gebhart/patrepeval huggingface dataset:
Production of Clean Pyrolytic Sugars for Fermentation (2014)

This study explores the separate recovery of sugars and phenolic oligomers produced during fast pyrolysis with the effective removal of contaminants from the separated pyrolytic sugars to produce a substrate suitable for fermentation without hydrolysis. The first two stages from a unique recovery system capture "heavy ends", mostly water-soluble sugars and water-insoluble phenolic oligomers. The differences in water solubility can be exploited to recover a sugar-rich aqueous phase and a phenolic-rich raffinate. Over 93 wt % of the sugars is removed in two water washes. These sugars contain contaminants such as low-molecular-weight acids, furans, and phenols that could inhibit successful fermentation. Detoxification methods were used to remove these contaminants from pyrolytic sugars. The optimal candidate is NaOH overliming, which results in maximum growth measurements with the use of ethanol-producing Escherichia coli.
CRM197: reduction of atherosclerotic stenoses in carotids of three elderly patients (2007)

Background: Many years ago, diphtheria toxin was shown to exert an antitumor effect in mice and humans. However, these old studies suggested that the molecule, expected to affect cancer with its toxicity only, could also act through an immunological mechanism. In recent years, this suggestion has been reappraised and crossreacting material (CRM)197 administered to advanced cancer patients has shown encouraging results. CRM197 is a nontoxic mutant of diphtheria toxin that cross-reacts immunologically with the native counterpart. Unexpectedly, a cancer patient treated with this molecule obtained, along with a small shrinkage of his lung tumor, a 27% reduction of an atherosclerotic stenosis of his internal right carotid. We were amazed at this result since we knew that the only drugs useful against atherosclerosis were statins. Objective: This study aimed at investigating whether CRM197 may also affect atherosclerotic stenosis. Patients & methods: Three elderly patients with moderate-to-severe carotid stenos...
New Fluorescent Model Compounds for the Study of Photoinduced Electron Transfer: The Influence of a Molecular Electric Field in the Excited State (1995)

The location of the âspacerâreceptorâ unit in a 4-aminonaphthalimide fluorophore, which undergoes internal charge transfer in the excited state, is crucial for the suitability of the compound as a pH sensor. In studies of the pH dependence of the fluorescence of the regioisomers 1 and 2, only 1 displayed desirable properties.
MicroRNA-98 and let-7 Confer Cholangiocyte Expression of Cytokine-Inducible Src Homology 2-Containing Protein in Response to Microbial Challenge (2009)

Posttranscriptional gene regulation by microRNAs (miRNAs) has been implicated in the fine-tuning of TLR-mediated inflammatory response. The cytokine-inducible Src homology 2-containing protein (CIS), one member of the suppressors of cytokine signaling family of proteins, is an important negative regulator for inflammatory cytokine signaling. Using in vitro models using normal human biliary epithelial cells (cholangiocytes), we demonstrated that LPS stimulation or infection with the parasitic protozoan Cryptosporidium parvum induced expression of CIS protein without a change in CIS mRNA levels by activating the TLR signaling pathway. Of those miRNAs expressed in cholangiocytes, we found that targeting of the 3'-untranslated region of CIS by microRNA-98 (miR-98) or let-7 resulted in translational repression, but not CIS mRNA degradation. LPS stimulation or C. parvum infection decreased cholangiocyte expression of miR-98 and let-7. Down-regulation of miR-98 and let-7 relieved miRNA-mediated translational suppression of CIS and contributed to LPS- and C. parvum-stimulated CIS protein expression. Moreover, gain-of-function (by overexpression of CIS) and loss-of-function (by siRNA interference) studies revealed that CIS could enhance IkappaBalpha degradation and regulate NF-kappaB activation in cholangiocytes in response to LPS stimulation or C. parvum infection. Our data suggest that miR-98 and let-7 confer cholangiocyte expression of CIS in response to microbial challenge, a process that may be relevant to the regulation of TLR-mediated epithelial innate immune response.
Direct Liquid Chromatography/Mass Spectrometry Analysis for Complete Characterization of Recombinant Adeno-Associated Virus Capsid Proteins (2017)

The requirement for robust analytical methods to characterize adeno-associated virus (AAV) vectors is immediate, as the field advances more AAV gene therapies into the clinic and onto commercialization. AAV capsid proteins (VPs) are critical for viral infectivity and vector potency. Thus, complete characterization of the constituent viral capsid proteins of AAV vectors, including their sequences and post-translational modifications (PTMs), is highly recommended to ensure AAV product quality and consistency. Typically, SDS-PAGE analysis followed by in-gel enzymatic digestion and liquid chromatography/tandem mass spectrometry (LC/MS/MS) is used for the characterization of viral capsid proteins. However, due to the limited recovery of digested peptides from the gel, determination of N-terminal sequences of VPs has not been reported to date. In this study, a direct liquid chromatography/mass spectrometry (LC/MS) intact protein analysis was developed to characterize viral capsid proteins in a variety of AAV serotypes. Both N- and C-terminal sequences of six AAV serotypes have been identified based on accurate mass measurement. This method can be used to confirm the identity of AAV serotype and monitor potential capsid protein heterogeneity. Complete sequence confirmation of AAV2 VPs was achieved through LC/MS/MS analysis of peptides generated using multiple enzymatic digestions. LC/MS/MS analysis confirmed the sequences for both N- and C-termini of capsid VPs and revealed acetylation on the N-termini of VP1 and VP3, consistent with LC/MS intact protein analysis.
Combining Ability in Loci for High Oleic and Low Linolenic Acids in Soybean (2001)

Two soybean [ Glycine max (L.) Merr.] germplasm lines have been identified for unique fatty acid content. The contents of oleic and linolenic acids in HOLL are controlled by ol and fan loci, respectively, and the very low content of linolenic acid in LOLL is controlled by fan and fanx a loci combined. The fan locus is identical for both HOLL and LOLL. Therefore, if ol and fanx a loci are independent, soybean germplasm could be developed with more unique and useful combinations of these fatty acids. The objectives of this study were to combine the loci of high oleic and low linolenic acids, and determine the effects of altered contents of oleic and linolenic acids on other fatty acids. HOLL was reciprocally crossed to LOLL. The data from F 2 seed indicated that the ol locus controlling high oleic acid was independently inherited from the fanx a locus controlling low linolenic acid. Thus, the germplasm (DHL) with the high oleic acid trait from HOLL, and very low linolenic acid trait from LOLL, was easily developed. The increases in oleic acid due to ol was associated completely with changes in linoleic acids, indicating a pleiotropic effect of the ol locus. Decreases in linolenic acid due to fan and fanx a were associated primarily with increases in linoleic acid. The development of DHL with increased contents of oleic acid and decreased contents of polyunsaturated fatty acids could open new markets for soybean oil.
Teacher Guided Architecture Search (2019)

Much of the recent improvement in neural networks for computer vision has resulted from discovery of new networks architectures. Most prior work has used the performance of candidate models following limited training to automatically guide the search in a feasible way. Could further gains in computational efficiency be achieved by guiding the search via measurements of a high performing network with unknown detailed architecture (e.g. the primate visual system)? As one step toward this goal, we use representational similarity analysis to evaluate the similarity of internal activations of candidate networks with those of a (fixed, high performing) teacher network. We show that adopting this evaluation metric could produce up to an order of magnitude in search efficiency over performance-guided methods. Our approach finds a convolutional cell structure with similar performance as was previously found using other methods but at a total computational cost that is two orders of magnitude lower than Neural Architecture Search (NAS) and more than four times lower than progressive neural architecture search (PNAS). We further show that measurements from only ~300 neurons from primate visual system provides enough signal to find a network with an Imagenet top-1 error that is significantly lower than that achieved by performance-guided architecture search alone. These results suggest that representational matching can be used to accelerate network architecture search in cases where one has access to some or all of the internal representations of a teacher network of interest, such as the brain's sensory processing networks.
Specific binding of leukemia oncogene fusion protein peptides to HLA class I molecules (1995)

Many human leukemias are characterized by chromosomal translocations yielding hybrid RNAs capable of encoding fusion chimeric proteins. The unique amino acid sequences found in these oncogenic fusion proteins represent true tumor-specific antigens that are potentially immunogenic. Although these leukemia-specific fusion proteins have an intracellular location, they might be recognized immunologically by T lymphocytes if peptides derived from the unique sequences are capable of presentation by the major histocompatibility complex (MHC) molecules on leukemic cells. The ability of a series of synthetic peptides corresponding to the junctional sequences of chronic myelogenous leukemia (CML)-derived bcr-abl and acute promyelocytic leukemia (APL)-derived PML-RAR alpha fusion proteins to bind to purified class I molecules was studied. A series of 152 peptides 8, 9, 10, and 11 amino acids in length, spanning the b3a2 and b2a2 breakpoints for CML and PML-RAR alpha A and B breakpoints for APL were analyzed for HLA A1, A2.1, A3.2, A11, A24, B7, B8, and B27 binding motifs. Twenty-one CML peptides and 4 APL peptides were predicted to be potential HLA class I binders. The peptides were tested for binding to appropriate purified HLA molecules in a competition radioimmunoassay. Four peptides derived from b3a2 CML breakpoint bound with high (< 50 nmol/L) or intermediate (< or = 500 nmol/L) affinity to HLA A3, A11, and B8. None of the CML b2a2 or PML-RAR alpha A or B junctional peptides showed affinity of this magnitude for the HLA class I molecules tested. This is the first evidence that tumor-specific breakpoint peptides can bind human MHC class I molecules and provides a rationale for developing a therapeutic vaccine strategy.
Novel therapeutic Strategies for Targeting Liver Cancer Stem Cells (2011)

The cancer stem cell (CSC) hypothesis was first proposed over 40 years ago. Advances in CSC isolation were first achieved in hematological malignancies, with the first CSC demonstrated in acute myeloid leukemia. However, using similar strategies and technologies, and taking advantage of available surface markers, CSCs have been more recently demonstrated in a growing range of epithelial and other solid organ malignancies, suggesting that the majority of malignancies are dependent on such a compartment.Primary liver cancer consists predominantly of hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (ICC). It is believed that hepatic progenitor cells (HPCs) could be the origin of some HCCs and ICCs. Furthermore, stem cell activators such as Wnt/β-catenin, TGF-β, Notch and Hedgehog signaling pathways also expedite tumorigenesis, and these pathways could serve as molecular targets to assist in designing cancer prevention strategies. Recent studies indicate that additional factors such as EpCAM, Lin28 or miR-181 may also contribute to HCC progression by targeting HCC CSCs. Various therapeutic drugs that directly modulate CSCs have been examined in vivo and in vitro. However, CSCs clearly have a complex pathogenesis, with a considerable crosstalk and redundancy in signaling pathways, and hence targeting single molecules or pathways may have a limited benefit for treatment. Many of the key signaling molecules are shared by both CSCs and normal stem cells, which add further challenges for designing molecularly targeted strategies specific to CSCs but sparing normal stem cells to avoid side effects. In addition to the direct control of CSCs, many other factors that are needed for the maintenance of CSCs, such as angiogenesis, vasculogenesis, invasion and migration, hypoxia, immune evasion, multiple drug resistance, and radioresistance, should be taken into consideration when designing therapeutic strategies for HCC. Here we provide a brief review of molecular signaling in liver CSCs and present insights into new therapeutic strategies for targeting liver CSCs.
Synthesis of Proteins by Native Chemical Ligation Using Fmoc-Based Chemistry (2005)

C-terminal peptide alpha-thioesters are valuable intermediates in the synthesis/semisynthesis of proteins by native chemical ligation. They are prepared either by solid-phase peptide synthesis (SPPS) or biosynthetically by protein splicing techniques. The present paper reviews the different methods available for the chemical synthesis of peptide alpha-thioesters using Fmoc-based SPPS.
Detection of natural peptide antibiotics in human nasolacrimal ducts. (2001)

The data suggest that the human efferent tear ducts produce a broad spectrum of antimicrobial peptides. Under inflammatory conditions, changes in the expression pattern occurred, revealing induction of the human inducible defensin HBD-2 and in some cases downregulation of HBD-1 and CAP37. Antimicrobial peptides have a therapeutic potential in dacryocystitis, in that they have a broad spectrum of antimicrobial activity and accelerate epithelial healing. However, caution is appropriate, because defensins also promote fibrin formation and cell proliferation, which are key elements in scarring processes, such as dacryostenosis.
Phosphor Free High-Luminous-Efficiency White Light-Emitting Diodes Composed of InGaN Multi-Quantum Well (2002)

We fabricated two types of high-efficiency white light-emitting diodes (LEDs) composed of an InGaN multi-quantum well (MQW), which emit light of two or three different colors without phosphors. The Type-1 white LED emits light of two colors (blue and yellow) from the MQW active layer, while the Type-2 LED emits light of three colors (blue, green and red). When the Type-1 white LED was operated at a forward current of 20 mA at room temperature, the color temperature (Tcp), average color rendering (Ra) and luminous efficiency were 7600 K, 42.7 and 11.04 lm/W, respectively. When the Type-2 white LED was operated at a forward current of 20 mA at room temperature, Tcp, Ra and luminous efficiency were 5060 K, 80.2 and 7.94 lm/W, respectively.
The coordination of signaling during Fc receptor-mediated phagocytosis (2004)

Phagocytosis by macrophages can be initiated by Fcgamma receptors (FcR) in membranes that bind to Fc regions of immunoglobulin G (IgG). Activated FcR transduce signals to cytoplasm, which regulate the internalization of IgG-coated particles into plasma membrane-derived vacuoles, phagosomes. Particles internalized by phagocytosis are much larger than FcR, which prompts questions of if and how the receptors are coordinated with each other. FcR-mediated signal transduction entails recruitment of proteins from cytoplasm to the receptor, largely via protein phosphorylation. These FcR signaling complexes then activate proteins that regulate actin, myosin, membrane fusion, and the production of reactive oxygen intermediates. Recent fluorescence microscopic studies of phagocytosis in macrophages indicate that signaling by FcR occurs as a sequence of distinct stages, evident in the spatial and temporal patterns of phosphoinositides, protein kinase C, and Rho-family GTPase activation on forming phagosomes. The coordination of these stages may be regulated by lipids or lipid-anchored proteins, which diffuse away from FcR complexes. Lateral diffusion of FcR-derived signals could integrate FcR-dependent responses over large areas of membrane in the forming phagosome.
Amino Acid Sequence and Disulphide-bridge Pattern of three gamma-Thionins from Sorghum bicolor (1995)

The complete primary structure of a new alpha-amylase inhibitor from Sorghum bicolor belonging to the gamma-thionin family has been determined and the amino acid sequences of two components of the family already elucidated have been corrected by combining the classical Edman degradation with advanced mass spectrometric procedures. The same integrated approach allowed us to define the pattern of the disulphide bridges in the three isoinhibitors. The arrangement of the cysteine pairing was determined as Cys3-Cys47, Cys14-Cys34, Cys20-Cys41 and Cys24-Cys43. The amino acid sequences of the alpha-amylase inhibitors share a high degree of similarity with the related plant gamma-thionins. All these proteins consist of 47 residues, contain eight cysteine residues forming four disulphide bridges, and show the presence of two clusters of basic amino acids located at both ends of the polypeptide chain. The pattern of S-S bridges determined for the isoinhibitors is identical to that inferred by NMR analysis in two related gamma-thionins, thus suggesting a highly conserved organization of the disulphide pairing. These results indicate that the structural similarities among the different gamma-thionins extend far beyond the primary structure and possibly concern the secondary structure and the general folding of the entire gamma-thionin family.
Quetiapine adjunct to selective serotonin reuptake inhibitors or venlafaxine in patients with major depression, comorbid anxiety, and residual depressive symptoms: a randomized, placebo-controlled pilot study (2006)

This double-blind, placebo-controlled study examined the efficacy and tolerability of quetiapine in combination with selective serotonin reuptake inhibitors (SSRIs)/venlafaxine in 58 patients with major depressive disorder, comorbid anxiety symptoms (HAM-A-14 score > or =14), and residual depressive symptoms (HAM-D-17 score > or =18, CGI-S score > or =4). Patients had received an SSRI/venlafaxine (at a predefined therapeutic dose) for > or =6 weeks. Overall, 62% (18/29) of quetiapine- and 55% (16/29) of placebo-treated patients completed the study. The mean change in HAM-D and HAM-A total scores from baseline to Week 8 (primary endpoint) was significantly greater with quetiapine (mean dose 182 mg/day) than placebo: -11.2 vs. -5.5 (P=.008) and -12.5 vs. -5.9 (P=.002), respectively. The onset of quetiapine efficacy (HAM-D/HAM-A/CGI-I) was rapid (by Week 1) and continued through to Week 8. Significant differences (P<.05) from baseline to Week 8 were observed between groups in 7/17 HAM-D (including feelings of guilt, suicide) and 6/14 HAM-A items (including tension, cardiovascular symptoms). Response (> or =50% decrease in total score) was higher for quetiapine than placebo: HAM-D, 48% vs. 28% (not significant, NS); HAM-A, 62% vs. 28% (P=.02). Remission (total score < or =7) was higher for quetiapine than placebo: HAM-D, 31% vs. 17% (NS); HAM-A, 41% vs. 17% (NS). CGI-S, CGI-I, and the Global Assessment Scale showed that quetiapine was significantly more effective than placebo. For quetiapine, adverse events (AEs) were similar to those previously observed; sedation/somnolence/lethargy was the most commonly reported. Here quetiapine was shown to be effective as augmentation of SSRI/venlafaxine therapy in patients with major depression, comorbid anxiety, and residual depressive symptoms, with no unexpected tolerability issues. Further studies are warranted.
Approaching hospital administration about adopting cooling technologies (2009)

The purpose of this article is to provide intensivists with information and examples regarding cooling technology selection, cost assessment, adaptation, barriers, and presentation to hospital administrators. A review of medical and business literature was conducted using the following search terms: technology assessment, organizational innovation, intensive care, critical care, hospital administration, and presentation to administrators. General recommendations for intensivists are made for assessing cooling technology with descriptions of common new technology implementation stages. A study of 16 hospitals implementing a new cardiac surgery technology is described. A description of successful implementation of an induced hypothermia protocol by one of the authors is presented. Although knowledgeable about the applications of new technologies, including cooling technology, intensivists have little guidance or training on tactics to obtain a hospital administration's funding and support. Intensive care unit budgets are usually controlled by nonintensivists whose interests are neutral, at best, to the needs of intensivists. To rise to the top of the large pile of requisition requests, an intensivist's proposal must be well conceived and aligned with hospital administration's strategic goals. Intensivists must understand the hospital acquisition process and administrative structure and participate on high-level hospital committees. Using design thinking and strong leadership skills, the intensivist can marshal support from staff and administrators to successfully implement cooling technology.
Interaction of Vibrio spp. with the Inner Surface of the Digestive Tract of Penaeus monodon (2015)

Several species of Vibrio are the causative agent of gastroenteritis in humans. In aquaculture, Vibrio harveyi (Vh) and V. parahaemolyticus (Vp) have long been considered as shrimp pathogens in freshwater, brackish and marine environments. Here we show by using scanning electron microscopy (SEM) that Penaeus monodon orally inoculated with each of these two pathogens via an Artemia diet had numerous bacteria attached randomly across the stomach surface, in single and in large biofilm-like clusters 6 h post-infection. A subsequent marked proliferation in the number of V. harveyi within the biofilm-like formations resulted in the development of infections in the stomach, the upper and middle midgut, but neither in the posterior midgut nor the hindgut. SEM also revealed the induced production of peritrichous pili-like structures by the Vp attaching to the stomach lining, whilst only a single polar fibre was seen forming an apparent physical bridge between Vh and the host's epithelium. In contrast to these observations, no such adherences or linkages were seen when trials were conducted with non-pathogenic Vibrio spp. or with Micrococcus luteus, with no obvious resultant changes to the host's gut surface. In naive shrimp, the hindgut was found to be a favorable site for bacteria notably curved, short-rod shaped bacteria which probably belong to Vibrio spp. Data from the current study suggests that pathogens of P. monodon must be able to colonize the digestive tract, particularly the stomach, where chitin is present, and then they use an array of virulent factors and enzymes to infect their host resulting in disease. Oral infection is a better way of mimicking natural routes of infection; investigating the host-bacteria interactions occurring in the digestive tract may lead to new strategies for the prevention or control of bacterial infections in penaeids.