cssi/SciSciGPT-SciSciNet huggingface dataset:
Do (Should) Brokers Route Standing Limit Orders Seeking to Trade U.S. Equity Options to Wholesalers

Exchange competition across U.S. options exchanges facilitates the tailoring and frequent modification of fees to attract particular order flow. We examine whether the maker-taker model or the payment for order flow (PFOF) model offers superior limit order execution quality. On the PHLX exchange, a set of select option classes recently changed pricing models from maker-taker to PFOF. We conduct difference-in-difference tests that suggest that options on stocks that change fee structures exhibit an improvement in limit order execution quality, including an increase in order fill rates, a decrease in order cancellation rates, and faster fills. We do, however, find that limit order volume, in terms of the number of orders submitted, declines following the change to PFOF pricing. Thus, our results seem to suggest that limit order traders on the PHLX exchange are made better off following the change in select options classes from maker-taker to PFOF.
Reoperative Options for Compressive Neuropathies of the Upper Extremity

In addressing failed surgery for compressive neuropathies about the arm, it is important to distinguish between what would truly be called recurrence vs. those who have a failure to improve in their symptoms. Evaluation of these patients does require some time in both obtaining a thorough history as well as performing a detailed clinical exam. Electromyographic and neural conduction velocity testing is helpful. In these cases, the surgeon needs to think both proximal and distal; that is, could the symptoms be coming from the neck or could there be areas of further compression proximally or distally about the peripheral nerve? Reoperating on previously operated nerve tissue can be quite stressful as the nerve tissue is frequently less forgiving than other soft tissue structures commonly encountered in the scar bed. The use of a microscope can sometimes be helpful in visualizing the tissue planes and/or nerve tissue. If mechanical reasons are found to explain the patient’s continued symptoms, then these points of compression can be surgically addressed if the patient is willing to accept the potential risks of nerve injury and further scarring, which sometimes precludes the patient from improving as much as both doctor and patient were hoping.
Perspectives of the Ideal Assisted Living Facilities from Depression Era Nurses

The diversity of the elderly combined with a prolonged life span means their response to changing care and health is varied. Today’s elderly population prefers to stay in their own homes. However, as their health declines they become more dependent. Their choice of housing is influenced by age, need for assistance, availability of their children, health care providers, services and facilities. One type of housing choice that has recently become popular for elderly persons is assisted living facilities. Little is known about how the rural elderly view what is important in an assisted living setting. The purpose of this qualitative study was to determine qualities of a senior living facility that retired rural elderly nurses would include in their vision of the optimal assisted living accommodations. Common themes that emerged were social environment, health and health care, diet and nutrition, exercise and recreation, social systems, and physical environment. Keywords: assisted living, rural elderly, health care, elderly housing http://dx.doi.org/10.14574/ojrnhc.v2i2.470
Development and Application of Histotripsy

Histotripsy is an experimental ablative technology conceived and developed at the University of Michigan. It uses acoustic energy generated from a piezoelectric transducer to create cavitation at a target location within the body. This unique mechanical mechanism of action is distinct when compared to conventional thermal ablative modalities. Other distinguishing features of histotripsy include its high precision, real-time monitoring and ultrasound feedback, and biologic effect of tissue liquefaction. Although histotripsy is a platform technology with a broad range of applications, much of the initial translational work was focused on BPH. During this process, enhanced understanding of cavitation bioeffects, refinement of treatment systems, and development of strategies to enhance treatment efficiency were realized and have facilitated application to other preclinical models of prostate cancer, renal masses, and renal calculi. Additionally, other non-urologic applications are also been explored at the University of Michigan and other groups across the country have started to published preclinical research studies utilizing variations of histotripsy technology. This growth in activity validates the concept of histotripsy tissue ablation and enhances the therapeutic impact of this new technology.
Cultural identity in the peri-urban African landscape: a case study from Pikine, Senegal

As African populations continue to urbanize at the highest rates worldwide, informal peri-urban landscapes have emerged in recent decades, becoming a norm throughout Africa’s cities. They continue ...
Future time perspective: Time horizons and beyond.

The articles in the present volume enhance the understanding of the role of perceived time in human development. Together, they point to the multifaceted nature of perceived future time and the associations different aspects of time have with goals, preferences, and well-being. Specifically, the articles showcase antecedents and consequences of perceived time left in life, consider ways to optimize measurement of future time horizons, and advance novel questions about the neural correlates of domain-specific aspects of subjective time. Findings are considered within the framework of socioemotional selectivity theory. Future directions for research on time horizons are discussed.
Dominance, Violence, and the Neurohormonal Nexus

Murder, the most extreme but usually unintended form of interpersonal violence, is explained as the escalation beyond normal bounds of face-to-face dominance competition. No neurohormonal substrate has been identified as a direct cause of face-to-face violence, but testosterone appears to play an indirect role, motivating dominant behavior. The relationship between testosterone and dominance is reciprocal, with elevations in the hormone as much a consequence of competition as its cause. A heightened testosterone may be especially prevalent among young men in “honor subcultures,” where threats to one’s personal reputation are ubiquitous, increasing the probability that dominance competitions, often triggered by trivial disagreements, result in tragic consequences.
Intergeneric Natural Plasmid Transformation between Escherichia coli and a Marine Vibrio Species

Because of the use of genetically engineered organisms in the environment, these has been renewed interest in transformation as a mechanism for horizontal gene transfer to the indigenous flora (Lorenz et al. 1988; Stewart and Sinigalliano 1990; Paul et al. 1991b). The potential for intergeneric, donor-mediated plasmid transfer to occur has not been widely investigated. There have been several reports of transfer of plasmid DNA from Escherichia coli cells to Bacillus subtilis (Van Randen and Venema 1984; Kosovich and Prozorov 1991). In this paper we describe the donor mediated transfer of plasmids between E. coli and Vibrio JT-1, the first report of intergeneric transformation involving a marine bacterium.
Genetic–Memetic Model of Mental Illness – Migration and Natural Disasters as Illustrations

In this chapter, we examine the differential effects of two generally accepted stressful situations – migration and natural disasters. The genetic composition of the individual interacts with the early memetic environment to predispose the individual to be stress-sensitive or stress-resistant. Another factor in this equation is the memes that the individual has absorbed in early life, memes for expressing dysphoria and memes for being “crazy,” and overarching memes that explain nature and misfortune. In the case of migration, the degree of conflict or congruence between the preexisting memes and the new meme pool of the new land would play a role, as well as the degree of support or filtering available from the submeme pool in the immigrant community playing a protective role. In natural disasters, genetic predisposition interacts with social support and perceived level of stress in the development of PTSD.
Some Functions of the Essential Trace Element, Selenium

In recent years there have been impressive increases in information concerning selenium biochemistry. After the initial discoveries that bacteria (Pinsent, 1954) and animals (Patterson et al., 1957; Schwarz and Foltz, 1957) require this trace element, almost 20 years elapsed before selenium was demonstrated to be an essential component of a mammalian enzyme, glutathione peroxidase,(Flohe et al., 1973; Rotruck et al., 1973) and a protein component of the Clostridial glycine reductase complex (Turner and Stadtman, 1973). Selenocysteine was determined to be the chemical form of selenium present in glycine reductase (Cone et al., 1976). Other prokaryotic selenoenzymes, several formate dehydrogenases (Stadtman, 1979, 1980a, 1980b, 1990 and 1996), a hydrogenase of Methanococcus vannielii (Yamazaki, 1982) and a clostridial nicotinic acid hydroxylase (Dilworth, 1982) were discovered. Mammalian glutathione peroxidase isoenzymes (Ursini et al., 1995) and selenoprotein P, a glycoprotein of unknown function, were isolated (Hill et al., 1991). Selenoprotein P is unusual in that it contains 10 selenocysteine residues in the polypeptide chain. Selenoprotein W, a 10 kDa muscle protein of unknown function was purified from normal muscle and partially characterized (Vendeland et al., 1993; Vendeland et al., 1995). The function of selenoprotein W is unknown but the occurrence of the selenocysteine residue in a Cys-x-x-Secys motif is suggestive of a redox role. The importance of selenium in mammalian physiology was magnified by the discovery of its occurrence in a 5' deiodinase that converts the prothyroid hormone, tetraiodothyronine, to the active hormone, 3,5,3'-tri-iodothyronine (Berry et al., 1991) and this established a direct role of selenium in eukaryotic developmental processes. Several years after the identification of selenocysteine in selenoproteins this unusual amino acid was shown to be inserted cotranslationally. An in-frame TGA codon was
Ending Overcriminalization and Mass Incarceration: Hope from Civil Society

Mass incarceration is an overwhelming problem and reforms are often difficult, leading to confusion about what to do and where to start. Ending Overcriminalization and Mass Incarceration: Hope from Civil Society introduces the key issues that need immediate attention and provides concrete direction about effective solutions systemically and relationally. In this work Anthony B. Bradley recognizes that offenders are persons with inherent dignity. Mass incarceration results from the systemic breakdown of criminal law procedure and broken communities. Using the principle of personalism, attention is drawn to those areas that directly contact the lives of offenders and determine their fate. Bradley explains how reform must be built from the person up, and once these areas are reformed our law enforcement culture will change for the better. Taking an innovative approach, Anthony B. Bradley explores what civic institutions need to do to prevent people from falling into the criminal justice system and recidivism for those released from prison.
Emulation of a Newborn’s Umbilical Scar

Background: Since the early ages of modern abdominoplasty, surgeons have paid special attention to the aesthetic aspects of the umbilicus. Studies have reported a variety of efforts to recreate a natural-looking belly button. This chapter presents another approach in this surgical field, which emulates the natural healing course of a newborn’s navel.
Nonlinguistic Cognitive Factors Predict Treatment-Induced Recovery in Chronic Poststroke Aphasia.

Abstract Objective To determine if pretreatment nonlinguistic cognition predicted language treatment outcomes and if so, which specific nonlinguistic cognitive subskills predicted naming therapy outcomes. Design Retrospective. Setting Research clinic. Participants Study 1 included data from 67 persons with aphasia who underwent language treatment and a pretreatment cognitive-linguistic assessment battery (N=67). Study 2 included data from 27 study 1 participants who completed additional pretreatment nonlinguistic cognitive assessments. Interventions 120-minute sessions of sentence comprehension (n=26) or naming treatment (n=41) 2 times per week for up to 10-12 weeks. Main Outcome Measures Proportion of potential maximal gain (PMG) (assessed immediately after treatment [10-12wk]; formula=mean posttreatment score–mean pretreatment score/total number of trained items–mean pretreatment score) and proportion of potential maximal gain maintained (PMGM) (assessed 12wk after posttreatment [22-24wk]; formula=mean maintenance score–mean pretreatment score/total number of trained items–mean pretreatment score) as outcome variables; and pretreatment assessment scores as predictor variables. Results In study 1, 37% of participants demonstrated nonlinguistic cognitive deficits. Principal component analyses reduced assessment data to 2 components: linguistic and nonlinguistic cognition. Backward elimination regression revealed that higher linguistic and nonlinguistic cognitive function significantly predicted higher PMG after language therapy. In study 2, principal component analysis of only the nonlinguistic cognitive measures identified 3 components: executive function, verbal short-term memory, and visual short-term memory. Controlling for pretreatment apraxia of speech and auditory comprehension deficits, regression analyses revealed that higher executive function and visual short-term memory significantly predicted higher PMG and PMGM after naming therapy. Conclusions Pretreatment nonlinguistic cognitive function significantly influenced language treatment outcomes and maintenance of therapy gains.
Aconcagua: A Novel Spatiotemporal Emotion Change Analysis Framework

In this paper, we introduce Aconcagua, a novel spatio-temporal emotion change analysis framework. Our current research uses Twitter tweets as the knowledge source for emotion analysis. The inputs for the emotion mapping and change analysis system, we are currently developing, are the location and time of the tweets and their corresponding emotion assessment score falling in the range [-1, +1], with +1 representing a very positive emotion and -1 representing a very negative emotion. We start by identifying spatial clusters that capture positive and negative emotion regions for batches of the dataset with each batch corresponding to a specific time interval, e.g. a single day. These obtained spatial clusters and their statistical summaries are then used as the input for Aconcagua which monitors change of emotions with respect to a set of unary and binary change predicates that are evaluated with respect to the set of spatial clusters; as the result of this process an emotion change graph is obtained whose nodes are spatial clusters and whose edges capture different types of temporal relationships between spatial clusters. An implementation of the change monitoring process is discussed which operates on top of a relational database and uses SQL queries to specify change predicates. To obtain more aggregated change summaries and ultimately change stories, the change graph further must be mined and summarized based on what aspects of change the analyst is interested in. To support such capabilities, our approach supports several types of change analysis templates called story types. We demo our approach using tweets collected in the state of New York in June 2014.
Independent Comparison of the Afirma Genomic Sequencing Classifier and Gene Expression Classifier for Cytologically Indeterminate Thyroid Nodules.

Background: For thyroid nodules with indeterminate cytology, the Afirma Gene Expression Classifier (GEC) identified benign nodules to reduce diagnostic surgery, though many nodules classified as su...
E-government as an anti-corruption tool: panel data analysis across countries:

Over the past two decades, many governments around the world have adopted e-government as an anti-corruption tool. However, there is a lack of empirical evidence on the impacts of e-government on c...
U.S. Food and Drug Administration Benefit‐Risk Assessment of Nilotinib Treatment Discontinuation in Patients with Chronic Phase Chronic Myeloid Leukemia in a Sustained Molecular Remission

On December 22, 2017, the U.S. Food and Drug Administration (FDA) updated the product label for nilotinib to include information for providers on how to discontinue this drug in certain patients. With the updated dosing recommendations, select patients with chronic phase myeloid leukemia (CML) taking nilotinib for 3 years or more and whose leukemia has responded with sustained molecular remission (MR4.5, BCR-ABL transcripts of ≤0.0032%) as determined by a FDA-approved test may be eligible to discontinue nilotinib. The updated dosing regimen was based on the efficacy results from two trials that measured how long patients could stop taking nilotinib without the leukemia returning (treatment-free remission). Trial results demonstrated that, among selected patients who received nilotinib as first-line therapy or after transition from imatinib, approximately 50% continued to be in remission at 96 weeks after stopping therapy. Relapses continued to occur throughout the study, indicating that long-term monitoring is needed for safety and disease monitoring. Discontinuation of treatment was associated with an increased risk of low grade musculoskeletal adverse events, some of which were prolonged. Overall, the results support the approval of updates to the dosing recommendations with regard to treatment discontinuation in selected patients who have received nilotinib for at least 3 years, are in a sustained molecular remission, and who can undergo appropriate monitoring. IMPLICATIONS FOR PRACTICE: The updated dosing information provides eligibility criteria for treatment discontinuation, strict monitoring criteria after nilotinib discontinuation, and guidance for treatment reinitiation in eligible patients with chronic phase myeloid leukemia. About half of appropriately selected patients remained in remission 96 weeks after treatment discontinuation. Patients may experience musculoskeletal pain on withdrawal of treatment, incidence of which appears to decrease over time; however, some patients may have long lasting events. The decision to withdraw or continue treatment with nilotinib should be based on clinical condition and patient preferences.
Statistical evaluation of satellite ocean color data retrievals

Abstract We develop a statistical approach to evaluate the performance of the ocean color data processing system for satellite-derived ocean color data products based on temporal stability of retrievals. We use the Multi-Sensor Level-1 to Level-2 (MSL12) ocean color data processing system to obtain the normalized water-leaving reflectance ρwN(λ) spectra from the Visible Infrared Imaging Radiometer Suite (VIIRS) measurements. The deviations of ρwN(λ) spectra from temporally and spatially averaged values are investigated, and the statistics with respect to various retrieval parameters are collected, including the solar-sensor geometry (solar-zenith, sensor-zenith, and relative azimuth angles), and various ancillary data (surface wind speed, surface atmospheric pressure, water vapor amount, and ozone concentration). The performance of MSL12 is also evaluated with respect to other intermediate retrieval parameters. The study shows that MSL12 produces statistically consistent VIIRS ocean color retrievals in the global open ocean, with respect to retrieval geometry parameters, as well as the ancillary inputs.
Kinematic analysis deconstructs the evolved loss of schooling behavior in cavefish

Fish display a remarkable diversity of social behaviors, from highly social to largely solitary. While social behaviors are likely critical for survival, surprisingly little is known about how they evolve in response to changing environmental pressures. With its highly social surface form and multiple populations of a largely asocial, blind, cave-dwelling form, the Mexican tetra, Astyanax mexicanus, provides a powerful model to study the evolution of social behavior. Given numerous morphological and behavioral differences between the surface and cave forms, a primary impediment to understanding how this behavior evolved is a lack of computational and statistical approaches that can precisely identify independent aspects of social behavior. Here, we use motion tracking and kinematic analysis to quantify social swimming patterns and argue that the absence of schooling in cavefish is not merely a consequence of their inability to see but rather a genuine behavioral adaptation that impacts the way they explore their cave environment. Surface fish school, maintaining both close proximity and alignment with each other. In the dark, surface fish no longer school, but we show that they still attempt to align and maintain proximity when they find themselves near another fish. Conversely, cavefish exhibit no preference for proximity or alignment, instead actively avoiding each other. Cavefish also slow down when more fish are present in the tank, which neither surface fish in the light or in the dark do. Using data-driven computer simulations, we show that those two traits -- active avoidance and collective slowdown -- are sufficient to shift the exploration strategy of cavefish from mostly-following-the-walls to exploring-the-entire-tank. Finally, we find that those differences in collective swimming patterns are largely consistent across independently-evolved cave populations, revealing an evolutionary convergence on this emergent social behavior.
Turbulence is an Ineffective Mixer when Schmidt Numbers Are Large

We solve the advection-diffusion equation for a stochastically stationary passive scalar $\ensuremath{\theta}$, in conjunction with forced 3D Navier-Stokes equations, using direct numerical simulations in periodic domains of various sizes, the largest being ${8192}^{3}$. The Taylor-scale Reynolds number varies in the range 140--650 and the Schmidt number $\mathrm{Sc}\ensuremath{\equiv}\ensuremath{\nu}/D$ in the range 1--512, where $\ensuremath{\nu}$ is the kinematic viscosity of the fluid and $D$ is the molecular diffusivity of $\ensuremath{\theta}$. Our results show that turbulence becomes an ineffective mixer when Sc is large. First, the mean scalar dissipation rate $⟨\ensuremath{\chi}⟩=2D⟨|\ensuremath{\nabla}\ensuremath{\theta}{|}^{2}⟩$, when suitably nondimensionalized, decreases as $1/\mathrm{log}\mathrm{Sc}$. Second, 1D cuts through the scalar field indicate increasing density of sharp fronts on larger scales, oscillating with large excursions leading to reduced mixing, and additionally suggesting weakening of scalar variance flux across the scales. The scaling exponents of the scalar structure functions in the inertial-convective range appear to saturate with respect to the moment order and the saturation exponent approaches unity as Sc increases, qualitatively consistent with 1D cuts of the scalar.
Critically Literate Citizenship: Moments and Movements in Second Grade:

With renewed emphasis on civic education in K–12 schools, educators and politicians call for young people to engage in civic action. Worth considering are the kinds of ideas taken up, the performan...
Pneumomyelia Secondary to Interlaminar Cervical Epidural Injection Causing Acute Cord Injury with Transient Quadriparesis.

Background Cervical radiculopathy and cervicalgia are commonly managed with spinal epidural steroid injections in the outpatient setting. Although cervical epidural injections are routinely performed, there is potential for significant complications if proper technique and safety measures are not followed. Spinal cord infarction and stroke following transforaminal injection have been described in the literature, whereas interlaminar injections have been associated with both epidural hematomas and direct cord injury. Case Description Here we describe a case of pneumomyelia after cervical interlaminar epidural steroid injection resulting in acute quadriparesis. The patient’s symptoms were caused by an inadvertent puncture of the cervical cord and injection of air present in the needle or syringe via an interlaminar approach. The initial computed tomography imaging showed a slit-like lesion at C7-T2 with density consistent with air that migrated rostrally on a follow-up scan. Conclusions Epidural steroid injections are often the treatment of choice in management of neck pain and cervical radiculopathy. Devastating complications can ensue if proper safety measures and technique are not used during the procedure regardless of the approach used.
Assessing the Impact of Communication Costs on International Trade

Abstract Communication costs are frequently cited as an important determinant of trade costs. We test this relationship by incorporating alternative measures of communication costs in a model of bilateral trade. We find that international variations in communication costs indeed have a significant influence on trade patterns. Furthermore, estimates using disaggregated data reveal that communication costs are more important for trade in differentiated products than for trade in homogenous products.
Internet Search Activity of Young People With Mood Disorders Who Are Hospitalized for Suicidal Thoughts and Behaviors: Qualitative Study of Google Search Activity.

Background: Little is known about the internet search activity of people with suicidal thoughts and behaviors (STBs). This data source has the potential to inform both clinical and public health efforts, such as suicide risk assessment and prevention. Objective: We aimed to evaluate the internet search activity of suicidal young people to find evidence of suicidal ideation and behavioral health–related content. Methods: Individuals aged between 15 and 30 years (N=43) with mood disorders who were hospitalized for STBs provided access to their internet search history. Searches that were conducted in the 3-month period prior to hospitalization were extracted and manually evaluated for search themes related to suicide and behavioral health. Results: A majority (27/43, 63%) of participants conducted suicide-related searches. Participants searched for information that exactly matched their planned or chosen method of attempting suicide in 21% (9/43) of cases. Suicide-related search queries also included unusual suicide methods and references to suicide in popular culture. A majority of participants (33/43, 77%) had queries related to help-seeking themes, including how to find inpatient and outpatient behavioral health care. Queries related to mood and anxiety symptoms were found among 44% (19/43) of participants and included references to panic disorder, the inability to focus, feelings of loneliness, and despair. Queries related to substance use were found among 44% (19/43) of participants. Queries related to traumatic experiences were present among 33% (14/43) of participants. Few participants conducted searches for crisis hotlines (n=3). Conclusions: Individuals search the internet for information related to suicide prior to hospitalization for STBs. The improved understanding of the search activity of suicidal people could inform outreach, assessment, and intervention strategies for people at risk. Access to search data may also benefit the ongoing care of suicidal patients.
The interplay of familial warmth and LGBTQ+ specific family rejection on LGBTQ+ adolescents' self-esteem.

Abstract Introduction Our study sought to assess the interplay of family dynamics, namely familial warmth and LGBTQ+ specific rejection, and its association to self-esteem in a non-probabilistic sample of LGBTQ+ adolescents in the United States. Methods Stratified by (1) cisgender and (2) transgender and non-binary LGBTQ+ adolescents (N = 8774), we tested multivariable regression analyses to assess the association between familial warmth and LGBTQ+ specific family rejection, adjusted for sociodemographic characteristics. We then conducted a sub-analysis with LGBTQ+ adolescents who reported being out to any family member about their LGBTQ+ identity; specifically, we tested a series of multivariable regression models to assess whether levels of LGBTQ+ specific family rejection attenuated the association between familial warmth and self-esteem. Results Full sample models indicated a positive association between familial warmth and self-esteem. Findings from our sub-analysis indicated that familial warmth remained positively linked to self-esteem and family rejection was negatively associated with self-esteem. Family rejection was a statistically significant moderator, attenuating the association between familial warmth and self-esteem. With respect to being out about one's sexual orientation, these findings were robust across gender stratification groups. Conclusions Families of origin serve as sources of stress and resilience for LGBTQ+ adolescents. Our findings contribute support to arguments that familial warmth and LGBTQ+ specific rejection are not mutually-exclusive experiences among LGBTQ+ adolescents. We provide recommendations for multilevel interventions to leverage activities that support positive family dynamics and self-esteem among LGBTQ+ adolescents.
Wormhole spacetimes in Palatini f(R) gravity and energy conditions

Traversable wormhole spacetimes are constructed in Palatini version of modified f(R) gravity theory. We impose that the matter supporting these spacetimes satisfies the null energy condition (NEC) and the weak energy condition (WEC). The gravitational field equations in Palatini approach are totally different to those field equations obtained in general relativity and f(R) metric approach. In this framework, by considering $$f(R)= R - \beta R^n$$ which is a given f(R) model that has consistent results with observations, the field equations have been simplified. To explicitly examine the NEC and the WEC, we take three different shape functions $$b(r)=r_0^2/r$$ , $$b(r)=\sqrt{r_0r}$$ , and $$b(r)=r_0^3/r^2$$ . Then, the existence of traversable wormholes in Palatini f(R) gravity is investigated in the absence of exotic matter. It is clearly demonstrated that the matter stress-energy tensor satisfies the NEC and the WEC.
RNA splicing analysis using heterogeneous and large RNA-seq datasets

The ubiquity of RNA-seq has led to many methods that use RNA-seq data to analyze variations in RNA splicing. However, available methods are not well suited for handling heterogeneous and large datasets. Such datasets scale to thousands of samples across dozens of experimental conditions, exhibit increased variability compared to biological replicates, and involve thousands of unannotated splice variants resulting in increased transcriptome complexity. We describe here a suite of algorithms and tools implemented in the MAJIQ v2 package to address challenges in detection, quantification, and visualization of splicing variations from such datasets. Using both large scale synthetic data and GTEx v8 as benchmark datasets, we demonstrate that the approaches in MAJIQ v2 outperform existing methods. We then apply MAJIQ v2 package to analyze differential splicing across 2,335 samples from 13 brain subregions, demonstrating its ability to offer new insights into brain subregion-specific splicing regulation.
Introduction: Climate Disruption and Governmental Action: Approaches, Obstacles, and Opportunities

This article is an introduction to a symposium issue of the Nova Law Review on "New Directions in Energy Law and Policy, Climate Disruption and Sea level Rise." The piece summarizes key points made in the symposium contributions of three prominent legal scholars: Professor David Driesen, Thomas McGarity, and Joseph Tomain. It notes two themes that are common to their articles and it discusses some of the implications of their work for the possible future direction of U.S. national and state policies regarding energy and the control of greenhouse gas emissions.
Type III Secretion Machinery and Effectors

The translocated effectors harbor many different activities and can be used in different combinations by various bacteria to exert highly specific and unique effects on the host cell. Additionally, even homologous effectors with identical enzymatic activity can vary enough in substrate specificity and delivery to make their effect on the host cell tailored for a given pathogen. In understanding the biology of these systems, moderate- and high-resolution structural information has often played a key role and, furthermore, revealed aspects and themes in the pathogenesis of these systems that were much less clear from data generated from more indirect experimental techniques. This chapter represents only a skimming of the surface in examining these systems from a structural point of view, but it is nonetheless informative. Composed of more than 20 proteins and related to the flagellar assembly apparatus, type III secretion systems are one of the most complex protein secretion systems to be discovered. Rather than presenting the structures based on their fold or biochemical activity or on the species which utilize them, the chapter is organized in biological themes and examines the structures in related functional contexts. Detailed structural analyses of type III secretion virulence systems are only in their infancy. The field awaits high-resolution work on the needle complex, the translocon, the bacterial side elements, and the remaining arsenal of effector molecules used by the different gram-negative pathogens utilizing this translocation system in plants and animals.
Shape and Energetics of DNA Plectonemes

The mechanics of DNA at length scales of few hundred nanometers is described by a fluctuating elastic rod model. In this paper we couple the fluctuating rod model with a variational method for describing plectonemes to unravel the mechanics of some recent single molecule experiments. We are able to reproduce some features seen in these experiments which analyze plectoneme formation in DNA under tension by continuously twisting it and tracking its end-to-end distance, torque, etc., as a function of the added link. Our model accounts for configurational entropy and electrostatics in the plectoneme. We find that configurational entropy makes a significant contribution to the mechanics of the plectoneme while electrostatics (in the presence of monovalent counterions) plays a relatively minor role.
A Mid-Infrared Survey of L1641N with ISOCAM

We present the results from our analysis of the Infrared Space Observatory (ISO) data on the L1641N outflow region located in the Orion A molecular cloud. The data were obtained with the array camera (ISOCAM) using two broadband filters, LW2 (6.7 μm) and LW3 (14 μm), and the narrowband circular variable filter (CVF), which provides low-resolution (R = λ/δλ ~ 40) spectra in the 5-17 μm region. We detect a total of 34 sources in the 765 × 840 region covered by the broadband filters. Four of these sources have no reported detection in previous studies of the region. The CVF data are available for only the central 32 × 32 portion of the total region, providing spectra for the brightest seven sources in that region. We find that the source previously identified as the near-IR counterpart to the IRAS-detected point source (IRAS 05338-0624) is not the brightest source in the wavelength region of the IRAS 12 μm filter. We find instead that a nearby object (within the beam of IRAS and not detected at near-IR wavelengths) outshines all other sources in the area by a factor of ~2. Despite its brightness, we conclude that this second object is unlikely to be the source detected by IRAS because that would imply a positional error of ~1' in the IRAS position. However, we also consider it unlikely that IRAS would not have spatially resolved and detected the second source. This implies that the second source must have brightened by at least 200 mJy in the decade between IRAS and ISO observations. A comparison of the near-IR (J - H vs. H - Ks) and mid-IR (H - Ks vs. [6.7 μm]-[14 μm]) color-color plots shows that while at near-IR wavelengths only four of the sources show evidence for emission above the values predicted from photospheric emission alone (hereafter referred to as excess emission), at least 85% of all sources show evidence for excess emission at mid-IR wavelengths. This result supports similar conclusions from L-band surveys. The CVF spectra suggest a range of evolutionary status in the program stars ranging from embedded young stellar objects to young disks. When combined with optical and near-IR age estimates, these results show active current star formation in the region that has been ongoing for at least 2 Myr.
Cross-origin javascript capability leaks: detection, exploitation, and defense

We identify a class of Web browser implementation vulnerabilities, cross-origin JavaScript capability leaks, which occur when the browser leaks a JavaScript pointer from one security origin to another. We devise an algorithm for detecting these vulnerabilities by monitoring the "points-to" relation of the JavaScript heap. Our algorithm finds a number of new vulnerabilities in the opensource WebKit browser engine used by Safari. We propose an approach to mitigate this class of vulnerabilities by adding access control checks to browser JavaScript engines. These access control checks are backwardscompatible because they do not alter semantics of the Web platform. Through an application of the inline cache, we implement these checks with an overhead of 1-2% on industry-standard benchmarks.
Magnetic Monopole Decay and Its Consequences

We return to further examination of the need for the existence of magnetic monopoles based on the decades old derivation [Sherman Frankel, Amer. Jour. of Physics, 44, 7, 683-6 1976], of both the monopole-charge force, vec(F) = eg(vec(r) * vec(v)/c)/r^3, as well as the Dirac angular momentum, vec(l_f) = eg hat(r), from P and T conservation alone, without any recourse whatsoever to Maxwell's Equations. The eg product also appeared in the charge conserving equation, deg/dt = 0 = edg/dt + gde/dt, and this paper examines the second possible solution, dg/dt = - de/dt, namely monopole decay, accounting for the non-observance of stable monopoles. It treats astrophysics and neutrino physics consequences and suggestions for experimental searches.
Sin pelos en la lengua : Rosario Ferré’s Last Interview

In this rare interview with Rosario Ferre, Frances Negron-Muntaner engages with the iconic author on a host of issues that remain controversial for critics a...
The roles of aerosol direct and indirect effects in past and future climate change

[1] Using the Geophysical Fluid Dynamics Laboratory's (GFDL's) fully coupled chemistry-climate (ocean/atmosphere/land/sea ice) model (CM3) with an explicit physical representation of aerosol indirect effects (cloud-water droplet activation), we find that the dramatic emission reductions (35%–80%) in anthropogenic aerosols and their precursors projected by Representative Concentration Pathway (RCP) 4.5 result in ~1 °C of additional warming and ~0.1 mm day−1 of additional precipitation, both globally averaged, by the end of the 21st century. The impact of these reductions in aerosol emissions on simulated global mean surface temperature and precipitation becomes apparent by mid-21st century. Furthermore, we find that the aerosol emission reductions cause precipitation to increase in East and South Asia by ~1.0 mm day−1 through the second half of the 21st century. Both the temperature and the precipitation responses simulated by CM3 are significantly stronger than the responses previously simulated by our earlier climate model (CM2.1) that only considered direct radiative forcing by aerosols. We conclude that the indirect effects of sulfate aerosol greatly enhance the impacts of aerosols on surface temperature in CM3; both direct and indirect effects from sulfate aerosols dominate the strong precipitation response, possibly with a small contribution from carbonaceous aerosols. Just as we found with the previous GFDL model, CM3 produces surface warming patterns that are uncorrelated with the spatial distribution of 21st century changes in aerosol loading. However, the largest precipitation increases in CM3 are colocated with the region of greatest aerosol decrease, in and downwind of Asia.
Convection heat and mass transfer in alloy solidification

Publisher Summary This chapter reviews that internal convection strongly influences alloy-solidification processes. Local cooling and solidification rates are affected by convection conditions, which, in turn, have a strong influence on the microstructural features of a casting. Moreover, advective transport of interdendritic liquid is responsible for macrosegregation. To improve solid/liquid-phase-change processes involving multicomponent materials, it is vital that engineers understand the convection conditions associated with the processes. However, obtaining a reliable knowledge base for guiding process improvements is made difficult by several complicating features associated with alloy solidification. The chapter highlights that single-domain models for binary solid/liquid-phase- change systems have contributed to enhancing the knowledge base, and the results of several computational studies were reviewed to demonstrate the potential of the models to predict convective transport phenomena for a wide variety of process conditions. Possible means of intelligently controlling alloy-solidification processes were discussed and the role of numerical simulation in developing control strategies was reviewed.
Ribonomic and short hairpin RNA gene silencing methods to explore functional gene programs associated with tumor growth arrest.

In this chapter, we present an approach using genomic and ribonomic profiling to investigate functional gene programs in a tumor growth model. To reach this goal, ribonomic profiling was combined with RNA interference in a tumor dormancy model. Strategies merging functional genomic technologies are outlined for the identification of novel posttranscriptionally regulated targets of p38 to show that they are functionally linked to the induction or interruption of cellular growth in cancer. In the first section of this chapter, we describe a method for the detection of mRNA subsets associated with RNA-binding proteins such as hnRNP A1 using (1) immunopurification of mRNA–protein complexes, from either whole cell lysates or subcellular fractions and (2) gene expression arrays to find those mRNAs bound to hnRNP A1. In the second section, short hairpin RNA technology was used to create a library of shRNAs that target p38 induced mRNAs expression libraries are utilized to “knockdown” the genes identified in the first section. Finally, this library of gene candidates is evaluated in vivo to address their functional role in the induction or maintenance of dormancy.
The Process of Cessation Among Current Tobacco Smokers: A Cross-Sectional Data Analysis From 21 Countries, Global Adult Tobacco Survey, 2009–2013

We analyzed data from the Global Adult Tobacco Survey (GATS) from 21 countries to categorize smokers by stages of cessation and highlight interventions that could be tailored to each stage. GATS is a nationally representative household survey that measures tobacco use and other key indicators by using a standardized protocol. The distribution of smokers into precontemplation, contemplation, and preparation stages varied by country. Using the stages of change model, each country can design and implement effective interventions suitable to its cultural, social, and economic situations to help smokers advance successfully through the stages of cessation.
Decision-making system for freeway incident response using sequential hypothesis testing methods

Recent research in advanced traffic management systems has emphasized incident detection and response to mitigate nonrecurring congestion. Existing incident response decision-making algorithms do not account for the expected losses associated with false alarms, undetected incidents, and delayed incident response. A freeway incident response decision-making system based on sequential hypothesis testing techniques is presented. The primary feature of this decision-making system is that it minimizes the sum of the expected losses associated with false response, nonresponse, and delayed responses to incidents through a dynamic programming algorithm. The results of simulation tests indicate that this algorithm performs better than typical Bayesian incident response algorithms for mean response time, false response rate, and nonresponse rate.
Fast Distributed Outlier Detection in Mixed-Attribute Data Sets

Efficiently detecting outliers or anomalies is an important problem in many areas of science, medicine and information technology. Applications range from data cleaning to clinical diagnosis, from detecting anomalous defects in materials to fraud and intrusion detection. Over the past decade, researchers in data mining and statistics have addressed the problem of outlier detection using both parametric and non-parametric approaches in a centralized setting. However, there are still several challenges that must be addressed. First, most approaches to date have focused on detecting outliers in a continuous attribute space. However, almost all real-world data sets contain a mixture of categorical and continuous attributes. Categorical attributes are typically ignored or incorrectly modeled by existing approaches, resulting in a significant loss of information. Second, there have not been any general-purpose distributed outlier detection algorithms. Most distributed detection algorithms are designed with a specific domain (e.g. sensor networks) in mind. Third, the data sets being analyzed may be streaming or otherwise dynamic in nature. Such data sets are prone to concept drift, and models of the data must be dynamic as well. To address these challenges, we present a tunable algorithm for distributed outlier detection in dynamic mixed-attribute data sets.
A World of Crisis and Progress: The American YMCA in Japan, 1890-1930

Three related themes weave through the experience of the American YMCA missionaries and Japanese Christians between 1890-1930: the connection between national identity and Christianity, resulting conflicts between these Christians, and an alternating sense of crisis and progress. In the 1920s, tensions between Americans and Japanese leaders led the American YMCA missionary movement to reevaluate its purpose and forced it away from nationalism.
The rules of global engagement for developing country firms

Purpose – This study aims to examine how property rights, financial liberalization and the control of corruption at the country level influence the inward and outward global engagement of domestic firms from developing countries. The author also examines whether firms with certain resource endowments such as human capital or technological capabilities are better positioned to globalize as the aforementioned institutional factors evolve. Design/methodology/approach – Using a sample of 18,365 firms from 57 developing countries and multilevel modeling, the author shows that institutional factors are related to inward and outward global engagement. Findings – The author finds that firms with human capital are more likely to move outward in the presence of lower levels of corruption. Domestic firms possessing technological capabilities are more likely to engage inward as financial liberalization eases the access to capital. Originality/value – Many existing studies that have investigated the impact of institut...