Miracle-dz/UniFAR-FTUs huggingface dataset:
A Prospective Trial on the Effect of Body Mass Index and Sex on Plasma Octreotide Levels in Patients Undergoing Long-Term Octreotide LAR Therapy

Objectives: Octreotide long acting repeatable (LAR) is commonly used to control the symptoms of patients with functional neuroendocrine tumors. Unfortunately, most patients escape control over time and require higher LAR doses or more frequent rescue therapy to remain asymptomatic. Previous work has shown that body weight and monthly LAR dose will significantly affect circulating plasma octreotide levels in patients undergoing therapy. Methods: To determine if other parameters change circulating plasma octreotide levels, we prospectively studied 82 patients undergoing long-term LAR therapy. Results: Multivariate analysis demonstrated that the plasma octreotide levels decrease by approximately 3.4% for each unit of body mass index (BMI) increase (P = 0.03), adjusting for sex and monthly LAR dose. Plasma octreotide levels for females were approximately 47.6% higher than those for males (P = 0.045), adjusting for BMI and monthly LAR dose. Initial and subsequent octreotide LAR doses should take into consideration sex and BMI. Males are estimated to require 14.1-mg (SD, 7.25) higher monthly LAR doses than females with the same BMI. Conclusions: We have shown that plasma octreotide levels are affected by not only monthly LAR dose but also BMI and sex. We hope these observations will make choosing initial and subsequent octreotide LAR doses easier for physicians.
Assimilation of Organic Contaminants in Wetlands: Processes and a Conceptual Model.

Laboratory studies and field measurements were conducted to quantify assimilative capacity of toxic organic contaminants in freshwater wetlands. Studies were conducted for hexachlorobenzene and naphthalene in a mineral-dominated bottomland hardwood forest and an organic matter-dominated freshwater marsh. In laboratory studies, sorption of hexachlorobenzene (HCB) in wetland soil and floodwater was strongly influenced by high levels of naturally occurring dissolved organic carbon (DOC). Organic matter-dominated wetlands (e.g., marshes) demonstrated no advantage over mineral-dominated wetlands (e.g., bottomland hardwood forests) for sorption of HCB due to partitioning in this DOC phase. Over the short-term, sorption of HCB was adequately described using a three-phase equilibrium model that included the DOC phase. Sorptive assimilation of HCB appears to be dependent on unique hydrological conditions that promote sedimentwater exchange rather than any enhanced sorptive ability of wetland substrates, themselves. Sorption of naphthalene was greater in the freshwater marsh due to the increased fraction of organic carbon and the lower affinity of naphthalene for DOC. Small, but measurable, differences were observed in sorption partition coefficients between aerobic and high-DOC, anaerobic incubations. Reductive dechlorination of HCB was observed under low redox conditions (— 200 mV) in both wetland soils. Substantial degradation of HCB (50-60% in the bottomland hardwood soil; 90% in the freshwater marsh soil) occurred over a period of 18 weeks. Mineralization of naphthalene was rapid in the freshwater marsh and bottomland hardwood soil when aerobic, high redox potential conditions were present. No mineralization was observed under anaerobic conditions. Shapes of mineralization curves were dependent on substrate concentration and were well fitted using a three-half order kinetic model. An assimilation model was developed to describe removal of toxic organics in a conceptually simple wetland. External assimilation fluxes are volatilization, reaction (e.g., biodegradation), outflow and burial. Sensitivity analysis indicated that assimilation of hydrophobic compounds (e.g., HCB) is inhibited by high concentrations of DOC. Removal of compounds such as naphthalene is controlled by volatilization. The assimilation model is suited for several uses including estimating the assimilation capacity of wetlands for organic contaminants, testing various treatment or fate scenarios, and estimating the fate of new compounds entering wetlands. CHAPTER
Investigation of solubilization and digestion methods for microsomal membrane proteome analysis using data‐independent LC‐MSE

To evaluate the implementation of various denaturants and their efficacy in bottom‐up membrane proteomic methods using LC‐MS analysis, microsomes isolated from tomato roots were treated with MS‐compatible surfactants (RapiGest SF Surfactant from Waters and PPS Silent Surfactant from Protein Discovery), a chaotropic reagent (guanidine hydrochloride), and an organic solvent (methanol). Peptides were analyzed in triplicate sample and technical replicates by data‐independent LC‐MSE analysis. Overall, 2333 unique peptides matching to 662 unique proteins were detected with the order of denaturant method efficacy being RapiGest SF Surfactant, PPS Silent Surfactant, guanidine hydrochloride, and methanol. Using bioinformatic analysis, 103 proteins were determined to be integral membrane proteins. When normalizing the data as a percentage of the overall number of peptides and proteins identified for each method, the order for integral membrane protein identification efficacy was methanol, guanidine hydrochloride, RapiGest SF Surfactant, and PPS Silent Surfactant. Interestingly, only 8% of the proteins were identified in all four methods with the silent surfactants having the greatest overlap at 17%. GRAVY analysis at the protein and peptide level indicated that methanol and guanidine hydrochloride promoted detection of hydrophobic proteins and peptides, respectively; however, trypsin activity in the presence of each denaturant was determined as a major factor contributing to peptide identification by LC‐MSE. These results reveal the complementary nature of each denaturant method, which can be used in an integrated approach to provide a more effective bottom‐up analysis of membrane proteomes than can be achieved using only a single denaturant.
UCC: update-conscious compilation for energy efficiency in wireless sensor networks

Wireless sensor networks (WSN), composed of a large number of low-cost, battery-powered sensors, have recently emerged as promising computing platforms for many non-traditional applications. The preloaded code on remote sensors often needs to be updated after deployment in order for the WSN to adapt to the changing demands from the users. Post-deployment code dissemination is challenging as the data are transmitted via battery-powered wireless communication. Recent studies show that the energy for sending a single bit is about the same as executing 1000 instructions in aWSN. Therefore it is important to achieve energy efficiency in code dissemination. In this paper, we propose novel update-conscious compilation(UCC) techniques for energy-efficient code dissemination in WSNs. An update-conscious compiler, when compiling the modified code, includes the compilation decisions that were made when generating the old binary. The compiler employs a detailed energy model and strives to match the old decisions for a more energy-efficient result. In most cases, matching the previous decisions improves the binary code similarity, reduces the amount of data to be transmitted to remote sensors, and thus, consumes less energy. In this paper, we develop update-conscious register allocation and data layout algorithms. Our experimental results show that they can achieve great improvements over the traditional, update-oblivious approaches.
Molecular Pathways Molecular Pathways : Involvement of ImmunePathways in the Therapeutic Response and Outcome in Breast Cancer

The immune system could mediate the antitumor activity of several anticancer treatments. Several chemotherapy compounds, including anthracyclines and oxaliplatin, induce immunogenic cell death that in turn activates antitumor immune response. Trastuzumab induces antibody-dependant cell-mediated cytotoxicity.On the basis of this background, immune markers have recently been the focus of intense translational research to predict andmonitor the efficacyof treatments.Gene expression arrays and immunohistochemistry have assessed immune activation and infiltration by macrophages, natural killer, and T and B lymphocytes. Using these approaches, several retrospective analyses of large trials have shown that activation of immune pathway may predict treatment efficacy and outcome in patients with breast cancers. As examples, intratumoral infiltration by lymphocytes and interferon-response in primary tumor predicted the efficacy of neoadjuvant chemotherapy. Intratumoral infiltration by lymphocytes was associated with good prognosis in patients with triple-negative breast cancer treated with adjuvant chemotherapy.More recently, it has been suggested that lymphocyte infiltration could also predict efficacy of trastuzumab. Finally, small retrospective studies have suggested that postchemotherapy lymphocyte infiltrates could be associated with better outcome in patients who did not reach pathologic complete response. This body of evidence suggests that assessing immune infiltration and activation could be useful in the future to stratify breast cancer patients. In addition, they provide evidence for the development of immunotherapies in breast cancer patients. Clin Cancer Res; 19(1); 1–6. 2012 AACR.
Crew familiarity: operational experience, non-technical performance, and error management.

INTRODUCTION Crew familiarity, in terms of having recent operational experience together as a crew, is seen as an important safety-related variable. However, little evidence exists to unpack the underlying processes with respect to familiarity. This study investigated the relationships between crew familiarity, non-technical performance, and error management. METHOD Data were collected during normal line operations at a commercial airline by observers using a methodology based on the Line Operations Safety Audit (LOSA). A total of 154 flights were analyzed, 31% of which were operated by an unfamiliar crew, with 69% operated by a familiar crew. RESULTS The rate of error occurrence was found to be higher for unfamiliar crews, and these crews were found to make different types of errors when compared with familiar crews. However, with respect to the management of error events, no significant difference was found between unfamiliar and familiar crews. No significant effect of crew familiarity was found with respect to crews' non-technical performance. However, strong correlations were found between crews' non-technical performance and the management of errors. DISCUSSION The findings indicate that crew familiarity, in terms of whether a crew has flown together recently or not, has little operational significance with respect to the management of error events during normal line operations. Accordingly, the suggestion that unfamiliar crews operate at a higher level of safety-related risk was not supported. Non-technical performance appears to be a stronger driver of effective error management than crew familiarity, and is highlighted as a focus for further investigation and intervention.
Detection and Molecular Characterization of J Subgroup Avian Leukosis Virus in Wild Ducks in China

To assess the status of avian leukosis virus subgroup J (ALV-J) in wild ducks in China, we examined samples from 528 wild ducks, representing 17 species, which were collected in China over the past 3 years. Virus isolation and PCR showed that 7 ALV-J strains were isolated from wild ducks. The env genes and the 3′UTRs from these isolates were cloned and sequenced. The env genes of all 7 wild duck isolates were significantly different from those in the prototype strain HPRS-103, American strains, broiler ALV-J isolates and Chinese local chicken isolates, but showed close homology with those found in some layer chicken ALV-J isolates and belonged to the same group. The 3′UTRs of 7 ALV-J wild ducks isolates showed close homology with the prototype strain HPRS-103 and no obvious deletion was found in the 3′UTR except for a 1 bp deletion in the E element that introduced a binding site for c-Ets-1. Our study demonstrated the presence of ALV-J in wild ducks and investigated the molecular characterization of ALV-J in wild ducks isolates.
The Endoplasmic Reticulum Binding Protein BiP Displays Dual Function in Modulating Cell Death Events1[W][OPEN]

The endoplasmic reticulum binding protein BiP can function as a positive and negative modulator of cell death events in plant cells. The binding protein (BiP) has been demonstrated to participate in innate immunity and attenuate endoplasmic reticulum- and osmotic stress-induced cell death. Here, we employed transgenic plants with manipulated levels of BiP to assess whether BiP also controlled developmental and hypersensitive programmed cell death (PCD). Under normal conditions, the BiP-induced transcriptome revealed a robust down-regulation of developmental PCD genes and an up-regulation of the genes involved in hypersensitive PCD triggered by nonhost-pathogen interactions. Accordingly, the BiP-overexpressing line displayed delayed leaf senescence under normal conditions and accelerated hypersensitive response triggered by Pseudomonas syringae pv tomato in soybean (Glycine max) and tobacco (Nicotiana tabacum), as monitored by measuring hallmarks of PCD in plants. The BiP-mediated delay of leaf senescence correlated with the attenuation of N-rich protein (NRP)-mediated cell death signaling and the inhibition of the senescence-associated activation of the unfolded protein response (UPR). By contrast, under biological activation of salicylic acid (SA) signaling and hypersensitive PCD, BiP overexpression further induced NRP-mediated cell death signaling and antagonistically inhibited the UPR. Thus, the SA-mediated induction of NRP cell death signaling occurs via a pathway distinct from UPR. Our data indicate that during the hypersensitive PCD, BiP positively regulates the NRP cell death signaling through a yet undefined mechanism that is activated by SA signaling and related to ER functioning. By contrast, BiP’s negative regulation of leaf senescence may be linked to its capacity to attenuate the UPR activation and NRP cell death signaling. Therefore, BiP can function either as a negative or positive modulator of PCD events.
Transcription Factor Binding Sites in the Long Control Region of Genital HPVs

The long control region (LCR) of papillomaviruses (PVs) is a genomic segment, without any major open reading frames, which contains a large number of cis-responsive elements that govern PV gene expression and replication. Its size ranges in different PVs from about 7 to 11% of the total genome, roughly 850 bp in the case of genital HPVs, and it is positioned between the end of the L1, and the start of the E6 gene. While even closely related PV LCRs do not show extensive nucleotide sequence similarities, there are a number of recognizable short motifs that are highly conserved, and it is apparent that in related PVs, e.g., in different genital human PVs (HPVs) [18], or different EVHPVs [29], there is a similar gross composition of these motifs. Since it is unlikely that a very low amount of overall sequence conservation, combined with highly conserved motifs, evolved by chance alone, most PV researchers share the hypothesis that these motifs would not exist unless each of them were involved in specific and important functions. Different laboratories disagree, however, as to the exact nature of these functions.
L-Theanine Administration Modulates the Absorption of Dietary Nutrients and Expression of Transporters and Receptors in the Intestinal Mucosa of Rats

L-theanine has various advantageous functions for human health; whether or not it could mediate the nutrients absorption is unknown yet. The effects of L-theanine on intestinal nutrients absorption were investigated using rats ingesting L-theanine solution (0, 50, 200, and 400 mg/kg body weight) per day for two weeks. The decline of insulin secretion and glucose concentration in the serum was observed by L-theanine. Urea and high-density lipoprotein were also reduced by 50 mg/kg L-theanine. Jejunal and ileac basic amino acids transporters SLC7a1 and SLC7a9, neutral SLC1a5 and SLC16a10, and acidic SLC1a1 expression were upregulated. The expression of intestinal SGLT3 and GLUT5 responsible for carbohydrates uptake and GPR120 and FABP2 associated with fatty acids transport were inhibited. These results indicated that L-theanine could inhibit the glucose uptake by downregulating the related gene expression in the small intestine of rats. Intestinal gene expression of transporters responding to amino acids absorption was stimulated by L-theanine administration.
A Stick-Breaking Likelihood for Categorical Data Analysis with Latent Gaussian Models

The development of accurate models and ecient algorithms for the analysis of multivariate categorical data are important and longstanding problems in machine learning and computational statistics. In this paper, we focus on modeling categorical data using Latent Gaussian Models (LGMs). We propose a novel stick-breaking likelihood function for categorical LGMs that exploits accurate linear and quadratic bounds on the logistic log-partition function, leading to an eective variational inference and learning framework. We thoroughly compare our approach to existing algorithms for multinomial logit/probit likelihoods on several problems, including inference in multinomial Gaussian process classication and learning in latent factor models. Our extensive comparisons demonstrate that our stick-breaking model eectively captures correlation in discrete data and is well suited for the analysis of categorical data.
Continuous wave and simulated GSM exposure at 1.8 W/kg and 1.8 GHz do not induce hsp16‐1 heat‐shock gene expression in Caenorhabditis elegans

Recent data suggest that there might be a subtle thermal explanation for the apparent induction by radiofrequency (RF) radiation of transgene expression from a small heat‐shock protein (hsp16‐1) promoter in the nematode, Caenorhabditis elegans. The RF fields used in the C. elegans study were much weaker (SAR 5–40 mW kg−1) than those routinely tested in many other published studies (SAR ∼2 W kg−1). To resolve this disparity, we have exposed the same transgenic hsp16‐1::lacZ strain of C. elegans (PC72) to higher intensity RF fields (1.8 GHz; SAR ∼1.8 W kg−1). For both continuous wave (CW) and Talk‐pulsed RF exposures (2.5 h at 25 °C), there was no indication that RF exposure could induce reporter expression above sham control levels. Thus, at much higher induced RF field strength (close to the maximum permitted exposure from a mobile telephone handset), this particular nematode heat‐shock gene is not up‐regulated. However, under conditions where background reporter expression was moderately elevated in the sham controls (perhaps as a result of some unknown co‐stressor), we found some evidence that reporter expression may be reduced by ∼15% following exposure to either Talk‐pulsed or CW RF fields. Bioelectromagnetics 29:92–99, 2008. © 2007 Wiley‐Liss, Inc.
Linear and O(n log n) time minimum-cost matching algorithms for quasi-convex tours

Let G be a complete, weighted, undirected, bipartite graph with n red nodes, n" blue nodes, and symmetric cost function c(x,y). A maximum matching for G consists of $\min\{n,n^\prime\}$ edges from distinct red nodes to distinct blue nodes. Our objective is to find a minimum-cost maximum matching, i.e., one for which the sum of the edge costs has minimal value. This is the weighted bipartite matching problem or, as it is sometimes called, the assignment problem. We report a new and very fast algorithm for an abstract special case of this problem. Our first requirement is that the nodes of the graph are given as a "quasi-convex tour. " This means that they are provided circularly ordered as x1,. ,xN, where N = n + n", and that for any $x_i, x_j, x_k, x_\ell$, not necessarily adjacent but in tour order, with xi, xj of one color and $x_k,x_\ell$ of the opposite color, the following inequality holds: \[ c(x_i,x_\ell) + c(x_j,x_k) \le c(x_i,x_k) + c(x_j,x_\ell). \] If $n = n^\prime$, our algorithm then finds a minimum-cost matching in $O(N \log N)$ time. Given an additional condition of ``weak analyticity," the time complexity is reduced to $O(N)$. In both cases only linear space is required. In the special case where the circular ordering is a line-like ordering, these results apply even if $n \ne n^\prime$. Our algorithm is conceptually elegant, straightforward to implement, and free of large hidden constants. As such we expect that it may be of practical value in several problem areas. Many natural graphs satisfy the quasi-convexity condition. These include graphs which lie on a line or circle with the canonical tour ordering, and costs given by any concave-down function of arclength --- or graphs whose nodes lie on an arbitrary convex planar figure with costs provided by Euclidean distance. The weak-analyticity condition applies to points lying on a circle with costs given by Euclidean distance, and we thus obtain the first linear-time algorithm for the minimum-cost matching problem in this setting (and also where costs are given by the $L_1$ or $L_\infty$ metrics). Given two symbol strings over the same alphabet, we may imagine one to be red and the other blue and use our algorithms to compute string distances. In this formulation, the strings are embedded in the real line and multiple independent assignment problems are solved, one for each distinct alphabet symbol. While these examples are somewhat geometrical, it is important to remember that our conditions are purely abstract; hence, our algorithms may find application to problems in which no direct connection to geometry is evident.
Localization of the AP-3 adaptor complex defines a novel endosomal exit site for lysosomal membrane proteins

The adaptor protein (AP) 3 adaptor complex has been implicated in the transport of lysosomal membrane proteins, but its precise site of action has remained controversial. Here, we show by immuno-electron microscopy that AP-3 is associated with budding profiles evolving from a tubular endosomal compartment that also exhibits budding profiles positive for AP-1. AP-3 colocalizes with clathrin, but to a lesser extent than does AP-1. The AP-3– and AP-1–bearing tubular compartments contain endocytosed transferrin, transferrin receptor, asialoglycoprotein receptor, and low amounts of the cation-independent mannose 6-phosphate receptor and the lysosome-associated membrane proteins (LAMPs) 1 and 2. Quantitative analysis revealed that of these distinct cargo proteins, only LAMP-1 and LAMP-2 are concentrated in the AP-3–positive membrane domains. Moreover, recycling of endocytosed LAMP-1 and CD63 back to the cell surface is greatly increased in AP-3–deficient cells. Based on these data, we propose that AP-3 defines a novel pathway by which lysosomal membrane proteins are transported from tubular sorting endosomes to lysosomes.