cssi/SciSciGPT-SciSciNet huggingface dataset:
Effects of recurrent antecedent hypoglycaemia and chronic hyperglycaemia on brainstem extra-cellular glucose concentrations during acute hypoglycaemia in conscious diabetic BB rats.

Our aim was to determine whether the divergent effects of chronic exposure to hyperglycaemia or hypoglycaemia on the glycaemic threshold for auditory brainstem dysfunction are reflected in the extra-cellular fluid (ECF) concentrations of glucose in the inferior colliculus during hypoglycaemia in the diabetic BB rat. Microdialysis was used to measure inferior colliculus ECF glucose concentrations under basal and hyperinsulinaemic (20 mU/kg·min) hypoglycaemic conditions. ECF glucose is increased under basal (hyperglycaemic) conditions and decreases during hypoglycaemia in both recurrently hypoglycaemic and chronically hyperglycaemic diabetic BB rats (to 0.5±0.1 and 0.8±0.2 mmol/L respectively), with no significant differences between groups. In both groups the plasma to ECF glucose ratio doubled during hypoglycaemia. Prior exposure to recurrent hypoglycaemia does not lead to increased ECF glucose concentrations in the inferior colliculus of diabetic BB rats. The resistance to impaired brainstem function seen in recurrently hypoglycaemic rats during hypoglycaemia cannot simply be attributed to increased blood-brain barrier glucose transport within this brain region.
Towards an embryocentric world: the current and potential uses of embryo technologies in dairy production

Structural features of the dairy industry make it well situated to use embryo technologies as tools for enhancing the genetic merit of dairy cattle and improving fertility. Technologies dependent upon embryo transfer have the potential to increase the efficiency of quantitative genetic selection as well as marker-assisted selection, simplify cross-breeding and germplasm conservation procedures and allow incorporation of transgenes into dairy cattle. In addition, embryo technologies may prove useful in improving fertility in infertile populations of lactating cows. The realisation of the promise of embryo technologies has been constrained by suboptimal efficiency in the production of embryos, alterations in embryonic and fetal survival and development associated with in vitro embryo production and cloning, as well as other technical and societal concerns. Solutions to many of these constraints are possible and the use of embryo technologies in both nucleus and commercial herds is likely to increase. Eventually, embryo transfer may compete with artificial insemination as a dominant method for establishing pregnancies in dairy cattle.
SEVA-INTEGRAL — An instrument for exploration of pathogenic zones

Spinning Electric Vector Analyzer, SEVA-INTEGRAL, is designed for wide-band operation exploration of natural spinning electric fields. It is believed that spinning fields trigger physical processes, which then make a considerable effect on the origination of geo-pathogenic zones, GPZ. Experiments on the influence of electric rotation in fundamental physical and biological processes have revealed considerable impact of the spinning fields on these processes. Due to this reason, GPZs are a serious social problem. Important studies of GPZs affecting human health, as well as the specific dangerous reaction of drivers in the crossing GPZs on roadways, is crucial. Operation of the instrument is based on perception of spinning fields by means of quadrupole sensor with further analyzing both amplitude and mean phase shift between parent vectors in a wide band up to 600 kHz. SEVA-INTEGRAL, unlike its predecessor SEVA, is more sensitive instrument to variation of electric spinning field intensity, and direction. Exploitation of the apparatus has revealed both periodic and irregular spots of electric spinning field activity on earth. The periodic active spots are manifestations of the global grid-like structures, known as meshes of Hartman, Curry and others; while irregular spots are the results of local electro-physical heterogeneities. Introduction of SEVA-Integral to the research field is a social necessity for preventing environmental hazard and promoting public health and safety concerns.
Exploring women's postpartum sexuality: social, psychological, relational, and birth-related contextual factors.

ABSTRACT Introduction Women's postpartum sexuality can be influenced by factors related to physical, personal, and relationship transitions after the newborn arrives. Despite this, many experiential and social factors remain unexplored. Aims This study aims to (i) investigate a range of variables thought to influence postpartum sexuality; (ii) expand the focus beyond latency to penis–vagina intercourse; and (iii) assess positive aspects of postpartum sexuality. Methods Via retrospective reporting on the first 3 months postpartum, 304 women completed an online questionnaire. Main Outcome Measures The main outcome measures were retrospective reports of sexual desire (Sexual Desire Inventory), latency to resumption of sexual activity, and perceptions of partner's sexual desire. Other measures were birth experience (Questionnaire Measuring Attitudes About Labor and Delivery), breastfeeding status, perceptions of social support (Multidimensional Scale of Perceived Social Support), stress (Perceived Stress Scale), and body image (Body Image Self‐Consciousness Scale). Results Significant differences in time to resumption were found. Women performed oral sex on their partners earlier than engaging in masturbation, which was followed by intercourse and then receiving oral sex. Post hoc analyses identified birth experience, social support, importance of partner's sexual fulfillment, and perception of partner's desire as contributors to this pattern. Women's postpartum sexual desire was influenced by their perceptions of their partner's postpartum sexuality and individual's level of fatigue. Results suggested that postpartum desire was not significantly influenced by breastfeeding status, vaginal issues, or psychosocial variables including stress, body image, or social support. Conclusion Results suggest that women's perceptions of their partner's sexuality impact postpartum sexuality more than the physical factors most commonly studied (e.g., vaginal trauma and breastfeeding). These results portray postpartum sexuality as a multidimensional phenomenon and highlight the need for further research that addresses its social context. Hipp LE, Kane Low L, and van Anders SM. Exploring women's postpartum sexuality: Social, psychological, relational, and birth‐related contextual factors. J Sex Med 2012;9:2330–2341.
The immunoglobulin response to individual HSV-1 viral polypeptides: kinetics of the response during primary and secondary experimental infection with herpes simplex virus.

Summary We studied the immunoglobulin response to individual viral polypeptides in experimental primary and secondary infection with herpes simplex virus (HSV)-1 in mice. After a single footpad inoculation with 105·6 pfu of HSV-1, immunoglobulin to proteins mol. wts (103) 44 and 75 appeared on day 7. Antibodies to gB, gC, gD, 42 × 103- and (48–52) × 103-mol. wt proteins appeared on day 11 and antibody to the major capsid protein, VP154, appeared on day 15 after infection. The secondary immune response was characterised by early production of antibody to gD on day 3 followed by antibodies against the 42 × 103- and 44 × 103-mol. wt proteins on days 4 and 5 respectively. Antibodies to glycoprotein gC and gB were delayed until day 7 of the secondary immune response. In both primary and secondary immune responses the responses against proteins of mol. wts (103) 42 and 44 were particularly intense and of high titre. We conclude that the kinetics of anti-polypeptide antibody appearance is markedly asynchronous; and that the anti-glycoprotein responses occur too late in primary infection to contribute to viral clearance.
The Role of Students' Perceptions of Study Strategy and Personal Attributes in Strategy Use.

ABSTRACT Drawing upon study strategy, metacognition, and attribution research literatures, the present study explored task, person, and strategy variables as determinants of strategy use. College students read and were tested over an expository passage and then were asked to report the strategies they used and their perceptions of themselves and of the strategies. The college students in the present study reported using a large number of strategies, more than eight per student on average. Reported use of skimming, anticipating the test, and selective rereading strategies predicted students’ performance on a short‐answer test. Reported use of each of these strategies was significantly predicted by one or more of the following factors: general knowledge of the strategy, specific strategy attributes, perceived learner attributes, match between strategy and learner attributes, and strategy efficacy.
Attenuation of LDH-A expression uncovers a link between glycolysis, mitochondrial physiology, and tumor maintenance

Alterations in cellular metabolism are among the most consistent hallmarks of cancer. Herein we have investigated the relationship between increased aerobic lactate production and mitochondrial physiology in tumor cells. To diminish the ability of malignant cells to metabolize pyruvate to lactate, lactate dehydrogenase A (LDH-A) levels were knocked down by means of LDH-A short hairpin RNAs. Reduction in LDH-A activity resulted in stimulation of mitochondrial respiration and decrease of mitochondrial membrane potential. It also compromised the ability of these tumor cells to proliferate under hypoxia. The tumorigenicity of the LDH-A-deficient cells was severely diminished, and this phenotype was reversed by complementation with the human ortholog LDH-A protein. These results demonstrate that LDH-A plays a key role in tumor maintenance.
Layout-aware text extraction from full-text PDF of scientific articles

The Portable Document Format (PDF) is the most commonly used file format for online scientific publications. The absence of effective means to extract text from these PDF files in a layout-aware manner presents a significant challenge for developers of biomedical text mining or biocuration informatics systems that use published literature as an information source. In this paper we introduce the ‘Layout-Aware PDF Text Extraction’ (LA-PDFText) system to facilitate accurate extraction of text from PDF files of research articles for use in text mining applications. Our paper describes the construction and performance of an open source system that extracts text blocks from PDF-formatted full-text research articles and classifies them into logical units based on rules that characterize specific sections. The LA-PDFText system focuses only on the textual content of the research articles and is meant as a baseline for further experiments into more advanced extraction methods that handle multi-modal content, such as images and graphs. The system works in a three-stage process: (1) Detecting contiguous text blocks using spatial layout processing to locate and identify blocks of contiguous text, (2) Classifying text blocks into rhetorical categories using a rule-based method and (3) Stitching classified text blocks together in the correct order resulting in the extraction of text from section-wise grouped blocks. We show that our system can identify text blocks and classify them into rhetorical categories with Precision1 = 0.96% Recall = 0.89% and F1 = 0.91%. We also present an evaluation of the accuracy of the block detection algorithm used in step 2. Additionally, we have compared the accuracy of the text extracted by LA-PDFText to the text from the Open Access subset of PubMed Central. We then compared this accuracy with that of the text extracted by the PDF2Text system, 2commonly used to extract text from PDF. Finally, we discuss preliminary error analysis for our system and identify further areas of improvement. LA-PDFText is an open-source tool for accurately extracting text from full-text scientific articles. The release of the system is available at http://code.google.com/p/lapdftext/ .
Angiotensin II (de)sensitization: Fluid intake studies with implications for cardiovascular control

Cardiovascular disease is the leading cause of death worldwide and hypertension is the most common risk factor for death. Although many anti-hypertensive pharmacotherapies are approved for use in the United States, rates of hypertension have increased over the past decade. This review article summarizes a presentation given at the 2015 meeting of the Society for the Study of Ingestive Behavior. The presentation described work performed in our laboratory that uses angiotensin II-induced drinking as a model system to study behavioral and cardiovascular effects of the renin-angiotensin system, a key component of blood pressure regulation, and a common target of anti-hypertensives. Angiotensin II (AngII) is a potent dipsogen, but the drinking response shows a rapid desensitization after repeated injections of AngII. This desensitization appears to be dependent upon the timing of the injections, requires activation of the AngII type 1 (AT1) receptor, requires activation of mitogen-activated protein (MAP) kinase family members, and involves the anteroventral third ventricle (AV3V) region as a critical site of action. Moreover, the response does not appear to be the result of a more general suppression of behavior, a sensitized pressor response to AngII, or an aversive state generated by the treatment. More recent studies suggest that the treatment regimen used to produce desensitization in our laboratory also prevents the sensitization that occurs after daily bolus injections of AngII. Our hope is that these findings can be used to support future basic research on the topic that could lead to new developments in treatments for hypertension.
Sharing the Stage: Analysis of social media adoption by Latin American journalists

Despite the proliferation of research on social media and journalism, only a few studies have analyzed how journalists in Latin America embrace the affordances of social platforms for journalism practice. Based on a survey of 877 Latin American reporters, this article examines the platforms journalists use and how they use them. The broad finding is that, despite the great popularity of Facebook in the region, Twitter is the most important platform for daily newsgathering and journalistic work. Journalists turn to Twitter to find sources and stories, showing an important openness to participatory journalism. Yet, they mistrust information provided from political sources. Our findings show that different regions in Latin America work with social media in different ways, and local journalistic cultures have an impact on these adoptions, especially in the case of Brazil. Further research and implications for the field are discussed.
The weight of evidence and the burden of authority: case histories, medical statistics and smallpox inoculation.

L'evaluation statistique de l'exercice medical est l'un des piliers de la medecine moderne. La vaccination contre la variole au XVIII e siecle en Angleterre est alors un exemple qui permet d'etablir une evaluation a partir de donnees numeriques
Vasoactive intestinal peptide prevents lung injury due to xanthine/xanthine oxidase

Reactive oxygen species mediate injury and inflammation in many tissues. The addition of xanthine and xanthine oxidase to perfused rat lungs led to increases in peak airway pressure and perfusion pressure, pulmonary edema, and increased protein content in bronchoalveolar lavage fluid. Treatment with 1-10 micrograms.kg-1.min-1 of vasoactive intestinal peptide (VIP), a widely distributed neuropeptide, markedly reduced or totally prevented all signs of injury. Simultaneously, VIP also diminished or abolished the associated generation of arachidonate products. Similar protection was provided by catalase (100 micrograms/ml) but not by the VIP-related peptides secretin or glucagon. The pulmonary vasodilator papaverine (0.15 mg/ml) was also ineffective. Injured lungs that were not treated with VIP released large amounts of this peptide in the perfusate. The results indicate that VIP has potent protective activity against injury triggered by xanthine/xanthine oxidase and may be a physiological modulator of inflammatory tissue damage associated with toxic oxygen metabolites.
Gold nanorod-incorporated gelatin-based conductive hydrogels for engineering cardiac tissue constructs.

Abstract The development of advanced biomaterials is a crucial step to enhance the efficacy of tissue engineering strategies for treatment of myocardial infarction. Specific characteristics of biomaterials including electrical conductivity, mechanical robustness and structural integrity need to be further enhanced to promote the functionalities of cardiac cells. In this work, we fabricated UV-crosslinkable gold nanorod (GNR)-incorporated gelatin methacrylate (GelMA) hybrid hydrogels with enhanced material and biological properties for cardiac tissue engineering. Embedded GNRs promoted electrical conductivity and mechanical stiffness of the hydrogel matrix. Cardiomyocytes seeded on GelMA-GNR hybrid hydrogels exhibited excellent cell retention, viability, and metabolic activity. The increased cell adhesion resulted in abundance of locally organized F-actin fibers, leading to the formation of an integrated tissue layer on the GNR-embedded hydrogels. Immunostained images of integrin β-1 confirmed improved cell-matrix interaction on the hybrid hydrogels. Notably, homogeneous distribution of cardiac specific markers (sarcomeric α-actinin and connexin 43), were observed on GelMA-GNR hydrogels as a function of GNRs concentration. Furthermore, the GelMA-GNR hybrids supported synchronous tissue-level beating of cardiomyocytes. Similar observations were also noted by, calcium transient assay that demonstrated the rhythmic contraction of the cardiomyocytes on GelMA-GNR hydrogels as compared to pure GelMA. Thus, the findings of this study clearly demonstrated that functional cardiac patches with superior electrical and mechanical properties can be developed using nanoengineered GelMA-GNR hybrid hydrogels. Statement of Significance In this work, we developed gold nanorod (GNR) incorporated gelatin-based hydrogels with suitable electrical conductivity and mechanical stiffness for engineering functional cardiac tissue constructs ( e.g. cardiac patches). The synthesized conductive hybrid hydrogels properly accommodated cardiac cells and subsequently resulted in excellent cell retention, spreading, homogeneous distribution of cardiac specific markers, cell-cell coupling as well as robust synchronized (tissue-level) beating behavior.
An assessment tool for evaluating cognitive-communicative problems in patients with right hemisphere damage: Preliminary findings.

This article briefly describes the primary characteristics ofthe communication problems associated with right hemisphere damage. It presents a test battery, the RIC Evaluation of Communication Prob...
Geostatistical facies modeling trends for oolitic tidal sand shoals

To assess prospective modeling trends for oolitic tidal sand shoals and explore potential patterns of reservoir heterogeneity, this study examines, quantifies, and models the cycle-scale architecture of the Holocene mobile oolitic tidal sand shoal complex at Schooner Cays, Bahamas. Process-based stratigraphic trends are captured in quantitative, geocellular models of the shoal from analyses of satellite imagery; two-dimensional, high-frequency seismic (chirp) data; and sediment cores. Data show that longitudinal tidal sand ridges extend up to 8 km (5 mi) along depositional dip, gradually transforming bankward into channel-bound, compound barforms consisting of linear, parabolic, and shoulder bars. These bars terminate into a laterally extensive (10 km [6 mi]), strike-elongate sand sheet. Each bar type includes distinct internal architecture, grain size, and sorting related to feedbacks among hydrodynamics, geomorphology, and sedimentology. Building on these data and concepts from the Holocene accumulations, this study demonstrates a methodology for quantifying and validating probabilistic stratigraphic trends prior to their inclusion in stochastic-based facies modeling algorithms. Inclusion of statistically robust facies probability volumes during truncated Gaussian simulation generated ordered and geologically accurate facies distributions relative to bar-crest centerlines, water depth, and geomorphic position. Petrophysical models that incorporate facies-specific porosity, permeability, and water saturation functions display pronounced cycle-scale heterogeneity that could provide insights into variable production rates and poor sweep efficiency commonly encountered during development of analogous oolitic reservoirs.
AJRCCM: 100-Year Anniversary.The Shifting Landscape for Lung Cancer: Past, Present, and Future

The past century has witnessed a transformative shift in lung cancer from a rare reportable disease to the leading cause of cancer death among men and women worldwide. This historic shift reflects the increase in tobacco consumption worldwide, spurring public health efforts over the past several decades directed at tobacco cessation and control. Although most lung cancers are still diagnosed at a late stage, there have been significant advances in screening high-risk smokers, diagnostic modalities, and chemopreventive approaches. Improvements in surgery and radiation are advancing our ability to manage early-stage disease, particularly among patients considered unfit for traditional open resection. Arguably, the most dramatic progress has occurred on the therapeutic side, with the development of targeted and immune-based therapy over the past decade. This article reviews the major shifts in the lung cancer landscape over the past 100 years. Although many ongoing clinical challenges remain, this review will also highlight emerging molecular and imaging-based approaches that represent opportunities to transform the prevention, early detection, and treatment of lung cancer in the years ahead.
Abstract 102: Model-Dependent Influence of Prior Splenectomy on Experimental Abdominal Aortic Aneurysm Progression

Objective: Abdominal aortic aneurysm (AAA) is a macrophage-driven, inflammatory vascular disease. Thus, mobilization of macrophage precursors from the bone marrow and/or splenic reservoir may represent a crucial initial step for AAA formation. Prior evidence suggests that splenic monocytes are important initial contributors to ischemic myocardial injury, their role in AAA pathogenesis remains unknown. We surgically removed the spleen prior to AAA creation to evaluate the influence of splenic monocytes on aneurysm pathophysiology. Methods: AAAs were created in either 1) male C57BL/6 mice by infrarenal intra-aortic porcine pancreatic elastase (PPE) infusion or 2) male ApoE deficient mice by continuous subdermal angiotensin II infusion (ApoE KO/Ang II model). Splenectomy was performed immediately prior to AAA creation in both models. Aortic diameter was serially monitored via ultrasonography, and aortae harvested at sacrifice for histopathology. Results: In sham splenectomy mice, PPE infusion led to significant aortic enlargement. AAA (≥50% aortic diameter increase) developed in all sham/PPE mice within 14 days (n=10). Splenectomy effectively eliminated PPE-induced aortic enlargement, with preservation of medial elastin and smooth muscle cell density and minimal inflammation compared to sham. In contrast, Ang II infusion in ApoE deficient produced similar-sized or larger AAA in splenectomized mice compared to sham, with elastin degradation, smooth muscle cell depletion undistinguishable between the groups. Conclusion: Splenectomy confers differential protection from AAA in mice, depending on the model/method employed for aneurysm formation. While this experiment underscores important limitations to mouse-based AAA modeling, the splenic monocyte reservoir may represent an important driver of AAA pathophysiology.
Co-Creation and Iterative Social Learning in Technology-Enabled Peer Assessment Environment (Double-Loop Mutual Assessment Approach)

This paper is motivated by IT-enabled peer assessment of complex task competencies as a social learning phenomenon. Despite popularity and evident validity of peer assessment techniques, several critical limitations, such as reliance on central authority and constraint to either formative or summative assessment, are present in existing designs of IT-enabled peer assessment systems. The present study contributes to the area of peer assessment literature by proposing theoretical justification for a new peer assessment technique, called Double-Loop Mutual Assessment (DLMA). This technique encompasses a simple but effective system of checks and balances that produces enhanced complex task competency development and assessment through formative and summative feedback. The resulting laissez-faire success metric is valid, reliable and does not require intervention of a moderator. The proposed technique can be applied in a wide variety of collective learning and/or co-creation setting where direct face-to-face interactions are difficult or anonymity is required.
Localizing Detroit’s Food System: Boundary-Work and the Politics of Experiential Expertise

Recently, different expert actors have attempted to localize Detroit’s food system to bring about greater justice citywide. At first, ‘professional experts’ dominated these efforts, claiming authority in the food system due to their knowledge based in qualified training and applied work experience. Yet a rival group of ‘experiential experts’ soon rose up to assert their power, arguing they and their unique race and place-based know-how merited greater influence. Within just a few years, experiential experts successfully replaced professional ones in commanding much area food localization. I show that experiential experts achieved this power largely through strategic boundary-work, including expulsion, expansion, and protection of autonomy. Nonetheless, some Detroiters and professional experts themselves questioned experiential experts’ legitimacy in removing professional experts from the food system altogether. I thus introduce a fourth form of boundary-work that experiential experts deployed to maintain ...
Identifying arbitrary parameter zonation using multiple level set functions

Abstract In this paper, we extended the analytical level set method [1] , [2] for identifying a piece-wisely heterogeneous (zonation) binary system to the case with an arbitrary number of materials with unknown material properties. In the developed level set approach, starting from an initial guess, the material interfaces are propagated through iterations such that the residuals between the simulated and observed state variables (hydraulic head) is minimized. We derived an expression for the propagation velocity of the interface between any two materials, which is related to the permeability contrast between the materials on two sides of the interface, the sensitivity of the head to permeability, and the head residual. We also formulated an expression for updating the permeability of all materials, which is consistent with the steepest descent of the objective function. The developed approach has been demonstrated through many examples, ranging from totally synthetic cases to a case where the flow conditions are representative of a groundwater contaminant site at the Los Alamos National Laboratory. These examples indicate that the level set method can successfully identify zonation structures, even if the number of materials in the model domain is not exactly known in advance. Although the evolution of the material zonation depends on the initial guess field, inverse modeling runs starting with different initial guesses fields may converge to the similar final zonation structure. These examples also suggest that identifying interfaces of spatially distributed heterogeneities is more important than estimating their permeability values.
The Internationalists: How a Radical Plan to Outlaw War Re-Made the World, by Oona A. Hathaway and Scott J. Shapiro

This excellent volume should, in my opinion, be required reading for any scholar working in the field of just war and military ethics. The authors tell a compelling and largely unknown story of the...
Circadian misalignment and hepatocellular carcinoma incidence in the United States

Background: Circadian misalignment may increase the risk of developing hepatocellular carcinoma (HCC). The aim of this study was to examine the association between distance from time zone meridian, a proxy for circadian misalignment, and HCC risk in the United States adjusting for known HCC risk factors.Methods: Surveillance, Epidemiology, and End Results (SEER) provided information on 56,347 HCC cases diagnosed between 2000 and 2014 from 16 population-based cancer registries in the United States. Distance from time zone meridian was estimated using the location of each SEER county's Center of Population in a geographic information system. Poisson regression with robust variance estimation was used to calculate incidence rate ratios (IRRs) and 95% confidence intervals (CIs) for the association between distance from time zone meridian and HCC risk adjusting for individual-level age at diagnosis, sex, race/ethnicity, year of diagnosis, SEER registry, and county-level prevalence of health conditions, lifestyle factors, shift work occupation, socioeconomic status, and demographic and environmental factors.Results: A 5-degree increase in longitude moving east to west within a time zone was associated with a statistically significant increased risk for HCC (IRR, 1.07; 95% CI, 1.01-1.14, P = 0.03). A statistically significant positive association was observed among those <65 years old, while no association was observed among individuals ≥65 years old (Pfor interaction < 0.01).Conclusions: Circadian misalignment from residing in the western region of a time zone may impact hepatocarcinogenesis.Impact: Circadian misalignment may be an independent risk factor for HCC. Cancer Epidemiol Biomarkers Prev; 27(7); 719-27. ©2018 AACR.
Understanding the motivations of serious leisure participation: a self-determination approach

The purpose of this study was to examine the associations between serious leisure (SL) and quality of motivation, in line with self-determination theory (SDT). The SL perspective was used to descri...
TreeSwift: a massively scalable Python package for trees

Background: Phylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical. Results: This article describes TreeSwift, a Python package for traversing and manipulating trees that does not require any external dependencies, and it then compares its performance against that of Bio.Phylo, DendroPy, and the ETE Toolkit. Conclusions: TreeSwift is a freely available, open source, and scalable Python package for traversing and manipulating trees. Source code and documentation are publicly available on GitHub (www.github.com/niemasd/TreeSwift), and it can easily be installed from PyPI (www.pypi.org/project/treeswift) using pip. Keywords: phylogenetics; tree; traversal; Python; scalable
Béla Szőkefalvi-Nagy

When Paul Butzer asked me to take advantage of this meeting and tell you something about the celebrant, our friend Bela Szőkefalvi-Nagy, I was pleased and at the same time embarrassed. I have known and admired Nagy for almost a quarter of a century, but I didn’t know as much about his life as I should have liked to know. All I could think of at first was a report consisting of two sentences — “He is a great mathematician. He is a nice guy.” — but surely those sentences are so well known that they need not be said again. To solve the problem, I did some historical research (that helped some), and I made use of some friendly spies (that helped a lot). My most effective spies were Ferenc Marta, a chemist colleague and a long-time friend of Nagy, and Ciprian Foias. Let me tell you what I learned.
Epiphrenic diverticula of the esophagus

Epiphrenic diverticula are among the more unusual lesions of the esophagus that are often misdiagnosed and misunderstood. Occurring alone or in association with other lesions, they are a potential source of difficulty to the patient and may develop severe complications. The etiology and clinical picture of these diverticula have been presented with emphasis on the roentgen diagnosis. When the diverticula are symptomatic, either conservative or surgical treatment is indicated.
Patient-Centered Outcomes with Second Kidney Transplant.

Kidney transplantation is the treatment of choice for patients with ESKD, yet the underutilization of transplantation in the United States suggests that these advantages are not adequately recognized ([1][1]). The proportion of the prevalent dialysis population currently waitlisted is low (15.5% in
Redescription of the enigmatic Pronyssa hennigi (W. Horn), comb. nov. (Coleoptera: Cicindelidae).

When Walther Horn described Heptodonta hennigi from Assam in 1898, on the basis of a single female, he was completely uncertain about which genus he should classify this species in. He wrote that he could not identify the genus, but that the closest looking species he knew were Heptodonta tricondyloides Gestro, which is now placed in the genus Dilatotarsa Dokhtouroff, and Euryoda (= Prothyma Hope) lucidicollis Chaudoir. He was especially confused by the shape of the pronotum, but also by the lack of pubescens on the lateral margin of the metacoxae, which is a typical character for the genus Heptodonta Hope (see also Fowler 1912). Hence, twelve years later, Horn (1910) transferred hennigi to the Madagascan genus Physodeutera Lacordaire, which he regarded as a "group" of the genus Prothyma Hope. After more than eighty years, Wiesner (1992) placed the species in the Philippine Prothyma subgenus Symplecthyma Rivalier, but also indicated his classification as doubtful with a question mark. Cassola (2002) suggested for the first time a possible affiliation to the genus Pronyssa Bates. Just one year later, Karl Werner visited the collection Senckenberg Deutsches Entomologisches Institut in Muncheberg, Germany, and labelled the still only known specimen with the handwritten note: "Genus / Pronyssa! / Werner det'.03".
Experimental Pulmonary Hypertension Is Associated With Neuroinflammation in the Spinal Cord.

Rationale: Pulmonary hypertension (PH) is a rare but fatal disease characterized by elevated pulmonary pressures and vascular remodeling, leading to right ventricular failure and death. Recently, neuroinflammation has been suggested to be involved in the sympathetic activation in experimental PH. Whether PH is associated with neuroinflammation in the spinal cord has never been investigated. Methods/Results: PH was well-established in adult male Wistar rats 3-weeks after pulmonary endothelial toxin Monocrotaline (MCT) injection. Using the thoracic segments of the spinal cord, we found a 5-fold increase for the glial fibrillary acidic protein (GFAP) in PH rats compared to controls (p<0.05). To further determine the region of the spinal cord where GFAP was expressed, we performed immunofluorescence and found a 3 to 3.5-fold increase of GFAP marker in the grey matter, and a 2 to 3-fold increase in the white matter in the spinal cord of PH rats compared to controls. This increase was due to PH (MCT vs. Control; p<0.01), and there was no difference between the dorsal versus ventral region. PH rats also had an increase in the pro-inflammatory marker chemokine (C-C motif) ligand 3 (CCL3) protein expression (~ 3-fold) and (2.8 to 4-fold, p<0.01) in the white matter. Finally, angiogenesis was increased in PH rat spinal cords assessed by the adhesion molecule CD31 expression (1.5 to 2.3-fold, p<0.01). Conclusion: We report for the first time evidence for neuroinflammation in the thoracic spinal cord of pulmonary hypertensive rats. The impact of spinal cord inflammation on cardiopulmonary function in PH remains elusive.
Mutant EGFR is a preferred SMURF2 substrate of ubiquitination: role in enhanced receptor stability and TKI sensitivity

ABSTRACT We previously reported that differential protein degradation of TKI-sensitive [L858R, del(E746-A750)] and resistant (T790M) epidermal growth factor receptor (EGFR) mutants upon erlotinib treatment correlates with drug sensitivity. However, the molecular mechanism remains unclear. We also reported SMAD ubiquitination regulatory factor 2 (SMURF2) ligase activity is important in stabilizing EGFR. Here, using in vitro and in vivo ubiquitination assays, mass spectrometry, and super-resolution microscopy, we show SMURF2-EGFR functional interaction is critical in receptor stability and TKI sensitivity. We found that L858R/T790M EGFR is a preferred substrate of SMURF2-UBCH5 (an E3-E2) complex-mediated K63-linked polyubiquitination, which preferentially stabilizes mutant receptor. We identified four lysine (K) residues (K721, 846, 1037 and 1164) as the sites of ubiquitination and replacement of K to acetylation-mimicking asparagine (Q) at K1037 position in L858R/T790M background converts the stable protein sensitive to erlotinib-induced degradation. Using STochastic Optical Reconstruction Microscopy (STORM) imaging, we show that SMURF2 presence allows longer membrane retention of activated EGFR upon EGF treatment, whereas, siRNA-mediated SMURF2 knockdown fastens receptor endocytosis and lysosome enrichment. In an erlotinib-sensitive PC9 cells, SMURF2 overexpression increased EGFR levels with improved erlotinib tolerance, whereas, SMURF2 knockdown decreased EGFR steady state levels in NCI-H1975 and PC9-AR cells to overcome erlotinib and AZD-9291 resistance respectively. Additionally, by genetically altering the SMURF2-UBCH5 complex formation destabilized EGFR. Together, we propose that SMURF2-mediated preferential polyubiquitination of L858R/T790M EGFR may be competing with acetylation-mediated receptor internalization to provide enhanced receptor stability and that disruption of the E3-E2 complex may be an attractive alternate to overcome TKI resistance.
F1 lightning: HTAP as a service

The ongoing and increasing interest in HTAP (Hybrid Transactional and Analytical Processing) systems documents the intense interest from data owners in simultaneously running transactional and analytical workloads over the same data set. Much of the reported work on HTAP has arisen in the context of "greenfield" systems, answering the question "if we could design a system for HTAP from scratch, what would it look like?" While there is great merit in such an approach, and a lot of valuable technology has been developed with it, we found ourselves facing a different challenge: one in which there is a great deal of transactional data already existing in several transactional systems, heavily queried by an existing federated engine that does not "own" the transactional systems, supporting both new and legacy applications that demand transparent fast queries and transactions from this combination. This paper reports on our design and experiences with F1 Lightning, a system we built and deployed to meet this challenge. We describe our design decisions, some details of our implementation, and our experience with the system in production for some of Google's most demanding applications.
Wildlife responses to livestock guard dogs and domestic sheep on open range

Abstract Domestic sheep (Ovis aries) are an attractant to carnivores; however, sheep are often accompanied by humans and livestock guardian dogs (LGDs; Canis familiaris), which defend sheep from depredation. Sheep also compete directly with wildlife for grazing resources. Although practiced for millennia in much of the world outside North America, the effect that transhumance has on wildlife is poorly understood. To test the effect of sheep bands (sheep, humans, and LGDs) on wildlife, we modeled the detection probability of wild mammals relative to the presence of sheep bands in the Northwestern United States. Sheep band presence was associated with a reduction of about half in the likelihood of detecting large carnivores (Ursus americanus, Ursus arctos, Canis lupus, and Puma concolor, p
Autophagic degradation of IRF3 induced by the small-molecule auranofin inhibits its transcriptional and proapoptotic activities

The ubiquitously expressed transcription factor interferon (IFN) regulatory factor 3 (IRF3) is critical for the induction of antiviral genes, e.g., type-I IFN. In addition to its transcriptional function, IRF3 also activates a nontranscriptional, proapoptotic signaling pathway. While the proapoptotic function of IRF3 protects against viral infections, it is also involved in harmful immune responses that trigger hepatocyte cell death and promote liver disease. Thus, we hypothesized that a small-molecule inhibitor of the proapoptotic activity of IRF3 could alleviate fatty-acid-induced hepatocyte cell death. We conducted a high-throughput screen, which identified auranofin as a small-molecule inhibitor of the proapoptotic activity of IRF3. In addition to the nontranscriptional apoptotic pathway, auranofin also inhibited the transcriptional activity of IRF3. Using biochemical and genetic tools in human and mouse cells, we uncovered a novel mechanism of action for auranofin, in which it induces cellular autophagy to degrade IRF3 protein, thereby suppressing IRF3 functions. Autophagy-deficient cells were unable to degrade IRF3 upon auranofin treatment, suggesting that the autophagic degradation of IRF3 is a novel approach to regulate IRF3 activities. Using a physiologically relevant in vitro model, we demonstrated that auranofin inhibited fatty-acid-induced apoptotic cell death of hepatocytes. In summary, auranofin is a novel inhibitor of IRF3 functions and may represent a potential therapeutic option in diseases where IRF3 is deleterious.
n / s − q ^ / T 3 relation at next-to-leading order in QCD

The relation between the specific shear viscosity $\ensuremath{\eta}/s$ and the dimensionless jet quenching parameter $\stackrel{^}{q}/{T}^{3}$ in perturbative QCD is explored at next-to-leading order in the coupling constant. It is shown that the relation changes little, although both transport coefficients independently are subject to large modifications at the next-to-leading order level. This finding confirms that the relationship is robust.
Chapter 12 Radioreceptor Assays

Publisher Summary This chapter discusses the radioreceptor assays. It bears witness to the importance of analytic techniques for understanding the chemical nature of neurotransmission. During the past century, this science has advanced from rudimentary biological assays, to the use of highly sophisticated and expensive electronic equipment. Sensitivity, specificity, versatility, precision, speed, simplicity and cost are the chief considerations when contemplating the use or development of an analytical procedure. As is evident from this chapter, no assay has yet been developed that is superior to all others in every category. The ability to measure trace quantities of biological chemicals and drugs has been a driving force in the advancement of biomedical science. The development of increasingly more sensitive assays has facilitated the study of known agents in addition to aiding in the identification and quantification of biologically important substances that were unknown to the last generation of scientists.
Syntheses and characterization of zirconium and hafnium complexes of amido-fluorenyl ligands [(NBut)SiMe2CH2(C13H8)]2− and [(NPri)SiMe2CH2(C13H8)]2−

Abstract The reaction of PriN(H)SiMe2CH2Cl with two equivalents of fluorenyllithium in THF led to [PriN(H)SiMe2CH2(C13H8)]Li(THF) (1) in high yield. X-ray diffraction studies of 1 revealed a monomeric structure with an η2-coordinated fluorenyl ligand. Lithiation followed by the treatment with zirconium or hafnium tetrachloride afforded the corresponding dichloro complexes [(η1-NPri)SiMe2CH2(η5-C13H8)]ZrCl2 (2) and [(η1-NPri)SiMe2CH2(η5-C13H8)]HfCl2 (3). These metal adducts were characterized by NMR spectroscopy, and in the case of 3 also by X-ray diffraction. Compound 3 shows a weak interaction between the formally 14-electron Hf center and the C-H of the isopropyl group. The dialkyl compound [(η1-NBut)SiMe2CH2(η5-C13H8)]Zr(CH2SiMe3)2 (4) was prepared from Me3SiCH2MgCl and [(η1-NBut)SiMe2CH2(η5-C13H8)]ZrCl2. The NMR spectroscopic and X-ray data point to a fairly congested environment around the zirconium atom. In contrast to the —SiMe2— bridged analogs, the —SiMe2CH2— linked amido-fluorenyl complex 4 features a relatively unstrained ligand backbone with a close to ideal trigonal planar geometry at the amido nitrogen atom.
A seawater filtration method suitable for total dissolved inorganic carbon and pH analyses

High biomass and heavy particle loads may interfere with carbonate chemistry analyses of samples from experimental aquaria and cultures used to investigate the impact of ocean acidification on organisms, as well as from biologically productive coastal regions. For such samples, a filtration method is needed that does not change the dissolved CO2 content, and consequently does not alter the total dissolved inorganic carbon and pH of the sample. Here, a filtration method is presented in which the sample seawater is pumped by a peristaltic pump through a replaceable 0.45 µm filter in a 50 mm polycarbonate filter holder and then into the sample bottle. Seawater samples of known carbonate composition were filtered to confirm that the filtration method did not alter the CO2 content, and compromise the subsequent sample analysis and data usefulness. Seawater samples with added phytoplankton concentrations in the range of 1–5 × 105 cells mL−1 were also filtered successfully. Finally, seawater with added biogenic CaCO3 was tested to prove that the method could successfully filter out such particles and produce dependable results. This approach will help to ensure more consistent and reliable carbonate chemistry measurements in coastal environments and from ocean acidification aquaria and cultures, by providing a well-tested method for sample filtration.
Assessing Cumulative Evidence within ‘Macro’ Research: Why Meta-Analysis Should be Preferred Over Vote Counting

Understanding the conclusions a body of evidence offers involves accumulating findings. Two recent articles used vote counting to assess the evidence related to important macro theories: transaction cost theory and resource-based theory. Each concluded that its focal theory is not well supported. In contrast, recent meta-analyses of the same theories concluded that both are strongly supported. We explain why macro researchers should trust the findings of meta-analyses but not those of vote counts. A direct implication is that researchers interested in advancing transaction cost and resource-based theories need to build upon the meta-analytic evidence. A broader implication is that, as the preferred method for accumulating evidence, meta-analysis can be a catalyst for the re-evaluation of established theories and the development of new theory.