cssi/SciSciGPT-SciSciNet huggingface dataset:
Inductive matrix completion for predicting gene-disease associations.

Motivation: Most existing methods for predicting causal disease genes rely on specific type of evidence, and are therefore limited in terms of applicability. More often than not, the type of evidence available for diseases varies—for example, we may know linked genes, keywords associated with the disease obtained by mining text, or co-occurrence of disease symptoms in patients. Similarly, the type of evidence available for genes varies—for example, specific microarray probes convey information only for certain sets of genes. In this article, we apply a novel matrix-completion method called Inductive Matrix Completion to the problem of predicting gene-disease associations; it combines multiple types of evidence (features) for diseases and genes to learn latent factors that explain the observed gene–disease associations. We construct features from different biological sources such as microarray expression data and disease-related textual data. A crucial advantage of the method is that it is inductive; it can be applied to diseases not seen at training time, unlike traditional matrix-completion approaches and network-based inference methods that are transductive. Results: Comparison with state-of-the-art methods on diseases from the Online Mendelian Inheritance in Man (OMIM) database shows that the proposed approach is substantially better—it has close to one-in-four chance of recovering a true association in the top 100 predictions, compared to the recently proposed Catapult method (second best) that has <15% chance. We demonstrate that the inductive method is particularly effective for a query disease with no previously known gene associations, and for predicting novel genes, i.e. genes that are previously not linked to diseases. Thus the method is capable of predicting novel genes even for well-characterized diseases. We also validate the novelty of predictions by evaluating the method on recently reported OMIM associations and on associations recently reported in the literature. Availability: Source code and datasets can be downloaded from http://bigdata.ices.utexas.edu/project/gene-disease. Contact: ude.saxetu.sc@68agan
Development of an Empirical Lag Time Equation

A regression analysis was performed on measured lag times from gauged watersheds to develop a lag time equation. The watersheds are part of the Agricultural Research Service’s database. They are located in several states and are comprised of varying terrain. The goal of the analysis was to develop a lag time equation that is useful in hydrologic modeling. The study included measurements from approximately 10,000 direct runoff events from 52 watersheds to determine which watershed parameters are best for predicting lag time. The lag time was found to correlate strongly with the longest hydraulic length of the watershed. Therefore an equation was developed that used only this parameter. The inclusion of any other watershed characteristics in the equation did not improve its ability to predict the lag time. Finally, the National Resource Conservation Service procedures for calculating watershed lag time were used to determine the lag times of the watersheds. These estimated lag times were then compared with ...
Preliminary evidence that American bullfrogs (Rana catesbeiana) are suitable hosts for Escherichia coli O157:H7.

We orally inoculated Rana catesbeiana tadpoles (n = 23) and metamorphs (n = 24) to test their suitability as hosts for Escherichia coli O157:H7. Tadpoles were housed in flowthrough aquaria and did not become infected. Metamorphs were housed in stagnant aquaria, and 54% tested positive through 14 days postinoculation, suggesting that they are suitable hosts for E. coli O157:H7.
“Coming Into My Own as a Teacher”: Identity, Disequilibrium, and the First Year of Teaching

This study examines the experiences of ten first-year English teachers in various school contexts in two Northeastern states. Through a phenomenological approach to in-depth interviewing, teachers were interviewed at the end of their first year of teaching. Commonalities in teachers' experiences include former teachers' influences on their teacher personae, negotiating their authoritative role in the classroom, understanding how and why to set boundaries with students, and demonstrating resilience and resolve in the face of multiple challenges. Implications for teacher education and induction programs are to address the disequilibrium of the self in early teaching experiences and to model habits of mind that promote “productive disequilibrium.”
Low Cost, Broadband Tunable Ferroelectric Filters for JTRS Cluster 5 Applications

Tunable ferroelectric ceramic capacitors have shown great promise in reducing the size, weight, and power (SWAP) of traditional varactor-based devices. Ferroelectric devices fabricated from Barium Strontium Titanate (BST) have been demonstrated in the laboratory and are just now becoming available for commercial narrowband applications. This paper presents some of the tradeoffs in designing a small form factor (SFF), easily manufacturable, broadband tunable filter utilizing high volume, low-cost BST devices. Development status for filters that cover the 225 MHz to 2.7 GHz frequency range with superior narrowband performance, low in-band insertion loss, and high out-of-band rejection that is directly applicable to the stringent requirements of Joint Tactical Radio System (JTRS) Cluster 5 Software Defined Radio (SDR) is also presented. These Manufacturing Readiness Level (MRL) 4 filters currently provide a 50% reduction in size over traditional approaches, and future short-term plans promise further reducti...
Comparative vessel anatomy of arctic deciduous and evergreen dicots

Arctic tundra plant species exhibit striking variation in leaf character and growth form. Both are likely related to differences in vessel anatomy, and all may affect responses to climate changes in the Arctic. To investigate the relationships among leaf character, growth form, vessel anatomy, and susceptibility to freeze-thaw-induced xylem cavitation, xylem vessel characteristics were compared among six deciduous and six evergreen arctic dicot species of erect and prostrate growth forms. We hypothesized that deciduous and erect species would have larger and longer vessels than evergreen and cushion/mat-forming species. Vessel lengths, diameters, and densities were measured for each species. Theoretical vessel flow rates were calculated using Poiseuille’s law for ideal capillaries. Flow rates were used to determine the susceptibility of vessels to cavitation induced by freeze-thaw events that may become more frequent with global warming. Vessel diameters were larger in deciduous species compared to evergreens, and in shrubs/trees vs. cushion/mat-forming plants. Vessel length distributions, however, did not differ for growth form or leaf character. Vessel density was greater in cushion/mat-forming species than in shrub/tree species. Deciduous plants showed a greater contribution to total conductivity by relatively larger vessels than evergreens. One of the deciduous species, Vaccinium uliginosum, is predicted to be susceptible to freeze-thaw-induced cavitation. These results have important implications for future arctic species composition and plant community structure.
Geographic information system‐system dynamics procedure for bus rapid transit ridership estimation

This article presents a two-step procedure for estimating the total daily ridership (TDR) of a new bus rapid transit route that runs along a corridor without a competing regular bus service. Bus rapid transit (BRT) is defined as a high-performance bus mode that combines a variety of infrastructure and operational features into a high-quality transit service. The authors describe the use of a Geographic Information System (GIS)-Business Analyst desktop to analyze and extract population statistics, including annual growth rates. The outputs of the GIS-BA desktop are the total population, employed population, number of households, and their respective annual growth rates in the buffer ring. The second step of the procedure uses a simulation model that embeds the known relationships between the demographic variables and the proposed BRT system's infrastructure and operational features; this step estimates the TDR of the base year. The authors then validate this two-step procedure with actual demographic and ridership data from the Las Vegas MAX BRT line and the Los Angeles Orange Line, respectively. They also apply the model to the proposed BRT route along Mesa St. in El Paso, Texas, as a case study. They conclude that this two-step procedure offers a new and relatively simple approach that complements the three known BRT ridership estimation methods currently acceptable by the U.S. Federal Transit Administration. The new procedure more directly links a BRT corridor’s TDR with the BRT system’s features, and the demographic and socioeconomic characteristics of the corridor it serves.
Translation Initiation on Mammalian mRNAs with Structured 5′UTRs Requires DExH-Box Protein DHX29

Eukaryotic protein synthesis begins with assembly of 48S initiation complexes at the initiation codon of mRNA, which requires at least seven initiation factors (eIFs). First, 43S preinitiation complexes comprising 40S ribosomal subunits, eIFs 3, 2, 1, and 1A, and tRNA(Met)(i) attach to the 5'-proximal region of mRNA and then scan along the 5' untranslated region (5'UTR) to the initiation codon. Attachment of 43S complexes is mediated by three other eIFs, 4F, 4A, and 4B, which cooperatively unwind the cap-proximal region of mRNA and later also assist 43S complexes during scanning. We now report that these seven eIFs are not sufficient for efficient 48S complex formation on mRNAs with highly structured 5'UTRs, and that this process requires the DExH-box protein DHX29. DHX29 binds 40S subunits and hydrolyzes ATP, GTP, UTP, and CTP. NTP hydrolysis by DHX29 is strongly stimulated by 43S complexes and is required for DHX29's activity in promoting 48S complex formation.
Initiation of spontaneous epileptiform activity in the neocortical slice

Tsau, Yang, Li Guan, and Jian-Young Wu. Initiation of spontaneous epileptiform activity in the neocortical slice. J. Neurophysiol. 80: 978–982, 1998. Cortical local circuitry is important in epilep...
Subclavian Artery Trauma: Endovascular Management

The treatment of traumatic vascular injuries has evolved with endovascular therapy becoming an important tool to deal with these difficult and often complex injuries. The technical aspects of vascular exposure and repair in the setting of trauma are often more challenging than in other settings. Open surgical repair of traumatic arterial injury is often complicated by distorted anatomy secondary to associated hematomas or pseudoaneurysms. The exposure of the great vessels of the arch is associated with significant morbidity and mortality. Depending on the location, an open approach could require a median sternotomy, thoracotomy, and supraclavicular, infraclavicular, or clavicular transection.
Staining fungi associated with Dendroctonus adjunctus in pines

Two wood-staining fungi were isolated from Dendroctonus adjunctus- killed ponderosa pines in southeastern New Mexico. One is described as a new species of Ceratocystis and the other as a new specie...
Cancer patients’ preferences for return of somatic and germline whole-exome sequencing results: Data from the CANSEQ study.

1535 Background: The introduction of whole-exome sequencing (WES) into routine cancer care presents novel challenges for patient education and informed consent. In light of the recent American Coll...
Introduction: Evidence-based in vitro fertilization treatment of fresh versus frozen embryo transfer: peeling away the layers of the onion.

This introduction to this Views and Reviews examines the current evidence for elective fresh versus frozen embryo transfer, delineates complexities that arise as we sift through the available evidence, and speculates on the ideal design of studies to arrive at an evidence-based consensus. Current gaps in the literature, including a lack of reporting on important outcomes such as live birth and maternal and perinatal adverse events, are noted. The difficulty in designing trials is reviewed, including the choice of the time point in the cycle to randomize patients, how to account for all the patients and embyros that are involved in the trial, whether to incorporate prenatal genetic screening, and the best type of study design to address the risk/benefit ratio of these practices.
The demand for money and the rate of interest

Within traditional Keynesian economics money serves as a means of payment and a store of wealth. These two functions of money were used by Keynes to undermine the classical dichotomy between the real and monetary sectors of the economy. The end result was his liquidity preference theory of the demand for money which allowed changes in the monetary sector to be transmitted to the real sector through changes in the rate of interest. But Keynes also assumed, along with everyone else, that the supply of money was exogenously determined. An exogenous money supply is simply another way of saying that the central bank (through its use of open market operations, the discount rate, and reserve requirements) can adjust the overall volume of money, in response to changes in the demand for it, to that level consistent with its policy objectives.
Discourse, Gender, and the Meaning of Work Rearticulating Science, Technology, and Engineering Careers Through Communicative Lenses

In this chapter, we offer communicative perspectives and challenges related to gender representation and the gendered organizing and career processes in science, technology, engineering, and math (STEM) areas. We focus on the meaning of work in STEM and how these meanings are (re)created and communicated through d/Discourses. Using a discursive approach, new perspectives on the issue of the underrepresentation of women in STEM careers derive from the constructed nature of STEM work itself and its meaningfulness to different groups, particularly women. Engagement in STEM careers also provides a context to evaluate and expand theory, research, and practice in communication. We use multi-disciplinary lenses to examine developmental, educational, media, technological, socio-cultural, and organizational perspectives on STEM work and careers. In summary, this chapter examines the discursive roots of contemporary constructions and images of STEM work, careers, education, and organizations, offering an opportunit...
Hill, Archibald A. (1902–1992)

Archibald A. Hill's (1902–1992) publications span the period from 1931 to 1975. They range in topics from literary and pedagogical to applied and theoretical linguistics. His contribution was not so much theoretical as it was practical, and the best representative of his linguistic work is his 1958 Introduction to linguistic structures: from sound to sentence in English. A four-volume Festschrift dedicated to him, with more than 150 linguists contributing, was published from 1976 to 1979.
Dupuytren’s Disease: Anatomy, Pathology, and Presentation

Dupuytren’s disease has been recognized for approximately four centuries. A thorough knowledge of the palmar fascial complex anatomy is imperative for understanding Dupuytren disease pathology. Its presentation, although seemingly constant, is actually variable, depending on the structures involved. Dorsal skin changes in Dupuytren disease are a source of confusion. These can be either in the form of dorsal Dupuytren’s nodules, which are similar to palmar nodules and pathognomonic of the disease or dorsal cutaneous pads, which are encountered equally in Dupuytren disease and in the normal population. There are also two distinct clinical entities associated with palmar fascial proliferation, classic Dupuytren disease and atypical, so-called non-Dupuytren disease. These two types differ in presentation, etiology, treatment, and prognosis. Authors of future epidemiological and outcome studies should not confuse these two clinical entities.
Primate-specific miR-515 family members inhibit key genes in human trophoblast differentiation and are upregulated in preeclampsia

Dysregulation of human trophoblast invasion and differentiation can result in preeclampsia (PE), a hypertensive disorder of pregnancy with significant morbidity and mortality for mother and offspring. miRNA microarray analysis of RNA from human cytotrophoblasts (CytT), before and after differentiation to syncytiotrophoblast (SynT) in primary culture, revealed that members of miR-515 family-including miR-515-5p, miR-519e-5p, miR-519c-3p, and miR-518f, belonging to the primate- and placenta-specific chromosome 19 miRNA cluster (C19MC)-were significantly down-regulated upon human SynT differentiation. The proto-oncogene, c-MYC, which declines during SynT differentiation, interacted with E-boxes upstream of pri-miR-515-1 and pri-miR-515-2, encoding these mRNAs, to enhance their expression. Predicted targets of miR-515-5p, known to be critical for human SynT differentiation, including hCYP19A1/aromatase P450, glial cells missing 1 (GCM1), frizzled 5 (FZD5), WNT2, Sp1, and estrogen receptor-α (ERα) mRNA, were markedly up-regulated during SynT differentiation. Notably, overexpression of miR-515-5p in cultured primary human trophoblasts impaired SynT differentiation and specifically decreased expression of hCYP19A1, GCM1, and Fzd5, which were validated as its direct targets. Interestingly, miR-515-5p levels were significantly increased in PE placentas, whereas mRNA and protein levels of targets, hCYP19A1, GCM1, and FZD5, were significantly decreased, compared with placentas of normotensive women. Thus, miR-515-5p may serve a key role in human trophoblast differentiation; its aberrant up-regulation may contribute to the pathogenesis of PE.
Earthicle: The Design of a Conceptually New Type of Particle

The conception and the steps made in the design of a conceptually new type of composite particle, so-called “earthicle”, are being described. This particle is meant to roughly mimic the layered structure of the Earth, having zerovalent iron core, silicate mantle, and a thin carbonaceous crust resembling the biosphere and its geological remnants. Particles are made in a stable colloidal form in an aqueous medium, involving chemical precipitation and pyrolysis of citric acid in the solution. The effects of various synthesis parameters were studied, including borohydride and oleate concentrations, APTES/TEOS molar ratio, chemical nature of the carbon precursors, and others. XRD analysis confirmed the predominantly zerovalent iron composition of the core, amorphous silica and crystalline iron silicate/silicide composition of the mesolayer, and the carbonaceous, amorphous graphitic composition of the surface coating. The atomically thin carbon shell was also detected as a distinct shoulder on the broad n−π* ab...
A Very Brief History

It stands to reason that a fetus, as it nears completion, needs a passage to the outer world that is commensurate with its size exactly at the time of parturition. The discrepancy between the pelvic canal and the fetus in most mammals is so large and the pelvis so rigid that a special mechanism must exist which corrects this discrepancy if a species is to persist. Here is one of the few examples where biology has to submit to reason. The birth canal cannot be opened during gestation because of the danger of premature fetal loss, and at the end of gestation the opening of the canal must be coordinated with a dramatic over-all shift of the endocrine balance which causes potentially damaging uterine contractions. This set of circumstances is well known to endocrinologists and explains Hisaw’s experiments with pregnant guinea pig serum. Only a hormone could cause such a change, and most hormones travel from the gland of origin to the site of action by the blood stream. Serum from pregnant animals with relaxed symphyseal joints was a plausible place to search for this factor. Once virgin guinea pigs had been treated with estrogen they responded to the pregnancy serum by significant widening of the symphysis pubis.1 This was a momentous discovery albeit overshadowed by the discovery of insulin, the pancreatic disulfide homologue of relaxin, at about the same time. Insulin took center stage at once because it saved lives and relaxin fell by the wayside because humans had developed a surgical procedure to overcome the problems of pelvic insufficiency. Nonetheless, relaxin researchers had an inkling that insulin and relaxin had something in common (Fig. 2.1). A condensed pictorial summary of both factors as they evolved through their stages of discovery is shown in Figure 2.2.
Evolved Standards, Evolving Justices?

In its Eighth Amendment cases, the Supreme Court has often cited counter-majoritarian considerations as the basis for exercising judicial restraint. As a result, excessive and draconian punishments persist in the United States, with the Court being hesitant to use the Constitution to bar state punishment practices. The Court’s evolving standards of decency doctrine, however, is majoritarian. As this Article argues, the doctrinal framework of the Court alleviates the counter-majoritarian difficulty, as the Court’s applications of the Eighth Amendment mirror majoritarian practices and only strike down outlier punishments. Given the lack of justification for judicial restraint under the Eighth Amendment, the Article maps a series of possible applications of the Constitution in this area, both on a micro-level—to limit punishments in certain circumstances—and on a macro-level—to bar certain punishments altogether. In particular, the Article reveals the current ability of the Court to apply its Eighth Amendment doctrine to abolish the death penalty and juvenile life-without-parole sentences. In short, the Article demonstrates that society’s standards with respect to criminal punishments have evolved. The question remains whether the justices themselves will evolve accordingly.
Chern-Simons theory and Wilson loops in the Brillouin zone

Berry connection is conventionally defined as a static gauge field in the Brillouin zone. Here, the authors show that for three-dimensional (3D) time-reversal invariant superconductors, a generalized Berry gauge field behaves as a fluctuating field of a momentum-space Chern-Simons gauge theory, which is the effective theory of the system. Furthermore, the gapless nodal lines in the momentum space which may arise in such superconductors play exactly the role of Wilson loop observables, and their linking and knot invariants modify the gravitational theta angle which can be evaluated from the Chern-Simons action. This angle induces a topological gravitomagnetoelectric effect where a temperature gradient induces a rotational energy flow. The authors also show how this idea may be potentially generalized to realize topological strings in six-dimensional phase space, where the physical space defects play the role of topological D-branes.
Parental Decision-Making Associated With Pediatric Emergency Department Use for Asthma

SS Mudd, CJ Ogborn, ME Bollinger. Ann Allergy Asthma Immunol. 2016;117(5):490–494 To identify common caregiver factors contributing to emergency department (ED) utilization for asthma care among inner city children. One hundred and fifty children aged 3 to 12 years were recruited during an ED visit for acute asthma care. Inclusion criteria were physician-diagnosed persistent and uncontrolled asthma, 2 or more ED visits or 1 or more hospitalizations for asthma during the past year, and living in the Baltimore metropolitan area. Children were primarily African American (95%) with male predominance (64%) and a mean age of 6.4 years …
Give me 3': Do minimum distance passing laws reduce bicyclist fatalities?

Abstract Safely integrating bicyclists onto roadways in the United States has become an important issue as the number of cyclists has steadily increased in recent decades. These concerns have led many city and state legislatures to pass laws requiring drivers to provide a minimum amount of distance between their vehicle and cyclists when passing them on roadways. Many believe these laws are ineffective in reducing the number of bicyclist fatalities because they are difficult for police to enforce, contain loopholes, and the minimum distance required is inadequate. This paper tests this claim empirically using data on 18,534 bicyclist fatalities from the Fatality Analysis Reporting System and a differences-in-differences approach, in a negative binomial model, to identify the effect of minimum distance passing laws on bicyclist fatalities. The analysis fails to find a significant effect of enacting a minimum distance passing law on the number of cyclist fatalities after controlling for differences in weather, demographics, bicycling commuter rates, state level traffic, and time variation.
Risk Reduction Strategies for Setting Remedial Priorities: Hazardous Waste

The usual approach to overcoming community opposition to the siting of a hazardous waste facility is to offer compensation to the host community. Most communities have refused to serve as hosts to hazardous waste facilities regardless of the amount of compensation. A risk-risk approach is proposed as an alternative where the increased risk to the community as a result of the new hazardous waste facility is offset by a reduction in risk by the hazardous waste generators in the community. This could be accomplished by a reduction in the generation of hazardous waste or toxic emissions by these firms. A multiobjective programming model is proposed to evaluate this alternative policy.
A framework for modeling scenario-based barrier island storm impacts

Abstract Methods for investigating the vulnerability of existing or proposed coastal features to storm impacts often rely on simplified parametric models or one-dimensional process-based modeling studies that focus on changes to a profile across a dune or barrier island. These simple studies tend to neglect the impacts to curvilinear or alongshore varying island planforms, influence of non-uniform nearshore hydrodynamics and sediment transport, irregular morphology of the offshore bathymetry, and impacts from low magnitude wave events (e.g. cold fronts). Presented here is a framework for simulating regionally specific, low and high magnitude scenario-based storm impacts to assess the alongshore variable vulnerabilities of a coastal feature. Storm scenarios based on historic hydrodynamic conditions were derived and simulated using the process-based morphologic evolution model XBeach. Model results show that the scenarios predicted similar patterns of erosion and overwash when compared to observed qualitative morphologic changes from recent storm events that were not included in the dataset used to build the scenarios. The framework model simulations were capable of predicting specific areas of vulnerability in the existing feature and the results illustrate how this storm vulnerability simulation framework could be used as a tool to help inform the decision-making process for scientists, engineers, and stakeholders involved in coastal zone management or restoration projects.
The Irving–Williams series and the 2-His-1-carboxylate facial triad: a thermodynamic study of Mn 2+ , Fe 2+ , and Co 2+ binding to taurine/α-ketoglutarate dioxygenase (TauD)

Taurine/α-ketoglutarate (αKG) dioxygenase (TauD) is an E. coli nonheme Fe2+- and αKG-dependent metalloenzyme that catalyzes the hydroxylation of taurine, leading to the production of sulfite. The metal-dependent active site in TauD is formed by two histidine and one aspartate that coordinating to one face of an octahedral coordination geometry, known as the 2-His-1-carboxylate facial triad. This motif is found in many nonheme Fe2+ proteins, but there is limited information on the thermodynamic parameters that govern metal-ion binding to this site. Here, we report data from calorimetry and related biophysical techniques to generate complete thermodynamic profiles of Mn2+ and Co2+ binding to TauD, and these values are compared to the Fe2+ data reported earlier Henderson et al. (Inorg Chem 54: 2278–2283, 2015). The buffer-independent binding constants (K) were measured to be 1.6 × 106, 2.4 × 107, and 1.7 × 109, for Mn2+, Fe2+, and Co2+, respectively. The corresponding ΔG° values were calculated to be − 8.4, − 10.1, and − 12.5 kcal/mol, respectively. The metal-binding enthalpy changes (ΔH) for these binding events are − 11.1 (± 0.1), − 12.2 (± 0.1), and − 16.0 (± 0.6) kcal/mol, respectively. These data are fully consistent with the Irving–Williams series, which show an increasing affinity for transition metal ions across the periodic table. It appears that the periodic increase in affinity, however, is a result of a complicated summation of enthalpy terms (including favorable metal-ion coordination processes and unfavorable ionization events) and related entropy terms.
Supply chain controls for biomaterials and medical devices in the USA

Supply chain controls are designed to minimize risk to a finished product, from suppliers involved all along the linked activities, from the product’s initial creation in a field or lab through its final distribution to the end customer. Companies – and regulatory professionals – currently face a mix of guidance documents written by the Food and Drug Administration (FDA), regulatory agencies around the world, and non-governmental organizations such as the World Health Organization (WHO) and the Pharmaceutical Inspection Cooperative Scheme (PIC/S). This chapter reviews common supply chain issues and the ways in which FDA encourages organizations through guidance documents and regulatory harmonization activities to improve supply chain controls. It also reviews key steps in supply chain control, as well as advanced techniques for regulatory affairs executives to consider.
Exploring determinants of behavioral chronotype in a diurnal-rodent model of human physiology.

Abstract Numerous studies conducted with human participants have shown that differences in chronotype, defined as individual patterns of early or late beginning of daily activity, have implications for many biobehavioral processes, such as cognitive performance, mood, impulsivity, academic achievement of college students, and mental health. However, the determinants of individual variation in chronotype have not been investigated. Basic research on circadian rhythms has provided a basis for investigating the causes of chronotype variation, but experimental tests of pertinent hypotheses are difficult to conduct with human subjects. This limitation can be overcome by use of animal models. This study was conducted with a rodent species, the antelope ground squirrel (Ammospermophilus leucurus), that, like humans, is active during the daytime, exhibits a spread of chronotypes, and has a similar average free-running circadian period. We found chronotype to be a stable trait within individuals based on strong consistency of separate determinations made six months apart (correlation r = 0.91). We also found a moderate correlation of chronotype with the duration of the active phase (r = −0.51) and with free running period (r = 0.34), but weak correlation with rhythm robustness (r = 0.16), and no correlation with photic responsiveness or with masking responses. The best multiple regression model, incorporating the duration of the active phase, free-running period, and rhythm robustness, explained 38% of the variance in chronotype. Although 62% of the variance in chronotype remained unaccounted for, the results are encouraging because they document the possibility of using a diurnal rodent as a model for the investigation of the determinants of chronotype variation in humans.
The Implementation of Constitutional Rights: Insights from Law and Economics

The study of Law and Economics focuses most often on issues of efficiency and growth. The economic approach has made major contributions, for example, in the areas of regulation, liability, and contract. But an economic approach to the study of courts and law can also shed light on an area that is seldom investigated by traditional legal scholars: the implementation of judicial decisions. In this essay I demonstrate the relevance of the economic approach to the implementation of constitutional rights. In particular, I show that the economic analysis of law is central to understanding the efficacy of judicial decisions supportive of the interests of relatively powerless groups within society.' Supreme Court decisions are not self-implementing. As Alexander Hamilton pointed out long ago in The Federalist Papers, courts are particularly dependent on the actions of others. Hamilton argued in Federalist 78 that the judiciary "has no influence over either the sword or the purse . . . and must ultimately depend upon the aid of the executive arm even for the efficacy of its judgments."2 Without external support-from the other branches of government or directly from the citizenry-Court decisions announcing constitutional rights are unlikely to affect or change people's lives in important ways. In contrast to traditional legal analysis, the tools of economic analysis can help explain how Court-mandated constitutional rights of relatively powerless groups are actually implemented. In particular, economic analysis suggests that implementation is more likely to occur if at least one of three conditions is present:
Endothelial Cells Filopodia in the Anastomosis of Central Nervous System Capillaries.

In this Perspective we explore filopodia of endothelial cells in the developing central nervous system using the Golgi method and transmission electron microscopy. Filopodia of endothelial cells play a crucial role in the anastomosis of growing capillaries of the central nervous system. The leading endothelial cells filopodia from approaching capillaries interconnect forming complex conglomerates that precede the anastomotic event. The contacting filopodia form narrow spaces between them filled with proteinaceous basal lamina material. The original narrow spaces coalesce into larger ones leading to the formation of a single one that will interconnect (anastomose) the two approaching capillaries. The four leading endothelial cells (two for each approaching capillary) become the wall of the newly formed post-anastomotic CNS capillaries. These new CNS capillaries are very small with narrow and irregular lumina that might permit the passage of fluid but not yet of blood cells. Eventually, their lumen enlarges and permits the passage of blood cells.
A BlackCrit Analysis on Black Urban Youth and Suspension Disproportionality as Anti-Black Symbolic Violence.

Through an analysis of Black urban high school youth’s critical engagements with literacy, the authors examine school suspensions–particularly disproportionality–as anti-Black symbolic violence. By...
The food locker: an innovative, user-centered approach to address food insecurity on campus

Food insecurity is a growing problem on college campuses. By following a user-centered design process, our team envisioned how design can be a tool for enacting social justice. By posing the question "How might we support college students challenged by food insecurity?" we designed a product called the Food Locker that paired an online ordering system with a collection of lockers for students to discreetly and conveniently retrieve items from the campus food pantry. In this experience report, we introduce the growing problem of food insecurity on college campuses, discuss how this issue connects to concerns of inclusion, equity and access, and then detail the steps we took to design the Food Locker. We conclude by reflecting on the process, exploring next steps and calling for continued focus on using design to identify interventions for social justice through UCD.
Dietary Estrogen Protects Against NaCl-Sensitive Hypertension in Estrogen-Depleted Female Spontaneously Hypertensive Rats.

P169 In male spontaneously hypertensive rats (SHR) a high NaCl diet produces a rapid and sustained increase in hypertension. In contrast, in female SHR a high NaCl diet causes only a small, transient increase in arterial pressure. Elimination of most endogenous estrogen (via ovariectomy) produces mild NaCl-sensitive hypertension in female SHR, but simultaneous ovariectomy and elimination of exogenous dietary plant estrogens (phytoestrogens) nearly quadruples the hypertensive effect of the high NaCl diet, although phytoestrogen removal has a negligible effect on blood pressure in SHR fed a basal NaCl diet. This suggests that phytoestrogens (particularly genistein, the primary dietary phytoestrogen) protect ovariectomized female SHR from NaCl-sensitive hypertension. However, other reports suggest that the beneficial effects of phytoestrogens may only be present when genistein is combined with a high soy diet. The present study tests the hypothesis that genistein can independently reduce NaCl-sensitive hypertension in estrogen-depleted female SHR. Female SHR were ovariectomized at 3 weeks of age and placed on one of four casein-based, non-soy containing, diets (AIN-76A), i.e., a high (8%) or basal (0.6%) NaCl diet with or without genistein (0.06%; the approximate phytoestrogen concentration in the diet) added to the diet. After 5 weeks, femoral arterial catheters were implanted and 3 days later arterial pressures were recorded from all rats. The high NaCl diet increased arterial pressure by 68 ± 6 mm Hg in the phytoestrogen-free SHR, but produced only a 17 ± 5 mm Hg rise in arterial pressure in the genistein-supplemented group (similar to the rise previously observed in ovariectomized SHR fed a normal high NaCl diet). These results demonstrate that dietary genistein reduces NaCl-sensitive hypertension in ovariectomized female SHR. This work was supported by NHLBI Grant HL-37722.
Data Portals and Analysis

The development of powerful and scalable methods to analyze cancer genomic data has transformed the practice of medicine by bridging the gap between complex genomic data and their use in research and clinical translation. Of particular significance are the data portals and analysis platforms available that make genomic data more accessible to the research community, as they enable translational research by providing scientists with the information, tools, and frameworks necessary to perform integrative analyses on cancer genomic data.
Physical and data structure of 3D genome.

With the textbook view of chromatin folding based on the 30-nm fiber being challenged, it has been proposed that interphase DNA has an irregular 10-nm nucleosome polymer structure whose folding philosophy is unknown. Nevertheless, experimental advances suggest that this irregular packing is associated with many nontrivial physical properties that are puzzling from a polymer physics point of view. Here, we show that the reconciliation of these exotic properties necessitates modularizing three-dimensional genome into tree data structures on top of, and in striking contrast to, the linear topology of DNA double helix. These functional modules need to be connected and isolated by an open backbone that results in porous and heterogeneous packing in a quasi–self-similar manner, as revealed by our electron and optical imaging. Our multiscale theoretical and experimental results suggest the existence of higher-order universal folding principles for a disordered chromatin fiber to avoid entanglement and fulfill its biological functions.
Clinical Utility of Lefamulin: If Not Now, When?

The looming threat of antimicrobial resistance requires robust stewardship and new developments in infectious diseases pharmacotherapy. This review discusses the pertinent spectrum and clinical data of lefamulin (Xenleta®), with a focus on potential real-world use. Lefamulin is a novel pleuromutilin antibiotic that obtained Food and Drug Administration labeling for community-acquired bacterial pneumonia (CABP) in 2019. Lefamulin is available in both intravenous and oral formulations, and it inhibits bacterial protein synthesis inhibition through interactive binding to unique sites of the peptidyl transferase center of the 50s bacterial ribosome subunit. Resistance, including cross-resistance with other antibiotics, is infrequent. Lefamulin demonstrates activity against most Gram-positive pathogens and other organisms commonly associated with CABP, i.e., Streptococcus pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Legionella pneumophila, and Chlamydophila pneumoniae. Lefamulin may also be an option for serious public health threats like methicillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and multi-drug-resistant organisms associated with sexually transmitted infections, e.g., Neisseria gonorrhoeae, Mycoplasma genitalium. Lefamulin lacks activity against Pseudomonas aeruginosa, Acinetobacter baumannii, Enterobacterales, most anaerobes, and E. faecalis. In Phase III trials, lefamulin monotherapy was non-inferior to moxifloxacin with or without linezolid for CABP. Lefamulin is a well-tolerated agent with a unique mechanism, availability in both IV and PO formulations, and it has been rigorously studied for safety and efficacy for CABP.
Deep Convolutional Neural Network for Parkinson’s Disease Based Handwriting Screening

In this paper, the use of a fine-tuned VGG-19 for screening Parkinson’s Disease (PD) based on a Kaggle handwriting dataset is investigated and experimented. The dataset including 102 wave and 102 spiral handwriting patterns was pre-processed where images were resized and a data augmentation based on image rotation was adopted to minimize overfitting. The Convolutional Neural Network (CNN) model was then trained on the pre-processed dataset and validated using both 4-fold and 10-fold cross validation techniques. The CNN model achieved an accuracy of 88%, 89%, and a sensitivity of 89%, 87% on the wave and spiral patterns respectively when a 10-fold cross validation was used. The proposed approach offers a promising solution for assessing and screening PD based on handwriting drawings and achieves a comparable high performance on the two different handwriting patterns as compared with the-state-of-the-art architecture that adopted a fine-tuned AlexNet.
UHD-DPDK Performance Analysis for Advanced Software Radio Communications.

Research conducted in LTE and 5G wireless communications systems uses common off-the-shelf hardware components and commercial software defined radio (SDR) hardware. One of the more popular SDR platforms is the Ettus USRP product line which uses the UHD driver and transport protocol framework. System performance can be increased using kernel bypass frameworks along with UHD. This paper investigates UHD with DPDK in an SDR environment using srslTE as the SDR application. We present measurement results using the iperf3 network performance application that show performance improvements when employing a kernel bypass framework to facilitate data transfer over the network interface between the SDR application and the radio hardware.
Impacts of climate change on terrestrial hydrological components and crop water use in the Chesapeake Bay watershed

Abstract This study assessed the impacts of climate change on terrestrial hydrological components and Crop Water Use (CWU) over the Chesapeake Bay watershed using a combination of Global Climate Models (GCMs) and a land surface model. To better understand the impacts of climate change on the hydrological cycle, long-term simulations of multiple earth system models from the Coupled Model Intercomparison Project (CMIP Phase 5) are statistically downscaled and bias-corrected using Multivariate Adaptive Constructed Analogs (MACA) scheme for use as model forcing. Precipitation indices from the twenty MACA-based GCMs are used to identify six best performing models. A mesoscale approach is developed, where CWU is estimated by accounting for the impacts of changing climate conditions and rising CO2 levels. Daily grid-based crop coefficients are derived from evapotranspiration data. The findings indicate a significant annual increase in precipitation (10 %) and temperature (+4.5 K) for the RCP 8.5 scenario towards the end of the 21st century. A significant reduction (13 % and 17 % respectively) in CWU is estimated for corn and soybeans, resulting from increased total precipitation and rising CO2 levels suppressing evapotranspiration. Our results indicate that even in a warmer regime, crop water use decreased due to rising CO2 concentrations due to climate change.
Transdiagnostic Approaches to Sexual- and Gender-Minority Mental Health:

Sexual- and gender-minority individuals experience minority stress, which is hypothesized to underlie the mental-health disparities affecting these populations. Drawing on advances in the classific...
Pulsed focused ultrasound enhances mesenchymal stem cell homing to skeletal muscle in a murine model of muscular dystrophy and homing was suppressed by Ibuprofen

Homing of iv-infused stem cells to diseased tissues may be critical for cell therapies and is frequently an obstacle to successful cell therapy. We have previously shown that molecular responses from the mechanotransduction effects of pulsed focused ultrasound (pFUS) in normal murine skeletal muscle generate a “molecular zip-code” consisting of local increases in chemoattractants (cytokines, chemokines, cell adhesion molecules) that induced MSC homing, potentially improving cellular therapies for regenerative medicine. This study investigated whether pFUS could also enhance MSC homing to dystrophic skeletal muscle in a muscular dystrophy (MD) mouse model. Stem cell therapies for MD are promising, but have been hampered by poor cell homing and the need for direct injections that are invasive and ultimately, impractical clinically. Since molecular signals drive cell homing following iv injection, drugs used to treat MD could potentially interfere with pFUS-enhanced homing and undermine cell therapies for MD.
An Analytics Approach to Designing Clinical Trials for Cancer

Thesis (S.M. in Operations Research)--Massachusetts Institute of Technology, Sloan School of Management, Operations Research Center, 2013.
Consensus routing: the internet as a distributed system

Internet routing protocols (BGP, OSPF, RIP) have traditionally favored responsiveness over consistency. A router applies a received update immediately to its forwarding table before propagating the update to other routers, including those that potentially depend upon the outcome of the update. Responsiveness comes at the cost of routing loops and blackholes--a router A thinks its route to a destination is via B but B disagrees. By favoring responsiveness (a liveness property) over consistency (a safety property), Internet routing has lost both. Our position is that consistent state in a distributed system makes its behavior more predictable and securable. To this end, we present consensus routing, a consistency-first approach that cleanly separates safety and liveness using two logically distinct modes of packet delivery: a stable mode where a route is adopted only after all dependent routers have agreed upon it, and a transient mode that heuristically forwards the small fraction of packets that encounter failed links. Somewhat surprisingly, we find that consensus routing improves overall availability when used in conjunction with existing transient mode heuristics such as backup paths, deflections, or detouring. Experiments on the Internet's AS-level topology show that consensus routing eliminates nearly all transient disconnectivity in BGP.
Finite difference methods for the steady-state navier-stokes equations

Two iterative methods for numerically solving the incompressible 2D steady-state Navier-Stokes equation are presented. These are the Numerical Oseen (NOS) method and the Laplacian Driver (LAD) method. Unlike most methods, these are not time-dependent or even time-like in their iterations. The methods make use of recent advances in numerically solving 2D linear second-order partial differential equations with methods which are direct (i.e., non-iterative).