluorescence was found to be calcium dependent. The GFPN-EF1 and EF2-GFPC fragments were separated by ion exchange chromatography. The assembly of the fragments was found to be reversible and the complex was regained upon mixing, as evidenced by surface plasmon resonance (SPR) data. The affinity between GFPN-EF1 and EF2-GFPC as well as rates of association and dissociation were found to be Ca(2+)-dependent.
Searching for inaccuracy in clinical laboratory testing using Medicare data. Evidence for prothrombin time. (1993)

Examining patient outcomes subsequent to clinical laboratory testing may be a useful tool for clinical laboratory quality assurance.
Determining Fault Tolerance of XOR-Based Erasure Codes Efficiently (2007)

We propose a new fault tolerance metric for XOR-based erasure codes: the minimal erasures list (MEL). A minimal erasure is a set of erasures that leads to irrecoverable data loss and in which every erasure is necessary and sufficient for this to be so. The MEL is the enumeration of all minimal erasures. An XOR-based erasure code has an irregular structure that may permit it to tolerate faults at and beyond its Hamming distance. The MEL completely describes the fault tolerance of an XOR-based erasure code at and beyond its Hamming distance; it is therefore a useful metric for comparing the fault tolerance of such codes. We also propose an algorithm that efficiently determines the MEL of an erasure code. This algorithm uses the structure of the erasure code to efficiently determine the MEL. We show that, in practice, the number of minimal erasures for a given code is much less than the total number of sets of erasures that lead to data loss: in our empirical results for one corpus of codes, there were over 80 times fewer minimal erasures. We use the proposed algorithm to identify the most fault tolerant XOR-based erasure code for all possible systematic erasure codes with up to seven data symbols and up to seven parity symbols.
The efficacy of DNA vaccination is enhanced in mice by targeting the encoded protein to dendritic cells (2008)

DNA vaccines promote an immune response by providing antigen-encoding DNA to the recipient, but the efficacy of such vaccines needs improving. Many approaches have considerable potential but currently induce relatively weak immune responses despite multiple high doses of DNA vaccine. Here, we asked whether targeting vaccine antigens to DCs would increase the immunity and protection that result from DNA vaccines. To determine this, we generated a DNA vaccine encoding a fusion protein comprised of the vaccine antigen and a single-chain Fv antibody (scFv) specific for the DC-restricted antigen-uptake receptor DEC205. Following vaccination of mice, the vaccine antigen was expressed selectively by DCs, which were required for the increased efficacy of MHC class I and MHC class II antigen presentation relative to a control scFv DNA vaccine. In addition, a DNA vaccine encoding an HIV gag p41-scFv DEC205 fusion protein induced 10-fold higher antibody levels and increased numbers of IFN-gamma-producing CD4+ and CD8+ T cells. After a single i.m. injection of the DNA vaccine encoding an HIV gag p41-scFv DEC205 fusion protein, mice were protected from an airway challenge with a recombinant vaccinia virus expressing the HIV gag p41, even with 1% of the dose of nontargeted DNA vaccine. The efficacy of DNA vaccines therefore may be enhanced by inclusion of sequences such as single-chain antibodies to target the antigen to DCs.
On the definition of the cutoff frequency f<sub>T</sub> (1969)

The commonly used definition of cutoff frequency f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> of bipola transistors is predicated on the existence of a frequency domain in which the magnitude of the current gain β varies inversely with frequency. In the absence of such a domain, the definition is vague. The definition 1/f <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</inf> = d/df[lm (1/β)] for f →0 is proposed.