cssi/SciSciGPT-SciSciNet huggingface dataset:
The effects of internal and external competition on innovation breadth

Abstract Prior research shows that increasing the breadth of elements used to create a firm's innovations can improve its ability to successfully introduce innovations. Yet, our understanding of the antecedents of innovation breadth is limited. This study investigates how competition affects product managers' decision to expand the breadth of elements used to create an innovation. I build on the awareness–motivation–capability (AMC) framework to propose that inter-firm competition from rivals' innovations and intra-firm competition from a firm's own innovations both create pressures for product managers to increase innovation breadth, but that the greater awareness and motivation resulting from internal competition will lead managers to increase innovation breadth more in response to intra-firm competition. I find support for these propositions based on a longitudinal examination of mutual fund innovations. This study offers contributions by developing theory about how competition shapes managers' decision to expand the diversity of elements used to develop an innovation.
Redrawing the Criminal-Civil Boundary

Introduction The Problem 681 I. The Criminal-Civil Divide and its Legal and Social Collapse....... 687 II. A Brief History and Criticism of the Supreme Court's Responses ...694 A. The 1880s to the 1980s 694 B. A Brief Experiment with Hybrid Actions 697 C. A Hasty Retreat 700 III. The Potential Legislative and Procedural Ramifications of an All-or-Nothing Approach.........709 Conclusion A Compromise 719
Computerized Kinetic Modeling: A New Tool in the Quest for Adequacy in Peritoneal Dialysis:

Until recently, kinetic modeling of peritoneal dialysis (PD) was performed by engineers, scientists, or nephrologists at major teaching institutions. Now there are several “user-friendly” computer ...
Case records of the Massachusetts General Hospital. Case 27-2005. An 80-year-old man with fatigue, unsteady gait, and confusion.

An 80-year-old man had an abrupt onset of difficulty concentrating, followed by severe fatigue, insomnia, and unsteadiness. An evaluation revealed no evidence of infection, autoimmune diseases, or exposure to toxins. His cognitive function declined markedly over two months, and myoclonus and fasciculations developed. He became progressively obtunded and died.
Chemotherapy as an Adjuvant to Cystectomy and for Advanced Urothelial Cancer

SUMMARY The future needs in this area appear to be continued systematic research. The most immediate research needs include the following: (1) the identification of new drug agents with activity in experimental systems and initiation of subsequent Phase I and II studies; (2) increased numbers of drug trials with established single agents to define more clearly those with activity; (3) continuing combination studies incorporating single agents with definite antitumor activity; (4) prospective randomized evaluations comparing combinations of the more active single agents to see whether the enhancement of antitumor effect is significant with multi-drug regimens; and (5) continued research into incorporation of systemic therapy into combined modality approaches to the primary therapy of bladder cancer in the context of randomized trials employing large numbers of patients. 12
Adaptation to low-K+ media increases H(+)-K(+)-ATPase but not H(+)-ATPase-mediated pHi recovery in OMCD1 cells

Studies in rat and rabbit outer medullary collecting duct of inner stripe origin (OMCDis) suggest that both H(+)-ATPase and H(+)-K(+)-ATPase participate in H+ secretion. However, the relative contr...
Teaching NeuroImages: Noninfectious cyst as an unusual complication of deep brain stimulation

A 73-year-old woman with essential tremor complained of cognitive difficulties, right-sided weakness, and balance problems 3 months after bilateral deep brain stimulation (DBS) surgery. MRI brain showed a cyst adjacent to the DBS electrode on the left side along with vasogenic edema (figure 1). CSF and blood studies did not demonstrate any evidence of infection. Dexamethasone initiation led to a gradual improvement in symptoms and resolution of edema (figure 2).
Expression and Function of the CXCR7 Chemokine Receptor in Leukemias

Abstract Background: Bone marrow produced stromal-derived factor-1a (SDF-1a) is a key chemokine involved in chemotaxis, homing, mobilization, and expansion of hematopoietic stem and progenitor cells. While the majority of well-defined functions of SDF-1a are mediated via its receptor CXCR4, recent studies have characterized CXCR7 as an alternative receptor capable of binding SDF-1a. Although the functions of CXCR7 are still incompletely understood, the receptor was reported to promote migration and adhesion in certain cell types and function as a pro-survival factor in breast cancer cells. CXCR7 expression and function in human leukemia cells has not been characterized. In this study, we examined CXCR7 expression in leukemia cell lines and primary samples from patients with acute lymphoblastic leukemia (ALL) and utilized a small molecule inhibitor of CXCR7 to probe CXCR7's function. Materials and methods: CXCR4 and CXCR7 expression was determined by flow cytometry, real-time PCR (RT-PCR) and immunocytochemistry (ICC) in leukemic cell lines including AML (OCI-AML2, OCI-AML3, HL60, U937 NB4, Molm13), ALL (REH, Raji, RS4; 11, Nalm6, Molt4) and CML (KBM5, K562) cells. In primary ALL patient samples, CD34+CD19+ gating was applied to detect CXCR7 expression on pre-B leukemic cells by flow cytometry. The migration of leukemic cells towards SDF-1a was studied using a transwell system. CXCR4 inhibitor AMD3100 was purchased from Sigma, and CXCR7 inhibitor CCX-733 was provided by ChemoCentryx Inc., Mountain View, CA. Results: CXCR4 was found to be ubiquitously expressed on the cell surface of all leukemic cell lines tested. CXCR7 mRNA and protein expression was detectable only in Burkitt lymphoma Raji cells, as analyzed by flow cytometry (clone 11G8, RD11 (CXCR7 negative) cells. AMD3100 at 25μM significantly inhibited SDF-1a induced migration (from 38.5% to 12%); CCR733 at 10μM also inhibited SDF-1a induced migration (from 38.5% to 24%) and the combination of AMD3100 and CCR733 resulted in 81% inhibition of migration (from 38.5% to 7.2%). AMD3100 blocked SDF-1a induced migration of CXCR4+CXCR7− RS4;11 cells (from 36.5% to 15.8%), while CCR733 had no effect (36.5% and 39.2%). In conclusion, these studies demonstrate functional expression of the SDF-1 receptor CXCR-7 on Raji and primary ALL cells and suggest that CXCR7 plays an active role in the migration of leukemic cells. CXCR-7 may serve as an alternative receptor to CXCR4. Studies addressing the role of CXCR7 in adhesion, SDF-1a-mediated signaling and survival of leukemic cells are in progress.
Abstract 3310: Targeting MUC1-mediated metabolism sensitizes pancreatic cancer cells to radiation therapy

Overexpression of MUC1 promotes growth promoting metabolic alterations in pancreatic cancer cells. We investigated the role played by MUC1-mediated metabolic alterations in radiation response of pancreatic cancer cells. Our findings indicate that cell survival and clonogenicity of pancreatic cancer cells upon radiation treatment correlate with MUC1 expression. MUC1 expression reduced radiation-induced reactive oxygen species (ROS) production and DNA damage, whereas, increased glucose uptake and lactate secretion upon irradiation. Metabolomic analysis through liquid chromatography-coupled tandem mass spectrometry approach revealed that pancreatic cancer cells exhibit spontaneous metabolic alterations upon irradiation. MUC1 expression further altered radiation-induced carbon flux especially in glycolysis and pentose phosphate pathway. We further investigated radiation-sensitization of MUC1-expressing cells by targeting glycolysis or pentose phosphate pathway using metabolic inhibitors, and observed that pre-treatment with 3-bromopyruvate (BrPA) effectively abrogates MUC1-mediated radiation-resistance by elevating ROS and DNA damage. BrPA treatment also reduced MUC1-induced carbon flux into glycolysis and pentose phosphate pathway, upon irradiation. Hence, our findings demonstrate that MUC1-mediated radiation-resistance in pancreatic cancer cells can be effectively targeted through inhibition of glycolysis. Citation Format: Venugopal Gunda, Jaime Abrego, Surendra K. Shukla, Nina V. Chaika, Fang Yu, Tadayoshi Bessho, Chi Lin, Pankaj K. Singh. Targeting MUC1-mediated metabolism sensitizes pancreatic cancer cells to radiation therapy. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3310. doi:10.1158/1538-7445.AM2015-3310
Subpectoral Implantation of Internal Pulse Generators for Deep Brain Stimulation: Technical Note for Improved Cosmetic Outcomes

Background Deep brain stimulation is increasingly used to treat a variety of disorders. As the prevalence of this technology increases, greater demands are placed on neurosurgical practitioners to improve cosmetic results, maximize patient comfort, and minimize complication rates. We have increasingly employed subpectoral implantation of internal pulse generators (IPGs) to improve patient satisfaction. Objective To determine the complication rates of subpectorally placed IPGs as compared to those placed in a subcutaneous location. Methods We reviewed a series of 301 patients from a single institution. Complication rates including infection, hematoma, and lead fracture were recorded. Rates were compared for subcutaneously and subpectorally located devices. Results Of the records reviewed, we found 301 patients who underwent 308 procedures for initial IPG implantation. Of these, 275 were subpectoral IPG implantation, 19 were infraclavicular subcutaneous implantation, and 14 were subcutaneous implantation in the abdomen. A total of 6 IPG pocket infections occurred, 2 subpectoral and 4 infraclavicular subcutaneous. Of the IPG infections, 2 of the infraclavicular subcutaneous devices had associated erosions. Two patients had their devices relocated from a subpectoral pocket to a subcutaneous pocket in the abdomen due to discomfort. Two patients in the subpectoral group suffered from hematoma requiring evacuation. Two patients in the infraclavicular subcutaneous group had lead fracture occur. Conclusions Subpectoral implantation of deep brain stimulation IPGs is a viable alternative with a low complication rate. This technique may offer a lower rate of infection and wound erosion.
The Lived Experiences of Retired Collegiate Athletes With a History of 1 or More Concussions.

Context: Concussions remain misunderstood, underreported, and undiagnosed. Although most concussion symptoms resolve within 2 weeks, some patients experience persistent symptoms that adversely aff...
Ecological significance of mitochondrial toxicants.

Abstract Mitochondrial dysfunction with exposure to anthropogenic contaminants is a critical concern in biomedical and ecological health. Importantly, understanding the role of mitotoxicants in modulating organismal fitness and survival, particularly in the context of species’ resilience to shifts in abiotic factors with climate change, is emerging as a key consideration. To date, only a few studies have focused on effects of mitotoxicants on organismal responses to additional abiotic stressors ( e.g. , shifts in temperature, levels of oxygen, and salinity); however, these serve to demonstrate that chemical exposure could alter stress responses. Here a theoretical framework is presented to integrate mitochondrial dysfunction into organismal response to additional stressors, highlighting the importance of sustaining the capacity to conserve or regenerate a healthy population of mitochondria, i.e. , maintaining mitochondrial plasticity, in a multi-stressor environment. The complexity of mitochondria-associated processes and impact of mitotoxicants in the context of shifts in fate and transport of anthropogenic chemicals with climate change are also considered. Considering the crucial role of mitochondria in multi-stressor environments and their vulnerability to physical and chemical stressors, this review proposes the use of mitochondrial function as a physiological marker of species resilience to environmental change. Finally, impacts of contaminants on mitochondrial health of wildlife are important in their own right, but the potential use of these studies, especially mitochondrial DNA analyses, to inform long-term impacts of chemicals on mitochondria in a human health context is also discussed.
Development of a simulation model for pedestrian evacuation under fire condition

Understanding pedestrian behavior under emergency conditions is critical for emergency preparedness. However, the high cost associated with field experiments limited the opportunities for exploring large-scale pedestrian behavior under various emergency scenarios. As an alternative, pedestrian modeling and simulation has become increasingly important in emergency studies. An efficient and valid simulation model that can facilitate the analyses and tests of different emergency management plans is still needed. Thus, this study aims to develop an improved simulation model for analyzing pedestrian movement under fire evacuation. The proposed model was built upon conventional social force model but with extended module addressing pedestrian behavior changes. The model was incorporated in simulation under Unity context and verified from different aspects. The proposed model was then applied to a fire evacuation experiment. Comparative experiments were conducted and the simulation results suggest that the proposed model is more appropriate for simulating pedestrian behavior under fire evacuation.
Device Thrombosis After Percutaneous Left Atrial Appendage Occlusion Is Related to Patient and Procedural Characteristics but Not to Duration of Postimplantation Dual Antiplatelet Therapy

Background— Device-related thrombus (DRT) after left atrial appendage occlusion is a worrisome finding with little knowledge about when to expect it and how to prevent it. This study sought to investigate correlates of DRT after left atrial appendage occlusion, its time of diagnosis, and particularly, association with postimplantation dual antiplatelet therapy duration. Methods and Results— Consecutive patients (n=102) after left atrial appendage occlusion with AMPLATZER Cardiac Plug/Amulet (n=59) or WATCHMAN (n=43) were included in a prospective registry (October 2011–May 2016). Follow-up was done at 1.5, 3 to 6, and 12 months postimplantation. DRT was classified as early (at 1.5 month), late (at 3–6 month), or very late (at 12-month follow-up). Postimplantation dual antiplatelet therapy was recommended for 30 to 180 days and decided independently by attending physicians. Final analysis included 99 patients, 42 (42.4%) females, with median CHA 2 DS 2 -VASc of 4.0 (interquartile range [IQR], 3.0–5.0) and median HAS-BLED score of 2.0 (IQR, 1.0–3.0). DRTs were observed in 7 (7.1%) patients: 2 (28.6%) early, 2 (28.6%) late, and 3 (42.9%) very late. When compared with patients without DRT, those with DRT presented more often with a history of prior thromboembolism (5 [71.4%] versus 28 [30.4%]; P =0.04), had lower left ventricular ejection fraction (50.0 [IQR, 35.0–55.0] versus 60.0 [IQR, 55.0–66.0]; P P =0.04) and with larger devices implanted (30.0 mm [IQR, 27.0–33.0] versus 25.0 mm [IQR, 24.0–28.0]; P P =0.77). Conclusions— In this real-world series, DRT was observed early, late, and very late after left atrial appendage occlusion. It was related to patient and procedural characteristics but not to postimplantation dual antiplatelet therapy duration.
FOXP3+ Treg as a therapeutic target for promoting anti-tumor immunity

Introduction: Regulatory T cells (Treg) characterized by expression of FOXP3 and strong immunosuppressive activity play a key role in regulating homeostasis in health and disease.Areas covered: Hum...
Digital Data-Centric Geography: Implications for Geography's Frontier

The debate regarding geographic information systems (GIS) as tool, toolbox, or science still lingers in geography departments and among geographers. Analysis of geographic information is a vital co...
Simian herpesviruses and neoplasia.

Publisher Summary The chapter focuses on simian herpesviruses and the role these viruses play in neoplasia. It describes several simian herpesviruses, along with summarizing data related to this. It compares the oncogenic simian herpesviruses with Epstein-Barr virus (EBV), along with providing additional, indirect evidence for a causal relationship between EBV and some lymphomas in man. The studies of simian oncogenic herpesviruses have led to renewed efforts to transform lymphocytes from animals of the species susceptible to tumor induction by Herpesvirus saimiri (HVS) or Herpesvirus ateles (HVA) with EBV, and to induce lymphomas in some of the same animals. The great importance of nonhuman primate model systems is stated in the chapter for the opportunities they offer in studying the pathogenetic mechanisms of lymphoproliferative diseases induced by herpesviruses. Further use of these models for vaccination and therapeutic studies may lead to the control of these diseases in man.
MarTurtSI, a global database of stable isotope analyses of marine turtles

Marine turtles are both flagship species of conservation concern and indicators of ocean health. As highly migratory species, and despite substantial research effort focusing on nesting females and satellite tagging studies, we still know little about the trophic ecology and habitat use of immature stages and males. Consequently, marine turtle biologists began using stable isotope analyses in the last decade to elucidate various aspects of trophic ecology, including habitat use and trophic position. This has resulted in a burgeoning but largely disconnected literature of mostly single-species case studies. Here we comprehensively synthesize this body of work into a unified data repository, the MarTurtSI database. MarTurtSI contains stable isotope data from six of seven marine turtle species ranging from juveniles to adults, in different developmental, feeding, and breeding habitats across multiple ocean basins. MarTurtSI will be curated and updated with the aim of enabling continued comprehensive and global investigations into the trophic ecology of marine turtles especially in the face of climate change and other conservation challenges.
Role of Stress in Predisposing Trees to Insect Colonization: Implications for Plant Health Care

Abstract Plant health care is a program of preventive maintenance, based on the use of cultural, biological and chemical tactics, to enhance plant appearance, structure and vitality. Trees planted in the urban landscape are considered to be stressed and predisposed to successful colonization by many insects. This presumption that there is a simple index between vitality and stress, and that stressed trees are predisposed to colonization, may not always be true. The relationship between tree vitality and susceptibility to insect attack is highly complex. Tree susceptibility to insect colonization does not increase continuously with stress. Recent studies have indicated that mild stress may improve tree defenses and that a plant health care strategy aimed at maintaining rapid tree growth may not reduce susceptibility to insects. Extension specialists and researchers need to focus their efforts on understanding tree defense strategies and developing cultural recommendations aimed at improving defenses rather...
New Trends and Perspectives in Melatonin Research

ABSTRACT This presentation summarizes available information on the effects of environmental lighting and other factors on melatonin synthesis and secretion; it also comments on the possible physiologic roles of melatonin.
Physiologically‐Based Pharmacokinetic Modeling Approach to Predict Rifampin‐Mediated Intestinal P‐Glycoprotein Induction

Physiologically-based pharmacokinetic (PBPK) modeling is a powerful tool to quantitatively describe drug disposition profiles in vivo, thereby providing an alternative to predict drug-drug interactions (DDIs) that have not been tested clinically. This study aimed to predict effects of rifampin-mediated intestinal P-glycoprotein (Pgp) induction on pharmacokinetics of Pgp substrates via PBPK modeling. First, we selected four Pgp substrates (digoxin, talinolol, quinidine, and dabigatran etexilate) to derive in vitro to in vivo scaling factors for intestinal Pgp kinetics. Assuming unbound Michaelis-Menten constant (Km ) to be intrinsic, we focused on the scaling factors for maximal efflux rate (Jmax ) to adequately recover clinically observed results. Next, we predicted rifampin-mediated fold increases in intestinal Pgp abundances to reasonably recover clinically observed DDI results. The modeling results suggested that threefold to fourfold increases in intestinal Pgp abundances could sufficiently reproduce the DDI results of these Pgp substrates with rifampin. Hence, the obtained fold increases can potentially be applicable to DDI prediction with other Pgp substrates.
Surgical pericardial drainage procedures have a limited diagnostic sensitivity

Purpose Cardiothoracic surgeons are frequently called upon to perform surgical pericardial drainage procedures (pericardial window) for pericardial effusions. These procedures have therapeutic value, but the diagnostic value of such procedures is debated. We set out to determine the sensitivity of pericardial drainage to detect the disease when cytology, microbiology, and pathology are evaluated. Methods A retrospective chart review of patients who underwent pericardial windows from 1 July 2011 to 1 January 2018 at a single academic institution was conducted. All patients who had undergone a recent trauma or cardiac procedure were excluded. Cytology, microbiology, and pathology were examined. The charts were then carefully reviewed to determine if a clinical diagnosis was reached. Sensitivity was then calculated for all diseases and for those that should have been able to be detected. Results One hundred sixty-two patients who had undergone a pericardial drainage procedure were identified; 49 patients were excluded for recent cardiac procedure or trauma. Of the 113 patients who met our inclusion criteria, 56 patients (49.6%) were female with a mean age of 59.7 ± 15.1 years. A diagnosis based on the pathology, microbiology, or cytology was obtained for 27 patients. The most common pathologies detected were adenocarcinoma (11), bacteremia (9), and small cell lung cancer (3); 56 patients had underlying pathologies that would have been possible to detect with either pathology, microbiology, or cytology. The most common detectable diagnoses were adenocarcinoma (20), bacteremia (12), and lymphoma (7). The most common undetectable diagnoses were idiopathic (17), cardiorenal fluid overload (17), and viral (11). The sensitivity of a pericardial drainage procedure for detecting disease was 0.24 for all cases, and 0.48 when restricted to cases where a detectable disease was present. Conclusion Cytology, microbiology, and pathology for pericardial drainage procedures were unable to detect a diagnosis for 76% of all cases and greater than 50% of cases with the theoretically detectable disease. Pericardial drainage procedures have a clear therapeutic value, but they have limited diagnostic utility.
Identification of environmental drivers in urban greenway communities

Abstract Urban trails and greenspaces have become ubiquitous features in cities, in part due to their ability to provide ecological benefits to the built-up environment. A major factor in their popularity is their potential to enhance habitat connectivity by bridging the gaps between remnant patches across urbanized areas, however, information on the structure and function of greenways themselves is limited. In this study we examined how greenways serve as distinct habitats in their own right by characterizing the vegetative structure of the Capital Area Greenway (CAG) in Raleigh, NC. We conducted a systematic vegetation survey of woody vegetation along 39 km of trails (354 random plots) in 2016 and identified environmental variables related to site conditions (percent canopy cover, stream proximity, flood zones), management efforts (designated conservation areas), and local anthropogenic activities (percent impervious surface, street proximity). We preformed three types of multivariate analyses (non-metric multidimensional scaling (NMS), multi-response permutation procedures (MRPP), and indicator species analysis (ISA)) to distinguish potential influences on species distribution and community structure. We observed highly diverse riparian, upland mesic, and xeric forest communities within the CAG. Results from NMS and MRPP suggested that vegetation patterns can be differentiated based on local environmental variables. Sites located in conservation areas and floodplains, for instance, were typically found at further distances from streets and were characterized by greater basal area, canopy cover, and higher non-native species richness. Individual study sites were highly diverse and varied even within similar local environments. Our findings indicate that the CAG serves as established natural habitat for native vegetation, supporting the idea that greenways can be used to enhance environmental quality in cities as ecological corridors.
Comment: The Challenges of Multiple Causes

We begin by congratulating Yixin Wang and David Blei for their thought-provoking article that opens up a new research frontier in the field of causal inference. The authors directly tackle the chal...
Evolutionary signal in the gut microbiomes of 74 bird species from Equatorial Guinea

How the microbiome interacts with hosts across evolutionary time is poorly understood. Data sets including many host species are required to conduct comparative analyses. Here, we analyzed 142 intestinal microbiome samples from 92 birds belonging to 74 species from Equatorial Guinea, using the 16S rRNA gene. Using four definitions for microbial taxonomic units (97%OTU, 99%OTU, 99%OTU with singletons removed, ASV), we conducted alpha and beta diversity analyses. We found that raw abundances and diversity varied between the data sets but relative patterns were largely consistent across data sets. Host taxonomy, diet and locality were significantly associated with microbiomes, at generally similar levels using three distance metrics. Phylogenetic comparative methods assessed the evolutionary relationship between the microbiome as a trait of a host species and the underlying bird phylogeny. Using multiple ways of defining "microbiome traits", we found that a neutral Brownian motion model did not explain variation in microbiomes. Instead, we found a White Noise model (indicating little phylogenetic signal), was most likely. There was some support for the Ornstein-Uhlenbeck model (that invokes selection), but the level of support was similar to that of a White Noise simulation, further supporting the White Noise model as the best explanation for the evolution of the microbiome as a trait of avian hosts. Our study demonstrated that both environment and evolution play a role in the gut microbiome and the relationship does not follow a neutral model; these biological results are qualitatively robust to analytical choices.
Simultaneously Targeting the NS3 Protease and Helicase Activities for More Effective Hepatitis C Virus Therapy

This study examines the specificity and mechanism of action of a recently reported hepatitis C virus (HCV) nonstructural protein 3 (NS3) helicase–protease inhibitor (HPI), and the interaction of HPI with the NS3 protease inhibitors telaprevir, boceprevir, danoprevir, and grazoprevir. HPI most effectively reduced cellular levels of subgenomic genotype 4a replicons, followed by genotypes 3a and 1b replicons. HPI had no effect on HCV genotype 2a or dengue virus replicon levels. Resistance evolved more slowly to HPI than telaprevir, and HPI inhibited telaprevir-resistant replicons. Molecular modeling and analysis of the ability of HPI to inhibit peptide hydrolysis catalyzed by a variety of wildtype and mutant NS3 proteins suggested that HPI forms a bridge between the NS3 RNA-binding cleft and an allosteric site previously shown to bind other protease inhibitors. In most combinations, the antiviral effect of HPI was additive with telaprevir and boceprevir, minor synergy was observed with danoprevir, and modest...
Extracting chemical reactions from text using Snorkel

Enzymatic and chemical reactions are key for understanding biological processes in cells. Curated databases of chemical reactions exist but these databases struggle to keep up with the exponential growth of the biomedical literature. Conventional text mining pipelines provide tools to automatically extract entities and relationships from the scientific literature, and partially replace expert curation, but such machine learning frameworks often require a large amount of labeled training data and thus lack scalability for both larger document corpora and new relationship types. We developed an application of Snorkel, a weakly supervised learning framework, for extracting chemical reaction relationships from biomedical literature abstracts. For this work, we defined a chemical reaction relationship as the transformation of chemical A to chemical B. We built and evaluated our system on small annotated sets of chemical reaction relationships from two corpora: curated bacteria-related abstracts from the MetaCyc database (MetaCyc_Corpus) and a more general set of abstracts annotated with MeSH (Medical Subject Headings) term Bacteria (Bacteria_Corpus; a superset of MetaCyc_Corpus). For the MetaCyc_Corpus, we obtained 84% precision and 41% recall (55% F1 score). Extending to the more general Bacteria_Corpus decreased precision to 62% with only a four-point drop in recall to 37% (46% F1 score). Overall, the Bacteria_Corpus contained two orders of magnitude more candidate chemical reaction relationships (nine million candidates vs 68,0000 candidates) and had a larger class imbalance (2.5% positives vs 5% positives) as compared to the MetaCyc_Corpus. In total, we extracted 6871 chemical reaction relationships from nine million candidates in the Bacteria_Corpus. With this work, we built a database of chemical reaction relationships from almost 900,000 scientific abstracts without a large training set of labeled annotations. Further, we showed the generalizability of our initial application built on MetaCyc documents enriched with chemical reactions to a general set of articles related to bacteria.
In Memoriam David Lawrence Atherton 1935–2020

David Lawrence Atherton, Fellow of the Royal Society of Canada, Emeritus Professor of Physics and Computer Engineering at Queen’s University, passed away peacefully on 18 March 2020 at his home, Silverstone Farm on Sydenham Lake, north of Kingston, Ontario, Canada. He is survived by Joanna (nee Banham) his beloved wife and companion of 58 years, his two much loved daughters, Tamsin and Heather, and his brothers, Richard in Derbyshire, England, and Charles in Athens, Greece. He will be missed as the cherished grandfather of Caden, Serena, and Jude.
Emerging trends in biomedical imaging and disease diagnosis using Raman spectroscopy

Abstract The chapter discusses emerging applications of Raman spectroscopy in the areas of biomedical imaging of cells and tissues with the ultimate goal of clinical translation for disease diagnosis. The technological developments in lasers, detectors, and fiber optics during the last few decades have enabled identification of subtle molecular differences driving pathological transformations using Raman spectroscopy. The ex vivo studies conducted to examine biofluids, mineralized tissues, and solid tumors that demonstrated the initial feasibility of harnessing the specificity of Raman data for clinical diagnosis have been presented. Next, the resultant early in vivo studies conducted with the goal of establishing Raman spectroscopy as a real-time tool for intraoperative surgical margin assessment and endoscopic diagnosis have been reviewed. In addition, emerging preclinical studies for characterizing metastatic progression of cancer and response to therapy have been discussed. Finally, the biomedical applications enabled by integration of this spectroscopic modality with microscopy and incorporation of nanomaterials for surface selective electromagnetic enhancement of Raman signal have been briefly reviewed.
Vaccine Efficacy Needed for a COVID-19 Coronavirus Vaccine to Prevent or Stop an Epidemic as the Sole Intervention.

Introduction Given the continuing COVID-19 pandemic and much of the U.S. implementing social distancing owing to the lack of alternatives, there has been a push to develop a vaccine to eliminate the need for social distancing. Methods In 2020, the team developed a computational model of the U.S. simulating the spread of COVID-19 coronavirus and vaccination. Results Simulation experiments revealed that to prevent an epidemic (reduce the peak by >99%), the vaccine efficacy has to be at least 60% when vaccination coverage is 100% (reproduction number=2.5–3.5). This vaccine efficacy threshold rises to 70% when coverage drops to 75% and up to 80% when coverage drops to 60% when reproduction number is 2.5, rising to 80% when coverage drops to 75% when the reproduction number is 3.5. To extinguish an ongoing epidemic, the vaccine efficacy has to be at least 60% when coverage is 100% and at least 80% when coverage drops to 75% to reduce the peak by 85%–86%, 61%–62%, and 32% when vaccination occurs after 5%, 15%, and 30% of the population, respectively, have already been exposed to COVID-19 coronavirus. A vaccine with an efficacy between 60% and 80% could still obviate the need for other measures under certain circumstances such as much higher, and in some cases, potentially unachievable, vaccination coverages. Conclusions This study found that the vaccine has to have an efficacy of at least 70% to prevent an epidemic and of at least 80% to largely extinguish an epidemic without any other measures (e.g., social distancing).
Graded multifunctional piezoelectric metastructures for wideband vibration attenuation and energy harvesting

Unlike well-studied locally resonant (LR) metamaterials with a periodic array of identical resonators, "graded" LR metamaterials consist of an array of resonators with a spatially varying parameter, yielding wideband wave attenuation and mode trapping/localization, among other features. In this work, we explore a graded LR piezoelectric metamaterial-based structure (i.e. metastructure) in which the grading parameter, namely the inductive shunt resonant frequency of the unit cells, follows a predefined variation pattern in space (e.g. first-order, quadratic, or fractional). We investigate the effect of such patterns on (i) the vibration attenuation bandwidth, (ii) the localization of vibration modes, and (iii) the harvested power. To this end, we consider a piezoelectric bimorph cantilever hosting an array of piezoelectric unit cells with spatially varying inductive shunts. Fully coupled electromechanical equations describing the metastructure's linear transverse displacement and unit cell voltages are given with a modal analysis framework and solved using the matrix inversion method. The results show that (i) the first-order grading pattern yields the widest bandgap with 65% increase in the bandwidth compared to the standard uniform LR pattern, (ii) the localization of vibration modes follows in shape the corresponding frequency grading pattern, and (iii) the largest power is harvested for the fractional grading pattern. Furthermore, all of the graded resonator configurations result in wider bandwidth in energy harvesting as compared to the uniform resonators case. Overall, the results unveil the fundamental characteristics of this class of graded piezoelectric metastructures and support the design of such multifunctional piezoelectric metastructures for concurrent vibration attenuation and energy harvesting.
Genome-wide detection of short tandem repeat expansions by long-read sequencing

Short tandem repeat (STR), or “microsatellite”, is a tract of DNA in which a specific motif (typically < 10 base pairs) is repeated multiple times. STRs are abundant throughout the human genome, and specific repeat expansions may be associated with human diseases. Long-read sequencing coupled with bioinformatics tools enables the estimation of repeat counts for STRs. However, with the exception of a few well-known disease-relevant STRs, normal ranges of repeat counts for most STRs in human populations are not well known, preventing the prioritization of STRs that may be associated with human diseases. In this study, we extend a computational tool RepeatHMM to infer normal ranges of 432,604 STRs using 21 long-read sequencing datasets on human genomes, and build a genomic-scale database called RepeatHMM-DB with normal repeat ranges for these STRs. Evaluation on 13 well-known repeats show that the inferred repeat ranges provide good estimation to repeat ranges reported in literature from population-scale studies. This database, together with a repeat expansion estimation tool such as RepeatHMM, enables genomic-scale scanning of repeat regions in newly sequenced genomes to identify disease-relevant repeat expansions. As a case study of using RepeatHMM-DB, we evaluate the CAG repeats of ATXN3 for 20 patients with spinocerebellar ataxia type 3 (SCA3) and 5 unaffected individuals, and correctly classify each individual. In summary, RepeatHMM-DB can facilitate prioritization and identification of disease-relevant STRs from whole-genome long-read sequencing data on patients with undiagnosed diseases. RepeatHMM-DB is incorporated into RepeatHMM and is available at https://github.com/WGLab/RepeatHMM .
Cross-Study, Cross-Method Associations Between Negative Urgency and Internalizing Symptoms:

There is a small body of research that has connected individual differences in negative urgency, the tendency to report rash actions in response to negative emotions, with self-report depressive an...
Optimization of Glaucoma Management During a Pandemic: Drive-Through IOP Checks

Purpose : In this pilot study, we compared the efficacy of drive-through intraocular pressure (IOP) checks in combination with E-health visits to E-health visits alone in the management of glaucoma patients during the COVID-19 pandemic. Methods : We performed a retrospective chart review for visits from April 2020 - November 2020 to compare subjects that received E-health visits (Group 1) versus subjects that received E-health visits with a drive-through IOP check (Group 2). Drive-through visits consisted of temperature screening with a non-contact infrared thermometer, near visual acuity check, and IOP measurements using a Tono-Pen XL Tonometer (Reichert, Depew, NY) followed by a video E-health visit with a glaucoma specialist. Group 1 patients only attended a video visit. We compared the proportion of interventions done at the visit as well as changes in visual acuity (VA) and IOP after the tele-visits between the 2 groups. The 4 types of interventions were: change in drop type, change in drop frequency, change in number of drops, and recommending surgical or laser intervention. Results : 28 subjects were included in our pilot study (mean age 74.9 +/- 3.8 years, 57.1% female). There was no significant difference in baseline characteristics between group 1 (n=15) and group 2 (n=13, Table 1). 6.7% of Group 1 patients had an intervention done compared to 38.5% of group 2 patients. Fisher exact probability testing showed a significant increase in the proportion of interventions done in group 2 subjects compared to group 1 subjects (p=.041), with the most common interventions being changing number of drops and drop frequency. There was no significant difference in changes in VA or IOP between the 2 groups (Table 1). Conclusions : Drive-through IOP checks in combination with virtual visits resulted in more interventions than virtual visits alone in the care of glaucoma patients during the COVID-19 pandemic. This novel healthcare modality can address the mismatch between capacity and demand for glaucoma care both during a pandemic and can further expand access to sub-specialized care.
Mass violence and the self: from the French wars of religion to the Paris Commune

At the time of writing this review, Israel and Hamas are entering the second week of fighting. The popular video-sharing social networking service, TikTok, played a critical role in the outbreak of...
Linear equations in subspaces of operators

Given a subspace S of operators on a Hilbert space, and given two operators X and Y (not necessarily in S), when can we be certain that there is an operator A in S such that AX = Y ? If there is one, can we find some bound for its norm? These questions are the subject of a number of papers, some by the present authors, and mostly restricted to the case where S is a reflexive algebra. In this paper, we relate the broader question involving operator subspaces to the question about reflexive algebras, and we examine a new method of forming counterexamples, which simplifies certain constructions and answers an unresolved question. In particular, there is a simple set of conditions that are necessary for the existence of a solution in the reflexive algebra case; we show that — even in the case where the co-rank of X is one— these conditions are not in general sufficient. In a sequence of papers ( [2], [3], [4] ) the authors have studied the possibility of solving the operator equation AX = Y , where X and Y are given Hilbert space operators and A is an operator to be found. In those papers, the operator A is required to lie in the algebra associated with some commutative subspace lattice. Certain necessary conditions were derived in [3] for the existence of such an operator, and, in [4], we showed that those conditions are not sufficient. The construction of the counterexample in [4] was somewhat complicated, and the structure of the algebra studied there is obscure. In this paper we suggest a new way to construct counterexamples, which — on the one hand — connects the problems of finding unknown operators in CSL algebras with the problem of finding them in other operator subspaces, and — on the other — allows us to answer some unresolved questions about the sufficiency of the conditions derived in [3]. Throughout, H will represent a separable Hilbert space with inner product 〈·, ·〉; H will sometimes be finite-dimensional. A subspace is a closed linear manifold, and we will often identify the subspace with the orthogonal projection whose range it is. If L is a collection of projections (or subspaces) that is closed under the operations of meet and join, it is a lattice. If, in addition, it contains the zero and identity operators, and is closed in the strong operator topology, it is called a subspace lattice. If the projections in L all commute with each other, then L is a commutative subspace lattice, or CSL. The collection of operators that leave invariant all the projections in L is called Alg L, and it is easy to see that Alg L is a weakly closed algebra of operators. Standard terminology refers to the collection Alg L as a reflexive algebra, and — if L is a CSL — as a CSL algebra. Received by the editors April 22, 1998. 1991 Mathematics Subject Classification. Primary 47D25. c ©1999 American Mathematical Society
Laminar Boundary Layers Developed within Unsteady Expansion and Compression Waves

The paper analyzes unsteady laminar wall boundary layers formed within centered compression or expansion waves traveling into gas at rest, and also the resultant displacement effects on inviscid flow in a tube. For the boundary layer, a previous analysis by Cohen is generalized to include both compression and expansion flows and allow for wall surface temperature change as occurs with finite wall thermal conductivity. Solutions obtained by coordinate expansions show that at higher pressures the wall surface temperature change significantly reduces surface heat transfer, outweighing higher order effects of the previous analysis for wall temperature constant. For the displacement effect, the method of characteristi cs is used to obtain linearized solutions. Characteristic features of the boundary layer and its displacement effect on inviscid tube flow are compared for compression and expansion wave flows. For either type of wave, boundary-layer displacement acts to diminish the basic inviscid-flow changes produced by the wave.
Biophysically inspired development of a sand-swimming robot

Previous study of a sand-swimming lizard, the sandfish, Scincus scincus, revealed that the animal swims within granular media at speeds up to 0.4 body-lengths/cycle using body undulation (approximately a single period sinusoidal traveling wave) without limb use [1]. Inspired by this biological experiment and challenged by the absence of robotic devices with comparable subterranean locomotor abilities, we developed a numerical simulation of a robot swimming in a granular medium (modeled using a validated Molecular Dynamics technique) to guide the design of a physical sand-swimming device built with off-the-shelf servo motors. Both in simulation and experiment the robot swims limblessly subsurface and, like the animal, increases its speed by increasing its oscillation frequency. It was able to achieve speeds of up to 0.3 body-lengths/cycle. The performance of the robot measured in terms of its wave efficiency, the ratio of its forward speed to wave speed, was 0.34±0.02, within 8 % of the simulation prediction. Our work provides a validated simulation tool and a functional initial design for the development of robots that can move within yielding terrestrial substrates.
The ombudsman for research practice

We propose that institutions consider establishing a position of “Ombudsman for Research Practice”. This person would assume several roles: as asounding board to those needing confidential consultation about research issues — basic, applied or clinical; as afacilitator for those wishing to pursue a formal grievance process; and as aneducator to distribute guidelines and standards, to raise the consciousness regarding sloppy or irregular practices in order to prevent misconduct and to promote the responsible conduct of research. While there are compelling features to this position, many complex issues need to be considered and resolved. We invite readers to respond to questions we raise in the text.