cssi/SciSciGPT-SciSciNet huggingface dataset:
A Bit-Parallel, General Integer-Scoring Sequence Alignment Algorithm

Mapping of next-generation sequencing data and other pro-cessor-intensive sequence comparison applications have motivated a continued search for high efficiency sequence alignment algorithms. In one approach, which exploits the inherent parallelism in computer logic calculations, individual cells in an alignment scoring matrix are represented as bits in a computer word and the calculation of scores is emulated by a series of bit operations comprised of AND, OR, XOR, complement, shift, and addition. Bit-parallelism has been successfully applied to the Longest Common Subsequence (LCS) and edit-distance problems, producing solutions which are significantly faster than standard implementations. But, the intensive mental effort required to produce these solutions, which are closely tied to special properties of the problems, has limited efforts to extend bit-parallelism to more general scoring schemes. In this paper, we give the first bit-parallel solution for general, integer-scoring global alignment. Integer-scoring schemes, which are widely used, assign integer weights for match, mismatch, and insertion/deletion or indel. Our method depends on structural properties of the relationship between adjacent scores in the scoring matrix. We utilize these properties to construct a class of efficient algorithms, each designed for a particular set of weights, and we introduce a standard for characterizing the efficiency in terms of the average number of bit-operations per cell of the original scoring matrix.
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

This protocol describes how to annotate genomic variants using either the ANNOVAR software or the web-based wANNOVAR tool. Recent developments in sequencing techniques have enabled rapid and high-throughput generation of sequence data, democratizing the ability to compile information on large amounts of genetic variations in individual laboratories. However, there is a growing gap between the generation of raw sequencing data and the extraction of meaningful biological information. Here, we describe a protocol to use the ANNOVAR (ANNOtate VARiation) software to facilitate fast and easy variant annotations, including gene-based, region-based and filter-based annotations on a variant call format (VCF) file generated from human genomes. We further describe a protocol for gene-based annotation of a newly sequenced nonhuman species. Finally, we describe how to use a user-friendly and easily accessible web server called wANNOVAR to prioritize candidate genes for a Mendelian disease. The variant annotation protocols take 5–30 min of computer time, depending on the size of the variant file, and 5–10 min of hands-on time. In summary, through the command-line tool and the web server, these protocols provide a convenient means to analyze genetic variants generated in humans and other species.
Predicting Disease-Related Subnetworks for Type 1 Diabetes Using a New Network Activity Score

Abstract In this study we investigated the advantage of including network information in prioritizing disease genes of type 1 diabetes (T1D). First, a naive Bayesian network (NBN) model was developed to integrate information from multiple data sources and to define a T1D-involvement probability score (PS) for each individual gene. The algorithm was validated using known functional candidate genes as a benchmark. Genes with higher PS were found to be more likely to appear in T1D-related publications. Next a new network activity metric was proposed to evaluate the T1D relevance of protein-protein interaction (PPI) subnetworks. The metric considered the contribution both from individual genes and from network topological characteristics. The predictions were confirmed by several independent datasets, including a genome wide association study (GWAS), and two large-scale human gene expression studies. We found that novel candidate genes in the T1D subnetworks showed more significant associations with T1D than ...
PRESENTATION OF THE CHARLES SCHUCHERT AWARD OF THE PALEONTOLOGICAL SOCIETY TO MICHAEL J. FOOTE

One of the things that I love about citation speeches at The Paleontological Society luncheon is that the audience invariably is provided with little snippets about the awardees that give us glimpses into who they really are. I thought I knew Dave Raup pretty well, but it wasn't until the GSA meeting in Salt Lake City a few years ago, when Dave received the PS medal, that I learned from Steve Stanley that Dave was once an accomplished piano player. I know that Charles Marshall is a skilled speaker, but, until last year in Denver, when Doug Erwin presented the citation for Charles for the Schuchert award, I had no idea that Charles was once an award-winning debater. This presents me with a challenge. What can I tell the audience assembled today, as well as future generations of paleontologists who will read this citation in JP, that will reveal for them a glimpse of the inner Mike Foote? In pondering this, it wasn't easy to come with anything particularly enlightening. Mike is a good cook, sometimes brews his own beer, is a decent softball player, and used to wear two earrings in one ear. But so what? These are all fine qualities, but seem fairly pedestrian by the standards of previous citations. But then I realized that there was one thing, which I learned only last Spring, that probably sets Mike apart from most people in this room, not to mention most previous Schuchert awardees: Mike owns his own BOWLING BALL. And shoes. If you ask him about this, he'll probably give you some story about having purchased them for five bucks at a garage sale, and how they …
Two-Year Trial of Human Caloric Restriction

Calorie restriction (CR) retards aging and extends mean and maximal life span in most species tested (1 ). However, whether prolonged CR increases life span in long-lived species (such as primates) is still controversial. Although two independent studies addressing the effects of CR in monkeys have shown different outcomes on life span, both converge into the fact that CR delays the onset and impact of age-related diseases (,3). In humans, the evidence of 2beneficial effects of CR derives from observational stud-ies in longer-lived population in Okinawa, Japan () and 4from individuals who self-impose CR (,6). In the lat5 -ter, severe food restriction causes several metabolic and molecular changes associated with CR in animals that protect against age-related pathologies, including changes in markers for type 2 diabetes, hypertension, cardiovas-cular disease, cancer, and dementia (). However, only a 7limited number of people have the discipline to follow the duration and severity of the CR regimen that is required for optimal benefits. In light of this, it became an impor-tant research objective to assess the feasibility, safety, and health-related outcomes of prolonged CR in a well-con-trolled human clinical trial.In this edition of the
Discovering Innovation

Summary form only given. Some have called it the "big blue brain storm" (Business week Aug 8, 2006). Led by its CEO Sam Palmisano, IBM is reaching out to its worldwide workforce, calling on family and friends and business associates and inviting them to participate in a world innovation JAM. IBM has brought together over 104,000 participants in a marathon 76 hour online session in the hopes of linking ideas and technologies that will lead to new business for IBM, help to solve societal problems and maybe revolutionize industry. The technologies that IBM used as its started set were from its worldwide research centers. These included biometric authentication which uses secure identity cards with your biometric information as a way to protect you against identity theft. There's communication pattern analysis with collaborative organizational analysis technology that analyzes communications within a company to both uncover internal patterns and identify potential changes that can be made to improve the organization's efficiency. And the last example is Super Simulations. These are systems like IBM's Blue Gene that are able to handle very sophisticated mathematical models that use real-time streams of real-world data to simulate everything from the weather to biological processes, and allow us to begin making predictions about real-world behaviors. The JAM is the latest in IBM's continuing efforts to create a culture of innovative thinking in its company. But that's only one of the ways IBM thinks about innovation there are others. The Global Innovation Outlook (GIO), has opened up IBM's technical and business forecasting processes to include external leaders from business, academia, the public sector, NGOs and other influential constituents of the world community. The GIO takes a deep look at some of the most pressing issues facing the world and works toward providing solutions to those needs: the future of the enterprise; energy and the environment; and transportation and mobility
Species-Area Curves and Diversity-Productivity Relationships in Beaver Meadows of Voyageurs National Park, Minnesota, USA

Species richness (S) increases with area (A) as shown in the well-known power function proposed by Arrhenius: S=cA 2 . We show that the exponent of the species-area curves, z, was negatively correlated with aboveground annual production (biomass) but the coefficient of the curves, c, was positively correlated with production in two communities dominated by grasses and sedges in beaver meadows in northern Minnesota. The parameters of the species-area power function were not correlated with water table depth nor with soil nutrient availabilities. We then show that the often-reported unimodal relationship between richness and productivity can be derived from the negative correlation of z and the positive correlation of c with productivity. We also show that the productivity corresponding to maximum richness declines with increasing area sampled. All other correlations of c and z with productivity yield either monotonically increasing or decreasing richness with increasing productivity. The relationships between richness and productivity depend on the area censused and the correlations of the coefficient and exponent of the species-area curve with productivity. Interpretations of diversity-productivity relationships are sensitive to plot size and require specification of the species-area relationship for the community in question.
Molecular identification of an ABC transporter complex for manganese: analysis of a cyanobacterial mutant strain impaired in the photosynthetic oxygen evolution process.

Abstract During photosynthesis, the photosystem II (PSII) pigment-protein complex catalyzes oxygen evolution, a reaction in which a four-manganese ensemble plays a crucial role. Using a newly developed selection scheme, we have isolated BP13, a random photosynthesis-deficient mutant strain of the cyanobacterium, Synechocystis 6803. This mutant grew slowly under photoautotrophic conditions, and had a low oxygen evolution activity. Biochemical analysis revealed that the lesion in this mutant strain had specifically affected the Mn ensemble in PSII. Interestingly, incubation of BP13 cells with micromolar levels of added Mn induced rapid recovery of oxygen evolution activity. The mutant could be complemented with a fragment of wild-type chromosomal DNA containing three closely linked genes, mntA, mntB and mntC. These gene products showed significant sequence similarities with polypeptide components of bacterial permeases that are members of the 'ABC (ATP binding cassette) superfamily' of transporter proteins. We determined that in the BP13 strain, a single nucleotide change had resulted in the replacement of an alanine by an aspartic acid residue in MntA, a soluble protein containing ATP binding motifs. These results suggest that the mntCAB gene cluster encodes polypeptide components of a Mn transporter, the first such protein complex identified in any organism.
Fast-response room temperature hydrogen gas sensors using platinum-coated spin-capable carbon nanotubes.

We report the properties of a hydrogen (H2) gas sensor based on platinum (Pt)-coated carbon nanotubes (CNTs) in this paper. To fabricate the Pt–CNT composite sensor, a highly aligned CNT sheet was prepared on a glass substrate from a spin-capable CNT forest, followed by electrobeam (e-beam) deposition of Pt layers onto the CNT sheet. To investigate the effect of Pt on the response of the sensor, Pt layers of different thicknesses were deposited on the CNT sheets. A Pt thickness of 6 nm yielded the highest response for H2 detection, whereas Pt layers thinner or thicker than 6 nm led to a reduction of the surface area for gas adsorption and, consequently, decreased response. The Pt–CNT composite sensor detects H2 concentrations of 3–33% at room temperature and shows reproducible behavior with fast response and recovery times.
The Chemical Vapor Deposoitin of Pure Nickel and Nickel Boride Thin Films from Borane Cluster Compounds

Several borane cluster compounds, such as pentaborane(9) and their corresponding metal complexes have been investigated in our laboratory for their utility as unique source materials for synthesizing metal/metal boride thin films by MOCVD. In this paper we report the preparation of thin films of nickel boride from the thermal decomposition of nido-pentaborane(9) in the presence of anhydrous nickel chloride [NiCl2] in the vapor phase. Crystalline nickel boride thin films of controlled composition ranging from 0.1 to several microns have been readily prepared by controlling the temperature and the flow rate of the pentaborane(9) into the reaction chamber. The nickel boride films on GaAs were thermally annealed to form the Ni7B3 phase as hexagonal crystals in a Ni3B matrix. These films have been characterized by AA, AES, EDXA, SEM, XRD and electron diffraction. The phases were determined primarily by X-ray and electron diffraction experiments.
Abstract B46: Essential roles of SIRT1 for BCR-ABL transformation and genetic mutations

Resistance of cancer stem cells and acquired genetic mutations are daunting challenges facing targeted cancer therapy, but the underlying mechanisms are not clear. This is best exampled by the tyrosine kinase inhibitor imatinib that effectively treats chronic myelogenous leukemia (CML) whereas resistance develops due to persistence of CML stem/progenitor cells and acquired mutations of BCR‐ABL. SIRT1 is a mammalian stress response gene homologous to yeast silent information regulator 2 (Sir2), a nicotinamide adenine dinucleotide (NAD+) dependent protein deacetylase, and is involved in regulation of a variety of cellular functions including survival, glucose homeostasis and fat metabolism through deacetylating histones and non‐histone target proteins. Here we demonstrate that BCRABL transformation activates SIRT1 in hematopoietic stem/progenitor cells in both clinical CML patients and a CML‐like disease mouse model. Inhibition of SIRT1 by gene knockdown or pharmacological inhibitors suppresses CML cell proliferation and induces apoptosis in vitro. SIRT1 knockdown inhibits growth of CML tumor xenograft in immunodeficient mice. Homozygous knockout of SIRT1 gene inhibits BCR‐ABL transformation of mouse bone marrow cells and the development of a CML‐like myeloproliferative disease. We show that through deacetylation of Ku70, SIRT1 promotes BCR‐ABL mutations upon imatinib treatment and de novo genetic mutations upon DNA damage. Our results suggest an essential role of SIRT1 for BCR‐ABL oncogenic transformation and promoting cancer genome instability, and have implication for targeting SIRT1 to overcome resistance. These findings not only improve our understanding of SIRT1 functions in tumorigenesis, but also have translational implication for targeting SIRT1 for overcoming resistance in cancer treatment. Citation Information: Cancer Res 2009;69(23 Suppl):B46.
Can anaerobes be acid fast? A novel, clinically relevant acid fast anaerobe.

Introduction: Anaerobic acid fast bacilli (AFB) have not been previously reported in clinical microbiology. This is the second case report of a novel anaerobic AFB causing disease in humans. Case presentation: An anaerobic AFB was isolated from an abdominal wall abscess in a 64–year-old Caucasian diabetic male, who underwent distal pancreatectomy and splenectomy for resection of a pancreatic neuroendocrine tumour. The isolated bacteria were gram-variable and acid-fast, consisting of small irregular rods. The 16S rRNA gene sequence analysis showed that the isolate is a novel organism described in the literature only once before. The organism was studied at the CDC (Centers for Disease Control and Prevention) by the same group that worked with the isolates from the previous report; their findings suggest that the strain belongs to the suborder Corynebacterineae. Conclusion: This is the fifth reported case of an anaerobic AFB involved in clinical disease; its microbiological features and 16S RNA sequence are identical to previously reported cases. Clinical disease with this organism seems to be associated with recent history of surgery and abscess formation in deep soft tissues. Acquisition from surgical material is uncertain but seems unlikely.
37 Evaluation of the use of intra-aortic balloon pump in a tertiary centre

Introduction Intra-aortic balloon pump (IABP) has been the mainstay treatment for cardiogenic shock seen in patients presenting with myocardial infarction (MI). We evaluated the practice and complications of IABP. Methods This retrospective study included patients who had IABP inserted over a 16 month period. Data was collected from case notes, discharge summaries and BCIS database. Results 34 patients (26 males) had IABP inserted with an average age of 70.5 years. 76% of patients were admitted for primary percutaneous coronary intervention (PPCI), followed by unstable angina (8.8%), ventricular septal defect (VSD) in late presentation MI (5.8%), triple vessel disease (5.8%) and intractable pulmonary oedema (2.9%). Of these 57% had severe LV function and 62% were in CS. The main indication for IABP insertion was CS in 73% of cases followed by VSD (11.7%), refractory angina (8.8%) and prophylactic insertion. One third of patients presented with cardiac arrest. Majority (90%) of the IABPs were inserted within 24 h of admission. The complication rate was low at 0.03%. 70% patients were treated in CCU and the rest transferred to ITU. Of these a total of 73.5% were discharged alive with good outcome. Conclusions Of the 34 patients studied, 76% were admitted for PPCI. 73% of patients with CS had IABP inserted with low complication rate. Majority were treated in CCU, of these over 70% of the patients were discharged alive. Therefore, in our study the use of IABP was useful and effective leading to good clinical outcomes.
441 Case-Controlled Twin Study: Fatal Pulmonary Hemosiderosis with Study of SurvivIng Twin Etiology: Home Infested with Stachybotrys and Aspergillus Mold.

One fraternal twin, from a family living in a house contaminated with Stachybotrys chartarum and Aspergillus versicolor, A. niger, and A. fumigatus, died at 18 months of respiratory failure. Autopsy showed pulmonary hemosiderosis, with Aspergillus found by PCR matching of DNA in environmental sampling and in lung samples. Staining revealed antibodies to mycotoxin T-2 and aflatoxin in lung, liver, and brain. The surviving twin had elevated mycotoxin antibodies in serum by enzyme-linked immunosorbent assay (ELISA) testing, confirming a major exposure. The environmental samples confirmed the presence in bulk and dust samples from the house, of T-2 and aflatoxin and an additional 20 mycotoxins in amounts in the microgram range, per gram of test material. The surviving twin exhibited signs, symptoms, and diagnostic testing consistent with immune suppression (NK cells and IL-2), toxic leukoencephalopathy (neurocognitive testing, MRI, PET scanning), and pulmonary disease (HP by mold serology, RADS clinically). Treatment includes removal from the mold contaminated house, symptomatic pulmonary support with bronchodilators and antileukotrienes, itraconazole, supplemental support for mycotoxin detoxification. The house and contents were taken to a Class 3 hazardous waste facility for destruction to prevent any further contact with these molds and mycotoxins. Progressive clinical improvement was noted with treatment. Using a series of biomarkers of mold and mycotoxins, this confirms an etiology of environmental mold and mycotoxin exposure for pulmonary hemosiderosis in children.
Performance and carcass traits of early-weaned steers receiving either a pasture growing period or a finishing diet at weaning.

A 2-yr study was conducted to evaluate 1) steers fed ad libitum high concentrate after weaning (CONC), or 2) steers grown on pasture for 82 d, followed by high-concentrate finishing (PAST), on the performance and carcass traits of 74 early-weaned (117 d of age) steers. Potential breed differences were evaluated using crossbred steers of three types: 1) 3/4 Angus x 1/4 Simmental (BRI), 2) 3/4 Simmental x 1/4 Angus (CON), and 3) 1/2 Wagyu x 1/4 Angus x 1/4 Simmental (WAG). Steers were randomly assigned within breed to the two treatments. There was no interactions (P > .10), so the data were pooled over years. The CONC steers had an ADG that was .17 kg/d higher (P = .0001), intake 1.09 kg/d lower (P = .0001), and gain:feed ratio .013 unit better (.190 vs .177, P = .008) than PAST steers overall. Growing treatment did not affect total concentrate consumed (P = .97). The BRI steers required 31 d less than did CON steers (P = .008), and 23 d less than WAG steers (P = .05) when fed to a constant fat end point (1.1 cm). The BRI steers exhibited an ADG .16 kg/d higher (P = .0003), tended (P = .07) to have an ADG intake .49 kg/d higher, and exhibited gain:feed .01 unit better (.189 vs 180) than WAG steers. When compared with CON steers, BRI steers consumed 310 kg less total concentrate (P = .0003). No differences (P > .38) were observed between growing treatments for carcass characteristics or sensory attributes except that CONC steers tended (P = .11) to improve percentage of steers grading Average Choice or higher by 47% over PAST steers. The WAG steers had a 76-unit higher marbling score (1,000 = Small00, 1,100 = Modest00) (P = .006) than BRI steers, resulting in 19% more (P = .09) steers grading > or = Choice and 82% more (P = .03) grading > or = Average Choice. Liver (P = .15) and rumen (P = .01) weights as a percentage of hot carcass weight were reduced for CONC steers. The CONC steers had higher gain, lower intake, better efficiency, reduced liver and rumen weights, and consumed the same amount of total concentrate when compared with PAST steers. The BRI steers had less finishing days and lower daily intake compared with CON steers. The WAG steers had more days finishing, lower gain, lower intake, more undesirable efficiencies, consumed the same amount of total concentrate, and improved quality grades compared with BRI steers.
Discovery of Bivalent Kinase Inhibitors via Enzyme-Templated Fragment Elaboration

We have employed novel fragment-based screening methodology to discover bivalent kinase inhibitors with improved selectivity. Starting from a low molecular weight promiscuous kinase inhibitor, we appended a thiol for subsequent reaction with a library of acrylamide electrophiles. Enzyme-templated screening was performed to identify acrylamides that assemble into bivalent inhibitors of c-Src kinase. Upon identification of acrylamide fragments that improve the binding affinity of our lead thiol, we characterized the resulting bivalent inhibitors and identified a series of kinase inhibitors with improved potency and selectivity compared to the thiol-containing precursor. Provided that protein can be prepared free of endogenous reactive cysteines, our methodology is general and could be applied to nearly any enzyme of interest.
The Use of Recycled Fibers in Fashion and Home Products

As the textile, apparel, fashion, and retail industries move to become more sustainable, an area of interest is the use of recycled fiber, yarn, fabric, and product content in the development and production of new products. The decision to use recycled materials in products must occur during design and product development and continue throughout the manufacturing processes. There are several recognized stages in recycling collection, processing, and then use in a new product. Recycled materials used in textile and apparel products can be obtained throughout the textile and apparel supply chain and post-consumer collection methods. The use of recycled raw materials aligns with the larger movements of global industries toward a circular economy (vs. linear) and working to achieve a closed-loop production cycle. This chapter reviews the textile and apparel industry, factors that have influenced the generation and use of waste and recycling processes currently used today. Selected brands that have programs and products that contain recycled content are identified here.
Influence of clinical history on MRI interpretation of optic neuropathy

Abstract Background and purpose Clinical history is known to influence interpretation of a wide range of radiologic examinations. We sought to evaluate the influence of the clinical history on MRI interpretation of optic neuropathy. Materials and methods 107 consecutive orbital MRI scans were retrospectively reviewed by three neuroradiologists. The readers independently evaluated the coronal STIR sequence for optic nerve hyperintensity and/or atrophy (yes/no) and the coronal post-contrast T1WI for optic nerve enhancement (yes/no). Readers initially evaluated the cases blinded to the clinical history. Following a two week washout period, readers again evaluated the cases with the clinical history provided. Inter-reader and reader-clinical radiologist agreement was assessed using Cohen's simple kappa coefficient. Results Intra-reader agreement, without and with provision of clinical history, was 0.564–0.716 on STIR and 0.270–0.495 on post-contrast T1WI. Inter-reader agreement was overall fair-moderate. On post-contrast T1WI, inter-reader agreement was significantly higher when the clinical history was provided (p = 0.001). Reader-clinical radiologist agreement improved with provision of the clinical history to the readers on both the STIR and post-contrast T1WI sequences. Conclusions In the MRI assessment of optic neuropathy, only modest levels of inter-reader agreement were achieved, even after provision of clinical history. Provision of clinical history improved inter-reader agreement, especially when assessing for optic nerve enhancement. These findings confirm the subjective nature of orbital MRI interpretation in cases of optic neuropathy, and point to the importance of an accurate clinical history. Of note, the accuracy of orbital MRI in the context of optic neuropathy was not assessed, and would require further investigation.
Parallel associative reductions in halide

Halide is a domain-specific language for fast image processing that separates pipelines into the algorithm, which defines what values are computed, and the schedule, which defines how they are computed. Changes to the schedule are guaranteed to not change the results. While Halide supports parallelizing and vectorizing naturally data-parallel operations, it does not support the same scheduling for reductions. Instead, the programmer must create data parallelism by manually factoring reductions into multiple stages. This manipulation of the algorithm can introduce bugs, impairs readability and portability, and makes it impossible for automatic scheduling methods to parallelize reductions. We describe a new Halide scheduling primitive rfactor which moves this factoring transformation into the schedule, as well as a novel synthesis-based technique that takes serial Halide reductions and synthesizes an equivalent binary associative reduction operator and its identity. This enables us to automatically replace the original pipeline stage with a pair of stages which first compute partial results over slices of the reduction domain, and then combine them. Our technique permits parallelization and vectorization of Halide algorithms which previously required manipulating both the algorithm and schedule.
Financial Relationships With Industry of Editorial Board Members of the Three Journals of the American Society for Radiation Oncology.

Purpose To quantitate financial conflicts of interest (FCOIs) among radiation oncology peer-reviewers, specifically editorial board members of the 3 American Society for Radiation Oncology journals. Methods and Materials The public Centers for Medicare and Medicaid Services Open Payments database delineates payments in 3 categories (general payments, research funding, and company ownership). After excluding non-US and non-MDs, names of board members were searched. Values of each FCOI were extracted for 2013 to 2015 and compiled. Results Of 85 board members, 65 (76%) received any form of payment during the overall period. The majority of delivered payments were general payments: 59 (69%) received at least 1 general payment during these 3 years. In each year, 9 board members (11%) received research funding, and 3 board members (4%) reported company ownership. Over the studied period, all board members received a sum total of $5,387,985; this was composed of $665,801 (12%) in general payments, $3,758,968 (70%) in research funding, and $963,216 (18%) in company ownership. The mean general payment and research funding amounts (all members) were $2,621 and $14,741, respectively. Median (interquartile range) general payments and research funding only in board members receiving payments were $419 ($91-$5072) and $56,250 ($13,345-$200,000), respectively. When assessing general payments according to amount, the vast majority of editorial board members received lower-quantity or no such payments, along with a smaller proportion that received higher-volume payments. The most frequent sources of general payments were Varian, Elekta, and Bristol-Myers Squibb. Merck and Varian were the most frequent funding sources for research payments. Conclusions In this population, the majority of FCOIs were general payments, but research funding comprised the highest monetary sums. Large-volume FCOIs do not apply to the vast majority of editorial board members, implying that the maintained integrity of academic peer-review is likely not influenced to a large extent by FCOIs.
Penfluridol suppresses glioblastoma tumor growth by Akt-mediated inhibition of GLI1.

// Alok Ranjan 1 , Sanjay K. Srivastava 1, 2 1 Department of Biomedical Sciences and Cancer Biology Center, Texas Tech University Health Sciences Center, Amarillo, TX 79106, USA 2 Department of Immunotherapeutics and Biotechnology, Texas Tech University Health Sciences Center, Abilene, TX 79601, USA Correspondence to: Sanjay K. Srivastava, email: sanjay.srivastava@ttuhsc.edu Keywords: antipsychotic drug, glioblastoma, neurosphere, in vivo, intracranial Received: December 16, 2016 Accepted: March 03, 2017 Published: March 23, 2017 ABSTRACT Glioblastoma (GBM) is the most common brain tumor with poor survival rate. Our results show that penfluridol, an antipsychotic drug significantly reduced the survival of ten adult and pediatric glioblastoma cell lines with IC 50 ranging 2–5 μM after 72 hours of treatment and induced apoptosis. Penfluridol treatment suppressed the phosphorylation of Akt at Ser473 and reduced the expression of GLI1, OCT4, Nanog and Sox2 in several glioblastoma cell lines in a concentration-dependent manner. Inhibiting Akt with LY294002 and siRNA, or inhibiting GLI1 using GANT61, cyclopamine, siRNA and CRISPR/Cas9 resulted in enhanced cell growth suppressive effects of penfluridol. On the other hand, overexpression of GLI1 significantly attenuated the effects of penfluridol. Our results further demonstrated that penfluridol treatment inhibited the growth of U87MG tumors by 65% and 72% in subcutaneous and intracranial in vivo glioblastoma tumor models respectively. Immunohistochemical and western blot analysis of tumors revealed reduced pAkt (Ser 473), GLI1, OCT4 and increase in caspase-3 cleavage and TUNEL staining, confirming in vitro findings. Taken together, our results indicate that overall glioblastoma tumor growth suppression by penfluridol was associated with Akt-mediated inhibition of GLI1.
Bilateral Sternal Bar Turnover Flaps for Reconstruction of Inferior Sternal Cleft

The principles for reconstruction of inferior sternal clefts include: (1) rigid protection of the heart without compression, (2) preferable use of autologous tissue, (3) dynamic reconstruction of the thoracic cage, (4) uncompromised growth, and (5) minimal donor site morbidity.
When fascism met empire in Japanese-occupied Manchuria*

Focusing on the case of Japanese-occupied Manchuria, this article asks what set Japan, Germany, and Italy apart from other empires during the ‘fascist moment’ from the aftermath of the First World War to the defeat of the Axis powers in 1945. While scholars have examined the politics and culture of fascism in metropolitan Japan, there is virtually no literature on fascist imperialism. Indeed, the consensus term is ‘wartime empire’ and the dominant framework is of an empire mobilized for total war. One of the goals is to think through what the concept ‘fascist imperialism’ might mean and what the Japanese case might contribute to its definition. Detailed comparison with Germany and Italy is beyond the scope of this article, which builds a definition of fascism around four core elements drawn from the Japanese case: the ideology of Asianism and its vision for Japanese leadership over a regional movement of anti-colonial nationalisms; hyper-militarism that went well beyond military imperialism pursued since the late nineteenth century and that constituted a new celebration of military action and the aesthetics of violence; red peril thinking that propelled the creation of a police state targeting communist intellectuals, politicians, and labour activists within the archipelago as well as communist nationalists in the empire; and radical statism, which signified the turn to the state as the spear tip and staging ground of action to address the crisis. All four dimensions of fascism in Japan intensified in the process of territorial expansion from 1931 to 1945, and linked transformations across the nation-state-empire.
Rethinking the Hispanic advantage in cancer outcomes: Influence of birthplace.

1575Background: In the United States, the Hispanic advantage in cancer outcomes over Non-Hispanic Whites (NHW) derives from studies aggregating heterogeneous Hispanic subgroups and ignoring birthpl...
Social life and social death: Inclusion, ostracism, and rejection in groups:

Humans are social animals and they depend upon social relationships to fortify their physical and psychological well-being. Various types of social experiences can threaten these relationships, mak...
Income inequality, equities, household debt, and interest rates: Evidence from a century of data

Abstract Using Philippon’s (2015) recently published historical household debt data, this paper uses Diebold and Yilmaz’s (2012) generalized variance decompositions and generalized impulse responses to understand the relationship between interest rates, the stock market, household debt, and the distribution of income in the U.S. The results indicate that increases in the stock market and household debt increase income inequality. Moreover, the relationship between the interest rate and income inequality is found to be negative and statistically significant. We interpret our results as suggesting that high income earners derive a larger portion of their income from interest rate sensitive assets.
On elastic fields of perfectly bonded and sliding circular inhomogeneities in an infinite matrix

The solutions to classical problems of perfectly bonded and sliding circular inhomogeneities in a remotely loaded infinite matrix are constructed by using an appealing choice of dimensionless material parameters that represent the in-plane average normal stress and the maximum shear stress at the center of the inhomogeneity, scaled by the corresponding measures of remote stress. The ovalization of the inhomogeneity and the effects of material parameters on stress concentration are discussed. The range of material parameters is specified for which the inhomogeneity with a perfectly bonded interface can expand in vertical direction under horizontal remote loading. For some combination of material properties, the maximum compressive hoop stress in the matrix along the interface can be larger than the maximum hoop stress around a circular void under tensile remote loading. The strain energies stored in perfectly bonded and sliding inhomogeneities are evaluated and discussed.
The Effects of Skill Acquisition in Youth Jobs on Future Work and Earnings

Many studies have examined the effects that working as a youth has on work in the future. This study examines the effects of skill acquisition in youth jobs on future work and earnings. Data from a longitudinal survey of youth between the ages of 12-17 when first interviewed and between the ages of 25-31 when reported working as an adult are used to estimate income and pay from the adult occupation, ratings of skills used in the adult occupation, and the probability of working as an adult. The results predict that working as a youth and gaining general skills as well as the cumulative number of hours worked as a youth prove to have positive and significant effects on almost all examined aspects of the future adult work experience.
When Pleasure Causes Pain: Living with Interstitial Cystitis

Interstitial cystitis (IC) is a chronic inflammatory condition of the bladder wall associated with genital and bladder pain, urgency, and dyspareunia. Characterized by sterile urine culture, IC is poorly understood and resistant to treatment. This article contextualizes patients' experiences from the standpoint of age, ethnicity, gender, socioeconomic status, and the experience of concomitant disease. More than 90 percent of interstitial cystitis patients are women, an alarming number of whom have been misdiagnosed as having psychiatric disorders. Medical diagnosis and treatment are discussed from a feminist perspective. The sexual functioning of persons with IC is discussed in depth. Topics touched upon include menstrual cycle variations and pregnancy, sexual desire, pain during sexual activity, sexual side-effects of medications, sexual history, and sexual self-care.
Bioarchaeological Approaches to Southwestern Violence

Studies of violence in the Southwest need to include multiple lines of evidence in order to understand the social role of that violence. Focusing solely on ethnographic or archaeological reconstruc...
A “fonte da felicidade”: a instrução pública na província do Espírito Santo (1833-1844) / The source of hapiness: public instruction in the province of Espírito Santo (1833-1844)

Nos relatorios dos presidentes de provincia do Espirito Santo de 1833 a 1844, a instrucao publica aparece junto da religiao como pilar para a civilizacao, esta ultima carregada de sentidos como “habitos polidos e apropriados”, “bom governo” e catolicismo. Isso se dava em virtude dessas autoridades escreverem em um contexto intelectual herdeiro do iluminismo lusitano, marcado por limitacoes ao cartesianismo e pela valorizacao da religiao catolica. Em alguns desses relatorios tambem estao registrados dados relativos ao quantitativo de alunos nas aulas de primeiras letras (ensino primario) e maiores (ensino secundario), alem das remuneracoes dos professores. Esses dados foram contrastados com os discursos dos presidentes de provincia com objetivo de se comparar as ideias dessas autoridades sobre a instrucao publica, referenciadas nos elementos do iluminismo portugues herdados pela intelectualidade brasileira nas primeiras decadas do seculo XIX, com a pratica de seus governos para com a conducao da instrucao publica na provincia do Espirito Santo. * * * In reports of the presidents of the Espirito Santo province, from 1833 to 1844, public instruction appears with religion as a pillar for civiliza-tion, charged with meanings such as "polite and proper habits," "good gov-ernment," and Catholicism. This was due to the authorities writing in an in-tellectual context heir to the Lusitanian Enlightenment, marked by limita-tions to Cartesianism and valuation of the Catholic religion. Some of these reports also record data on the number of students in first-grade (primary) and higher classes (secondary), in addition to teachers' salaries. These data were contrasted with speeches of the provincial presidents in order to com-pare the ideas of these authorities on public education, referenced in the ele-ments of Portuguese enlightenment, inherited by Brazilian intelligentsia in the first decades of the nineteenth century, with the practice of their govern-ments towards the conduct of public instruction in the province of Espirito Santo.
Thoracoscopic Lung Biopsy

Recent advances in endoscopic surgery technology and techniques have dramatically transformed and ameliorated this approach to intrathoracic lesions in the paediatric patient. The anatomy of the thorax with its rigid rib cage and collapsible lung render it ideally suited to endoscopic procedures [1].
MJO teleconnections over the PNA region in climate models. Part I: Performance- and process-based skill metrics

AbstractWe propose a set of MJO teleconnection diagnostics that enables an objective evaluation of model simulations, a fair model-to-model comparison, and a consistent tracking of model improvemen...
Innovative Uses for an Online Survey Tool at WVU

West Virginia University (WVU) employees and students use a variety of online survey tools for research, polling, and feedback. In addition to these uses, survey tools have been used to develop complex online forms with workflows and email notifications, program reviews that allow collaborative responses over a six-month period, online tutorials with built-in quizzes, and ballots for student body elections. This paper focuses on WVU's "off label" uses of its most popular survey tool, Qualtrics, and includes a few best practices gleaned from lessons learned.
Chromatographic Analysis of Evolved Contaminants From Spacecraft Materials

The organic materials used in the inhabited area of manned spacecraft were examined for their atmospheric contaminating potential. A sample of each spacecraft material was sealed in a closed, environmentally-controlled chamber and the chamber gas from each sample was subjected to the following tests: (1) odor analysis, (2) carbon monoxide and carbon dioxide analysis, (3) total hydrocarbon content by flame ionization, and (4) qualitative and quantitative analysis of organic contaminants by gas chromatography using three different packed columns.
Small Town or Metropolis? Analyzing the Relationship between Population Size and Language

The variance in language used by different cultures has been a topic of study for researchers in linguistics and psychology, but often times, language is compared across multiple countries in order to show a difference in culture. As a geographically large country that is diverse in population in terms of the background and experiences of its citizens, the U.S. also contains cultural differences within its own borders. Using a set of over 2 million posts from distinct Twitter users around the country dating back as far as 2014, we ask the following question: is there a difference in how Americans express themselves online depending on whether they reside in an urban or rural area? We categorize Twitter users as either urban or rural and identify ideas and language that are more commonly expressed in tweets written by one population over the other. We take this further by analyzing how the language from specific cities of the U.S. compares to the language of other cities and by training predictive models to predict whether a user is from an urban or rural area. We publicly release the tweet and user IDs that can be used to reconstruct the dataset for future studies in this direction.
Management of Acute Sinusitis via e-Visit.

Background: Acute sinusitis is the most common diagnosis in online health care delivery and is the diagnosis most associated with antibiotic prescriptions in the outpatient setting. Few studies hav...
Making Evidence-Based Interventions Relevant for Users: A Comparison of Requirements for Dissemination Readiness Across Program Registries:

This study compares prevention program registries in current use on their level of support for users seeking to implement evidence-based programs. Despite the importance of registries as intermediaries between researchers and the public, and although previous studies have examined how registries define their standards for methodological soundness and evidence of efficacy, little research has focused on the degree to which registries consider programs' dissemination readiness. The result is that registry users are uncertain whether listed programs and their necessary support materials are even available for implementation. This study evaluates 11 publicly and privately funded prevention registries that review the evidence base of programs seeking to improve child health and prosocial outcomes on the degree to which they use dissemination readiness as an evidentiary criterion for rating programs, and the extent and type of information they provide about dissemination readiness to support real-world implementation. The results show wide variability, with few having standards about dissemination readiness or making evidence-based information about interventions easily accessible to users. Findings indicate the need for registries to (1) do more to assess dissemination readiness before including programs on their website and (2) offer more complete information on dissemination readiness and implementation support to users.
Microemulsion as a promising carrier for nose to brain delivery: journey since last decade

Tight junctions and efflux transporters are two chief bodyguards of the blood–brain barrier that protect the brain and create challenges for the treatment of neurological disorders by hampering the systemic delivery of conventional therapeutics to the brain. Approaches involving drug delivery across the brain are either invasive which require disruption of barrier integrity, leading to develop the risk of neurological changes and brain abscess, or non-invasive patient friendly approach like intranasal delivery. Several investigations have strongly confirmed the direct connection between nose and brain via olfactory and trigeminal pathway which deliver neurotherapeutics directly to the brain bypassing obstructive barriers. Since last two decades, extensive researches are ongoing for intranasal delivery of drugs in the form of different novel colloidal carriers wherein, microemulsion with their unique composition and small globule size (< 100 nm) have shown higher efficacy in-vivo and revealed their great potential to treat severe brain disorders where rapid onset of action is needed. In this discussion, why intranasal delivery of microemulsion seems to be promising for brain targeting is the foremost focus while, the importance of delivery device for efficient brain targeting is also covered. Considering the translation of positive in-vivo outcomes further into clinical studies and humans, future direction should be aimed at evaluating the suitability of microemulsion with an efficient intranasal delivery device capable of delivering formulation into upper nasal segment. Limitations associated to intranasal delivery of microemulsion such as performing brain distribution studies in most appropriate model resembling humans, impact of diseased condition on the drug absorption and toxicity related to prolonged use, etc. must be addressed in the near future to establish a strong bench to bedside platform.