cssi/SciSciGPT-SciSciNet huggingface dataset:
Global analysis of transcription factor-binding sites in yeast using ChIP-Seq.

Yeast strains with epitope-tagged TFs are most commonly used for ChIP-Seq, along with their matching untagged control strains. The initial step of ChIP involves the cross-linking of DNA and proteins. Next, yeast cells are lysed and sonicated to shear chromatin into smaller fragments. An antibody against an epitope-tagged TF is used to pull down chromatin complexes containing DNA and the TF of interest. DNA is then purified and proteins degraded. Specific barcoded adapters for multiplex DNA sequencing are ligated to ChIP DNA. Short DNA sequence reads (28–36 base pairs) are parsed according to the barcode and aligned against the yeast reference genome, thus generating a nucleotide-resolution map of transcription factor-binding sites and their occupancy.
Towards synthetic evolution of nanostructures

The aim of this chapter is to explore the key ingredients that are necessary to apply non-biological evolutionary processes at the nano scale. In such processes, large numbers of building blocks spontaneously self-organize into new irregular forms that were not directly pre-determined by a designer, but rather form solutions to a given functional requirements. Such structures are able to adapt their configuration and behavior in response to changing requirements and changing conditions, ultimately leading to a form of evolutionary materials. The motivation for looking into self-organizing phenomena like evolution at the nano scale is both for finding new ways to design structures, and to synthetically recreate and examine the evolutionary processes that gave rise to primordial life. The chapter discusses some lessons learnt from applying evolutionary processes at macro-level robotic structures, and postulates as to key ingredients that are necessary to complete an evolutionary cycle at the nano scale.
Mechanosensitive subcellular rheostasis drives emergent single-cell mechanical homeostasis

Mechanical homeostasis-a fundamental process by which cells maintain stable states under environmental perturbations-is regulated by two subcellular mechanotransducers: cytoskeleton tension and integrin-mediated focal adhesions (FAs). Here, we show that single-cell mechanical homeostasis is collectively driven by the distinct, graduated dynamics (rheostasis) of subcellular cytoskeleton tension and FAs. Such rheostasis involves a mechanosensitive pattern wherein ground states of cytoskeleton tension and FA determine their distinct reactive paths through either relaxation or reinforcement. Pharmacological perturbations of the cytoskeleton and molecularly modulated integrin catch-slip bonds biased the rheostasis and induced non-homeostasis of FAs, but not of cytoskeleton tension, suggesting a unique sensitivity of FAs in regulating homeostasis. Theoretical modelling revealed myosin-mediated cytoskeleton contractility and catch-slip-bond-like behaviours in FAs and the cytoskeleton as sufficient and necessary mechanisms for quantitatively recapitulating mechanosensitive rheostasis. Our findings highlight the previously underappreciated physical nature of the mechanical homeostasis of cells.
VIOLET LASER EMISSION BY UPCONVERSION EXCITATION OF NEODYMIUM-DOPED FLUORIDES

Upconversion excitation processes can be used to obtain laser operation at wavelengths that are shorter than that of the pump source. Efficient operation of such lasers is possible in materials with metastable intermediate energy levels that act as population storage reservoirs. Excitation of higher levels that emit short-wavelength radiation can occur by absorption of a second photon from the intermediate level, or by energy transfer processes involving two ions in an intermediate state. Stimulated emission by upconversion excitation using flashlamp pumping was fust reported in 1971.1
Hemostatic Resuscitation for Perioperative Bleeding

The perioperative resuscitation approach to hemorrhagic shock is changing due to recent military experience in managing traumatic injury. For the past few decades, resuscitation of perioperative hemorrhagic shock has most commonly consisted of crystalloids and colloids, followed by RBCs, after which, if indicated according to laboratory results, plasma and platelets. If used, empiric ratios of RBC to plasma units ranged between 10 and 4 units of RBCs to 1 unit of plasma, without platelets. This approach was the foundation of Advanced Trauma Life Support (ATLS).
Development of a scintillation proximity binding assay for high-throughput screening of hematopoietic prostaglandin D2 synthase.

Prostaglandin D2 synthase (PGDS) catalyzes the isomerization of prostaglandin H2 (PGH2) to prostaglandin D2 (PGD2). PGD2 produced by hematopoietic prostaglandin D2 synthase (H-PGDS) in mast cells and Th2 cells is proposed to be a mediator of allergic and inflammatory responses. Consequently, inhibitors of H-PGDS represent potential therapeutic agents for the treatment of inflammatory diseases such as asthma. Due to the instability of the PGDS substrate PGH2, an in-vitro enzymatic assay is not feasible for large-scale screening of H-PGDS inhibitors. Herein, we report the development of a competition binding assay amenable to high-throughput screening (HTS) in a scintillation proximity assay (SPA) format. This assay was used to screen an in-house compound library of approximately 280,000 compounds for novel H-PGDS inhibitors. The hit rate of the H-PGDS primary screen was found to be 4%. This high hit rate suggests that the active site of H-PGDS can accommodate a large diversity of chemical scaffolds. For hit prioritization, these initial hits were rescreened at a lower concentration in SPA and tested in the LAD2 cell assay. 116 compounds were active in both assays with IC50s ranging from 6 to 807 nM in SPA and 82 nM to 10 μM in the LAD2 cell assay.
Preventing Complications of Pediatric Tracheostomy Through Standardized Wound Care and Parent Education

Importance Pediatric tracheostomy is commonly performed for upper airway obstruction and prolonged mechanical ventilation. Children undergoing tracheostomy typically have multiple chronic medical problems that place them at high risk for readmission and additional complications. Objective To determine whether the institution of a postoperative protocol for parent education and wound care with a nurse trained in tracheostomy care decreases the rate of readmission and other complications. Design, Setting, and Participants A case series and medical record review was conducted of children 18 years and younger who underwent tracheostomy at a tertiary pediatric medical center between January 1, 2009, and December 31, 2014. Intervention A postoperative tracheostomy care and education protocol. Main Outcomes and Measures Overall 30-day readmission rate, 30-day tracheostomy-related readmission rate, tracheostomy wound complications, and additional factors that may have affected readmission rates and wound complications (age at the time of tracheostomy, discharge location, indication for tracheostomy). Results A total of 191 children (118 boys and 73 girls) were included; of these, 112 participated in the education protocol and 79 children did not. Following institution of the education protocol, there was no decrease in the overall readmission rate (26.8% before the protocol vs 26.6% after the protocol; difference, 0.2%; 95% CI, –12.5% to 13.0%) or in the tracheostomy-related readmission rate (10.1% before the protocol vs 7.1% after the protocol; difference, 3.0%; 95% CI, –5.0% to 11.0%). Overall, 68.6% of readmissions were associated with medical comorbidities (95% CI, 55.9% to 81.3%). There was a significant decrease in tracheostomy-related wound complications after institution of the protocol (31.6% to 17.9%; difference, 13.7%; 95% CI, 1.6% to 26.0%). Multiple logistic regression analysis showed that children who were discharged home were significantly more likely to be readmitted for a tracheostomy-related complication than were patients discharged to an advanced care facility (odds ratio, 14.47; 95% CI, 3.08 to 67.92). Conclusions and Relevance Tracheostomy care requires expertise for all caregivers and is challenging for people without specialized training. Specialized nursing and education protocols are associated with decreased complications of tracheostomy wounds. Children who are discharged directly to home are at higher risk for readmission compared with children discharged to advanced care facilities. Further development of caregiver education protocols is necessary to continue to reduce readmissions and tracheostomy-related complications.
Rule 2: Have a Financial Plan

Intelligent investing isn’t an open-ended process whereby investors use financial markets to get rich quickly. Neither is it a panacea, a one-size-fits-all process. It is rather a process that allows these investors to achieve certain financial goals. That’s why intelligent investing begins with financial planning, which includes the financial goals and priorities to be pursued; the financial constraints and the means of achieving them; and a strategy that allocates funds to different financial assets that help investors match financial goals and priorities with financial means and constraints. This means that different investors may pursue different investment strategies, as goals and priorities and means and constraints differ across individuals. Younger individuals, for instance, may pursue an investment strategy that provides maximum liquidity, as they may need the invested funds in the near future to pay for education or for a down payment to buy a house.
Estimating the Net Career Income of a Geriatrician and a Nurse Practitioner: Still Want to Be a Doctor?

Objectives With a continual shortage of geriatricians, adult-gerontology primary care nurse practitioners have assumed a greater role in the delivery of outpatient care for older adults. Given the long duration of physician training, the high cost of medical school, and the lower salaries compared with subspecialists, the financial advantage of a career as a geriatrician as opposed to a nurse practitioner is uncertain. This study compares the estimated career earnings of a geriatrician and an adult-gerontology primary care nurse practitioner. Methods We used a synthetic model of estimated net earnings during a 43-year career span for a 22-year old person embarking on a career as a geriatrician versus a career as an adult-gerontology primary care nurse practitioner. We estimated annual net income and net retirement savings using different annual compound rates and calculated the financial impact of forgiving medical student loans, shortening the duration of physician training, and reinstituting the practice pathway for geriatric medicine certification. Results Career net incomes for the geriatrician did not match the nurse practitioner until almost age 40. At 65 years of age, the difference between the geriatrician and nurse practitioner was 30.6%. A higher annual compound rate was associated with an even smaller percentage difference. Combining all three health policy interventions lowered the break-even age to 28 and more than doubled the difference in career earnings. Conclusions Small estimated differences in net career earnings exist between geriatricians and adult-gerontology primary care nurse practitioners. Health policy interventions had a dramatic positive effect on geriatricians' lifetime net earnings in calculated estimates.
Ultrasonic tomographic imaging of defects in industrial materials

Ultrasonic tomography has been fairly widely applied for imaging of inhomogeneities in isotropic materials, particularly in the medical field, however, little success has been made in its application to industrial materials. This is largely due to the complex nature of ultrasonic wave propagation in these anisotropic materials. The three dimensional characteristics of ultrasonic wave propagation in anisotropic materials have been thoroughly studied for single crystals and also studied recently for different composites [1,2,3]. Understanding these characteristics provides the theoretical background for developing appropriate ultrasonic tomographic imaging methods for industrial materials.
Cell repair: Revisiting the patch hypothesis.

ABSTRACTPlasma membrane damage elicits a complex and dynamic cellular response. A vital component of this response, membrane resealing, is thought to arise from fusion of intracellular membranous compartments to form a temporary, impermeant patch at the site of damage; however, this hypothesis has been difficult to confirm visually. By utilizing advanced microscopy technologies with high spatiotemporal resolution in wounded Xenopus laevis oocytes, we provide the first direct visualization of the membrane fusion events predicted by the patch hypothesis; we show the barrier formed by patching is capable of abating exchange of material across the plasma membrane within seconds. Profound changes also occur to the plasma membrane surrounding wounds; lipid remodeling is accompanied by membrane fusion events, both conventional (e.g., exocytosis) and novel (e.g., “explodosis”). Further, we reveal additional complexity in wound-induced subcellular patterning, supporting existing evidence that extensive interaction...
Neutralizing Homelessness, 2015: Tent cities and ten year plans

Since Peter Marcuse published Neutralizing Homelessness in 1988, The United States has undergone a dramatic shift in homeless policy away from the emergency shelter model toward an emphasis on Chro...
Room-temperature InGaAs/InP quantum-well-in-nanopillar laser directly grown on silicon

We demonstrate room-temperature transparency and optically pumped lasing with an InGaAs quantum well active region integrated in an InP nanoresonator cavity grown monolithically on silicon. As-grown silicon transparent lasers will enable on-chip optical interconnects.
Application of Micro-CT and MRI in Clinical and Preclinical Studies of Osteoporosis and Related Disorders

Advanced imaging techniques, which are noninvasive and nondestructive, can provide structural information about bone beyond simple bone densitometry. As the mechanical competence of trabecular bone is a function of its apparent density and 3D distribution, assessment of 3D trabecular structural characteristics may improve our ability to understand the pathophysiology of osteoporosis, to test the efficacy of pharmaceutical intervention, and to estimate bone biomechanical properties. We studied ovariectomy-induced osteopenia in rats with various treatments. Micro-CT is also useful for studying osteoporosis in mice and phenotypes of mice with gene manipulation. Micro-CT can quantify osteogenesis in mouse Ilizarov leg-lengthening procedures, osteoconduction in rat cranial defect models, and structural changes in arthritic rabbits, rats, and mice. Micro-CT can reproducibly quantify 3D microarchitecture of new bone formation inside the pores of titanium prosthesis implants is rabbits. In clinical studies, we evaluated longitudinal changes in iliac crests in premenopausal and postmenopausal women. Paired bone biopsies from post-menopausal women with osteoporotic fracture shows that 3D trabecular microstructure deteriorates in the iliac crest of postmenopausal osteoporotic women without active treatment. Three-dimensional microstructural parameters can predict fracture. Treatment of PTH in postmenopausal women with osteoporosis significantly improved trabecular morphology with a shift toward a more plate-like structure, increased trabecular connectivity, and increased cortical thickness. Paired bone biopsy specimens from the iliac crest in postmenopausal women with osteoporosis before and after beginning estrogen replacement therapy demonstrated in post-treatment biopsies a significant change in the ratio of plates to rods. High-resolution MR and µMR have received considerable attention both as research tools and potential clinical tools for assessment of osteoporosis. It has been used in studying human specimens or animal models of osteoporosis with various treatment strategies.
Two Trigonometric Designs: One-Sided Riesz Products and Littlewood Products

A solution of the recently-resolved Littlewood conjecture is here presented in two stages of proof: the development of one-sided Riesz products and the Littlewood-product construction. In addition, problems are listed having to do with exerting more control on drift damage, with filling in gaps in our knowledge of trigonometric designs, and with positive mass interpolation vs. the sup interpolations of the present paper.
Differences in the Lateral Compartment Joint Space Width After Anterior Cruciate Ligament Reconstruction: Data From the MOON Onsite Cohort:

Background:Anterior cruciate ligament (ACL) reconstruction can effectively return athletes to the playing field, but they are still at risk of developing posttraumatic osteoarthritis (PTOA). No stu...
Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference

Small interfering RNA (siRNA) represents a promising class of inhibitors in both fundamental research and the clinic. Numerous delivery vehicles have been developed to facilitate siRNA delivery. Nevertheless, achieving highly potent RNA interference (RNAi) toward clinical translation requires efficient formation of RNA-induced gene-silencing complex (RISC) in the cytoplasm. Here we coencapsulate siRNA and the central RNAi effector protein Argonaute 2 (Ago2) via different delivery carriers as a platform to augment RNAi. The physical clustering between siRNA and Ago2 is found to be indispensable for enhanced RNAi. Moreover, by utilizing polyamines bearing the same backbone but distinct cationic side-group arrangements of ethylene diamine repeats as the delivery vehicles, we find that the molecular structure of these polyamines modulates the degree of siRNA/Ago2-mediated improvement of RNAi. We apply this strategy to silence the oncogene STAT3 and significantly prolong survival in mice challenged with melanoma. Our findings suggest a paradigm for RNAi via the synergistic coassembly of RNA with helper proteins.
Clinic Director Roles and Expectations

The ambulatory clinic director oversees the clinical and education mission for residents, patients, and faculty. This includes making sure residents become exposed to and skilled in varied areas of medicine, including chronic disease management, preventative care, mental healthcare, substance abuse, acute care, and population management. The ambulatory clinic is a critical learning venue for developing the necessary skills to provide outstanding outpatient care.
Origins of n -type doping difficulties in perovskite stannates

Materials that are simultaneously transparent and electrically conductive play a key role in optoelectronic devices. Barium stannate has recently come to the forefront as a promising new transparent conductor, but its conductivity has been difficult to control. The authors have performed computational studies to determine the mechanisms that limit doping. They find that atomic-scale defects, such as vacancies in the crystal lattice, are responsible, but their formation can be controlled by tailoring the growth conditions. The authors also investigated related materials, such as strontium stannate and calcium stannate, which are transparent even in the ultraviolet. Calcium stannate is found to always be insulating, but guidelines are provided for maximizing the conductivity of the strontium compound.
“Stories to Meditate On”: Animals in Gaita’s Narrative Philosophy

Narrative philosophy is the Australian philosopher Raimond Gaita’s answer to the question of how to philosophize in a manner that directly informs efforts to answer the classic philosophical question of ‘how best to live’. Gaita claims, provocatively, that getting the world in view in a manner relevant to arriving at an answer involves challenges that, far from being merely theoretical, are such that we can only meet them by working on ourselves or, alternately, by reshaping our sense of what matters. A productive philosophical intervention would thus need to be in the business of directing our attitudes and would have to have the hallmark of literary discourse or “narrative.” This chapter lays out Gaita’s case for thinking that we need narrative philosophy, and it discusses some of Gaita’s efforts to present us with such a philosophy, specifically in relation to ethical thought about human-animal relations. An important virtue of Gaita’s approach is that it equips us to overcome the philosophically influential, but morally questionable, idea of tension between the moral standing of animals and the moral standing of severely cognitively disabled human beings.
Human medial efferent activity elicited by dynamic versus static contralateral noises

Abstract The medial olivocochlear reflex (MOCR) modifies cochlear amplifier function to improve encoding of signals in static noise, but conflicting results have been reported regarding how the MOCR responds to dynamic, temporally-complex noises. The current study utilized three MOCR elicitors with identical spectral content but different temporal properties: broadband noise, amplitude-modulated noise, and speech envelope-modulated noise. MOCR activity was assessed using contralateral inhibition of transient-evoked otoacoustic emissions in 27 normal-hearing young adults. Elicitors were presented contralaterally at two intensities of 50 and 60 dB SPL. Magnitude and growth of contralateral inhibition with increasing elicitor intensity were compared across the three elicitor types. Results revealed that contralateral inhibition was significantly larger at the elicitor intensity of 60 dB SPL than at 50 dB SPL, but there were no significant differences in the magnitude and growth of inhibition across the three elicitors, contrary to hypothesis. These results suggest that the MOCR responds similarly to both static and dynamic noise.
THE PROPERTIES OF A PURIFIED HEPATIC MICROSOMAL MIXED FUNCTION AMINE OXIDASE

A microsomal mixed function oxidase has been concentrated approximately 1000-fold from pork liver. The purified enzyme catalyzes the NADPH- and oxygen-dependent N-oxidation of a variety of secondary and tertiary amines, including tranquilizers, antihistamines, narcotics, tropine alkaloids, ephedrine and ephedrine-like compounds. The tertiary amines are oxidized only to the amine oxide. Secondary amines are oxidatively N-dealkylated, at least in part. The oxidase does not catalyze the oxidation of N-methyl substituted amides, carbamates or heterocyclic nitrogen compounds containing a polar group α or β to the amino group. The purified oxidase is a flavoprotein and lacks detectable amounts of cytochrome P-450. It contains (in mumoles component/mg protein) FAD, 12.8; non-heme iron, < 2.0; cytochrome b5, 0.55; and an undetermined amount of phospholipid.
THE SPECTROSCOPIST AND THE COMPUTER – A PARTNERSHIP

A partner is defined as a participant or a colleague. It is in this sense that we see the role of the new data systems in a partnership with spectrophotometers and with spectroscopists. At the heart of this role is communication between the partners. The electronic interface between instrument and computer is handled today in a more or less standard manner. Resolving the interface between the computer and the spectroscopist is a much more difficult problem. It is a problem in human engineering which requires great attention to the needs and thinking processes of the spectroscopist partner, the constraints and capabilities of the computer partner, and the capabilities of the instrument partner.
Proceedings of the 14th international conference on Hybrid systems: computation and control

It is our great pleasure to welcome you to the 14th ACM International Conference on Hybrid Systems: Computation and Control (HSCC 2011), held in Chicago, April 12-14, 2011. This year's conference continues its tradition of being the premier forum for presentation of research results and experience reports on leading edge issues on the theory and practice of embedded reactive systems involving the interplay between discrete and continuous dynamic behaviors. The mission of the conference is to share information on the latest advancements, both practical and theoretical, in the design, analysis, control, optimization, and implementation of hybrid systems. Previous editions of HSCC were held in Berkeley, 1998, Nijmegen, 1999, Pittsburgh, 2000, Rome, 2001, Palo Alto, 2002, Prague, 2003, Philadelphia, 2004, Zurich, 2005, Santa Barbara, 2006, Pisa, 2007, St. Louis, 2008, San Francisco, 2009 and Stockholm, 2010. The call for papers, which included for the first time a call for tool-presentation papers in addition to regular papers, attracted a large number of very competitive submissions from Asia, Canada, Europe, and the United States. After a very careful reviewing process and in-depth discussions, the program committee accepted 31 regular papers and 4 tool-presentation papers for presentation. All submitted papers were reviewed by at least 3 PC members with support from external reviewers. HSCC 2011 takes place under the umbrella of the 4th Cyber-Physical Systems Week (CPSWeek), which is the collocated cluster of five conferences and workshops: HSCC, the International Conference on Cyber-Physical Systems (ICCPS), the International Conference on Information Processing in Sensor Networks (IPSN), the Conference on Languages, Compilers, and Tools for Embedded Systems (LCTES), and the Real-Time and Embedded Technology and Application Symposium (RTAS). Through CPSWeek, the five conferences had joint plenary speakers, poster and demo sessions, workshops and tutorials as well as joint social events.
The Proton-Translocating Membrane ATPase (F1F0) in Streptococcus faecalis (faecium)

It is generally believed that a proton-translocating ATPase, referred to as the F1F0 ATPase, is present universally in bacterial cell membranes. It is also apparent that, at the level of quaternary structure, the bacterial enzyme is essentially identical to the F1F0 ATPase localized in membranes of mitochondria, photosynthesizing organelles, and certain secretory vesicles within eukaryotic cells. Theoretically, all F1F0 ATPases are considered to be reversible, but physiologically the enzyme may operate mainly or only in one direction. In mitochondria or respiring bacteria, for example, the enzyme mediates oxidative phosphorylation energized by a transmembrane electrochemical potential of H+ ions, the proton-motive force (PMF), generated by a respiratory chain. On the other hand, in an organism like S. faecalis (faecium), which lacks a respiratory chain, or in secretory vesicles, the F1F0 ATPase functions only as a hydrolase and ATP hydrolysis is coupled to the generation of a PMF. The PMF is then harnessed to drive active transport. Finally, in a facultative organism like E. coli, the enzyme may function either as an ATP synthetase or hydrolase depending on whether the organism derives its energy from respiration or from anaerobic glycolysis as dictated by environmental circumstances.
Superficial vein thrombosis.

Superficial vein thrombosis (SVT), also known as superficial thrombophlebitis, is historically thought of as a benign condition that can always be treated symptomatically with nonsteroidal antiinflammatory drugs (NSAIDs) and elastic compression. However, many studies have reported an association of SVT with venous thromboembolism (VTE), with rates of concomitant deep vein thrombosis (DVT) as high as 53% and pulmonary embolism (PE) as high as 33% with lung scanning. In addition, SVT recurrence and extension is often reported. Although well-designed, randomized, controlled trials are few in this patient population, data suggest that anticoagulation in general and low-molecular-weight heparins specifically are the most effective treatment for SVT for resolving symptoms, preventing SVT recurrence or extension, and preventing VTE. When the significant morbidity and mortality associated with VTE is considered, it is reasonable that anticoagulation be used in all patients with SVT.
Electronic motion in DNA

The question of whether DNA is like a wire or an insulator is a controversial one, with some experiments finding DNA is conducting and some not. A new experiment suggests that it may all depend on the DNA sequence — electron transfer in DNA only occurs with high efficiency between guanine bases. This mechanism may help explain previous disparate results.
Revising predictions

Making a prediction is essentially expressing a belief about the future. It is therefore natural to interpret later predictions as revisions of earlier ones and to investigate the notion of belief revision in this context. We study, both semantically and syntactically, the following principle of minimum revision of prediction: "as long as there are no surprises, that is, as long as what actually occurs had been predicted to occur, then everything which was predicted in the past, if still possible, should continue to be predicted, and no new predictions should be added."
The value of sharing disaggregated information in supply chains

Abstract We study a two-stage supply chain where the retailer observes two demand streams coming from two consumer populations. We further assume that each demand sequence is a stationary Autoregressive Moving Average (ARMA) process with respect to a Gaussian white noise sequence (shocks). The shock sequences for the two populations could be contemporaneously correlated. We show that it is typically optimal for the retailer to construct its order to its supplier based on forecasts for each demand stream (as opposed to the sum of the streams) and that doing so is never sub-optimal. We demonstrate that the retailer’s order to its supplier is ARMA and yet can be constructed as the sum of two ARMA order processes based upon the two populations. When there is no information sharing, the supplier only observes the retailer’s order which is the aggregate of the two aforementioned processes. In this paper, we determine when there is value to sharing the retailer’s individual orders, and when there is additional value to sharing the retailer’s individual demand sequences. In order to determine the magnitude of the value of information sharing we show how to compute the supplier’s mean squared forecast error under no sharing, order sharing, and demand sharing.
Response to Comment on Jiang Paper

This is in response to a comment on a paper published in JAI, "Introducing Excess Return on Time-Scaled Contributions: An Intuitive Return Measure and New Solution to the IRR and PME Problem."
Heart-Failure Therapy - New Drugs but Old Habits?

In 2015, empagliflozin, an inhibitor of sodium–glucose cotransporter 2 (SGLT2), lowered the composite cardiovascular end point in the EMPA-REG trial1 involving patients with type 2 diabetes mellitu...
Use of Computer Modeling to Streamline Care in a Psychiatric Emergency Room: A Case Report

Computer simulation using JaamSim tested the impact of changing the number of providers, proportion of independent to supervised providers, shift provider added, time to hospitalization, and the nu...
Custom-molded headcases have limited efficacy in reducing head motion for fMRI

Effectively minimizing head motion continues to be a challenge for the collection of functional magnetic resonance imaging (fMRI) data. The development of individual-specific custom molded headcases have been offered as a promising solution to minimizing motion during data collection, but to date, only a single published investigation into their efficacy exists in the literature. That study found headcases to be effective in reducing motion during short resting state fMRI scans (Power et al, 2019). In the present work, we examine the efficacy of these same headcases in reducing motion for a larger group of participants engaged in naturalistic scanning paradigms that consist of long movie-watching scans (~20-45min), as well as speaking aloud inside the MRI. Unlike previous work, we find no reliable reduction in head motion during movie viewing when comparing participants with headcases to those who were simply situated with foam pillows or foam pillows with medical tape. Surprisingly, we also find that for those wearing headcases, head motion is worse while talking relative to those situated with just foam pillows. These differences appear to be driven by large brief rotations of the head as well as translations in the z-plane as participants speak. Smaller, constant head movements appear equivalent with or without headcases. The largest reductions in head motion are observable when participants were situated with both foam pillows and medical tape, consistent with recent work by Kraus and colleagues (2019). Altogether, this work suggests that in a non-clinical, non-developmental population, custom-molded headcases may provide limited efficacy in reducing head motion beyond existing tools available to researchers. We hope this work can help improve the quality of custom headcases, motivate the investigation of additional solutions, as well as help researchers make more informed decisions about their data acquisition procedures.
Chapter 13 – Nuclear Power

Publisher Summary Nuclear fission is a mature though controversial energy technology where electricity is generated from the energy released when heavy nuclei break apart. In the case of nuclear fusion, much work remains in the effort to sustain the fusion reactions and then to design and build practical fusion power plants. The fuel for nuclear fusion is abundant, namely, light atoms such as the isotopes of hydrogen. Nuclear energy can be generated by fission (the splitting of a nucleus). Fission reactions do not generate greenhouse gases or the air pollutants that produce urban smogs and regional acid precipitation. A nuclear reactor power plant essentially consists of a uranium fuel core, a converter loop, a turbine-generator, and a condenser. Nuclear fission electric power plants give rise to issues regarding operating hazards, particularly the chances of a serious reactor accident, the difficulties of safeguarding the fissionable materials used as reactor fuels, and the still unresolved problem of long-term storage for radioactive wastes.
Trajectories of internalizing symptoms in early childhood: Associations with maternal internalizing symptoms and child physiology.

Research has shown that children's internalizing symptom development during early childhood are shaped by biopsychosocial processes including physiology and parental symptoms. However, associations between maternal internalizing symptoms, child physiology and trajectories of child internalizing symptoms are not well understood. We used growth curve models to examine how maternal internalizing symptoms, child physiology and the interaction between maternal internalizing symptoms and child physiology may be associated with trajectories of internalizing symptoms during early childhood. Mothers reported their children's internalizing symptoms when children were 3, 4, 5 and 6 years of age, and mothers self-reported their own internalizing symptoms when children were 3. Respiratory Sinus Arrhythmia (RSA) was collected when children were 3.5-years-old. Results showed that there is a non-linear, quadratic trajectory across all participants from age 3 to 6. Maternal internalizing symptoms were not associated with children's internalizing symptoms at age 6, but were associated with both linear and quadratic change. Lower resting RSA was associated with greater increases in children's internalizing symptoms over time. Interactions between maternal internalizing symptoms and RSA were not associated with children's internalizing symptom development. The findings demonstrate that maternal internalizing symptoms and child physiology are independently associated with internalizing symptom development during early childhood.
De novo assembly and annotation of the North American bison (Bison bison) reference genome and subsequent variant identification.

Genomic tools have improved the ability to manage bison populations and enhanced efforts to conserve this iconic species. These tools have been particularly useful for detecting introgression of cattle genome within bison herds but are limited by the need to use the cattle genome as a surrogate for mapping reads. This complicates efforts to distinguish the species of origin of chromosomal segments in individual bison at the genomic level. An assembly (Bison_UMD1.0) based on 75X genome coverage by Illumina and 454 reads was generated using the MaSuRCA assembler, generating a 2.81 Gigbases de novo reference genome from American bison. Comparison of bison and domestic cattle references identified 28 443 364 single nucleotide variants and 2 627 645 insertions/deletions distinguishing the species. Sequence alignment of an additional 12 modern bison samples and two historic bison samples to domestic cattle and bison references provides a dataset of genomic variants defining the different species and within-species variation. This first annotated draft assembly represents a resource for the management and conservation of bison, as well as a means to study the effects on the genome of interspecies hybridization. The comparisons of historical bison sequences with the new bison reference identified genomic differences between modern and pre-population bottleneck bison. The results support the application of genomics to enhance future research on disease, the establishment of satellite conservation herds and insight into bison and cattle speciation. The first genome assembly for bison and dataset provides a foundation that can be built upon as genetic technologies improve over the years.
Toward a Universal Visual Language of Law

There is a legal language that is more universal than text, that can communicate across language and cultural barriers: it is the language of visual images. Visual communication of law provides a means to transmit the content, meaning, and implications of law and legal analysis in legal documents and multimodal communications that are accessible and understandable not only to those trained in the law or highly literate in the dominant written language of the communication, but also to those whose basic language skills in the dominant language of the communication would otherwise not allow them to receive or understand the legal advice, rights, or requirements contained in the communication. In the very near future, visual legal rhetoric is anticipated to become a standard part of legal practice not just in litigation, but also in transactional practice and all areas of law because of the communicative and rhetorical power of visual media. The goal of this Article is to apply the lens of visual legal rhetoric, visual literacy analysis, visual cultural studies, and mise en scene analysis to evaluate and critique representative examples of legal communications that use visual images as a means to overcome language and cultural barriers. I hope to draw lessons in visual communication for lawyers, judges, legislators, and regulators to encourage them to make visuals a more integral part of legal works in transactional, litigation, legislative, regulatory, and legal informational contexts. Visuals can overcome barriers in communication that words alone cannot, and visual legal works can be made more universal in their communication, interpretation, performance, and enforcement.
Detection and partial characterization of extracellular inducers of persistence in Staphylococcus epidermidis and Staphylococcus aureus.

Introduction. This study describes the identification and partial characterization of persistence-inducing factors (PIFs) from staphylococci.Hypothesis/Gap Statement. Increases in persisters during mid-log phase growth indicate that quorum-sensing factors might be produced by staphylococci.Aim. To identify and partially characterize PIFs from Staphylococcus epidermidis RP62A and Staphylococcus aureus SH1000.Methodology. Others have demonstrated a significant increase in persister numbers during mid-log phase. Inducers of this mid-log increase have yet to be identified in staphylococci. Optical density at 600 nm (OD600) was used instead of time to determine when persister numbers increased during logarithmic growth. Concentrated culture filtrates (CCFs) from S. epidermidis and S. aureus were obtained at various OD600s and following incubation at 16 h. The CCFs were used to develop a PIF assay. The PIF assay was used to partially characterize PIF from S. epidermidis and S. aureus for sizing of PIF activity, temperature and protease sensitivity and inter-species communications.Results. The optimal OD600s for S. epidermidis and S. aureus PIF assays were 2.0 and 0.5, respectively. The highest PIF activity for both species was from CCF following incubation overnight (16 h). S. epidermidis' PIF activity was decreased by storage at 4 oC but not at 20 oC (16 h), 37 oC (1 h) or 100 oC (15 min). S. aureus' PIF activity was decreased following storage at 4 oC (2 weeks) and after boiling at 100 oC for 5 min but not after incubation at 37 oC (1 h). PIF activity from both species went through a 3000 molecular weight cutoff ultrafilter. Proteinase K treatment of S. aureus PIF decreased activity but did not decrease the PIF activity of S. epidermidis. PIF from S. epidermidis did not increase persisters when used to treat S. aureus cells and nor did PIF from S. aureus increase persisters when used to treat S. epidermidis cells.Conclusions. Attempts to discover PIFs for staphylococci were unsuccessful due to the time-based means used to identify mid-log. Both staphylococcal species produce extracellular, low-molecular-weight inducers of persistence when assayed using an OD600 -based PIF assay.
Complexity issues in circuits for neural computation

Artificial Neural Networks (ANNs) present a new model for massively parallel computation and a promising paradigm for solving large scale optimization problems. One common model for ANNs is the threshold circuit--a multilayer feedforward network of linear threshold gates. In this thesis, we provide a rigorous analysis of this model via a circuit complexity theoretic approach by focusing on the basic computational properties of threshold circuits with binary inputs. The size (i.e. number of gates) and the depth (i.e. number of layers) of a network measure the amount of hardware and the time for parallel computation, respectively. In this thesis, we shall present the best known results on the depth of threshold circuits in implementing common arithmetic functions such as multiplication, division, and sorting. While traditional logic circuits consisting of polynomially many (in n) arbitrary fan-in AND/OR gates would require at least $\Omega$(log n/log log n) depth to compute the product or the quotient of two n-bit numbers, such arithmetic computations can be carried out by polynomial size threshold circuits of small constant depth. For example, we can construct depth-4 threshold circuits of polynomial-size that compute the product of two n-bit numbers or the sorting of n n-bit numbers. An important problem in the application of neural networks is the tradeoff between the depth and the size. We demonstrate that a small increase in the depth can significantly decrease the size of the threshold circuit required for a special, but very useful class of functions, namely the symmetric functions. While the best known result requires O(n) gates for a depth-2 threshold circuit that computes any symmetric Boolean function (in n variables), we can show that only $O(\sqrt{n})$ threshold gates are needed for a depth-3 circuit. Moreover, using results from the theory of rational approximation, we provide the first known nontrivial lower bound results on the size of threshold circuits with depth more than two by showing that at least $\Omega(n\sp{1/2-\epsilon})$ for any $\epsilon >$ 0 threshold gates are needed (for a depth-3 threshold circuit) to compute any symmetric Boolean function.
Large Strain Analysis and Stresses in Linear Materials

A method is presented to determine stresses and strains in a greatly deformed body subjected to a state of plane stress when the modulus of elasticity of the material used is approximately constant within the range of natural strains being considered. To demonstrate the method, a birefringent disk is subjected to a series of large diametral compressive loads, and the principal stresses and strains are computed across the horizontal diameter by means of photoelasticity, grids, and thickness measurements. Natural strains and true stresses are used in the analysis. With this type of description, the mechanical properties of the material are linear to a strain of 0.15 with a deviation of less than 5% from linearity in Young’s modulus at a strain level of 0.18. Birefringence is linear to beyond 0.15 strain. Results are given in dimensionless form. Equilibrium checks are satisfactory for all levels of load applied.
Protease helps yeast find mating partners

The choice of mating partner by the yeast Saccharomyces cerevisiae involves the detection of mating pheromones produced by other yeast cells. A cell that is capable of mating deduces the position of its nearest mating partner from the spatial gradient of pheromone. While studying this process, we realized that, in the presence of many potential mating partners, the gradient might not point in the direction of the nearest partner. Here we show that degradation of some of the mating pheromone by protease enzymes helps to align the gradient in the direction of the nearest partner, which increases mating efficiency.
Extracting optimal paths from roadmaps for motion planning

We present methods for extracting optimal paths from motion planning roadmaps. Our system enables any combination of optimization criteria, such as collision detection, kinematic/dynamic constraints, or minimum clearance, and relaxed definitions of the goal state, to be used when selecting paths from roadmaps. Our algorithm is an augmented version of Dijkstra's shortest path algorithm which allows edge weights to be defined relative to the current path. We present simulation results maximizing minimum path clearance, minimizing localization effort, and enforcing kinematic/dynamic constraints.
A Discretionary Access Control Method for Preventing Data Exfiltration (DE) via Removable Devices

One of the major challenges facing the security community today is how to prevent DE. DE is the unauthorized release of information from a computer system or network of systems. Current methods attempt to address this issue by controlling the information that is released over the Internet. In this paper, we present a host-level discretionary access control method that focuses on exfiltration via removable devices (e.g. thumb drives or external hard drives). Using XML to store extended file attributes, we classify files based on user-defined distribution levels and the community of interest to which they belong. Files are classified with a distribution statement upon creation and re-classified (if necessary) when modified. By monitoring the access to all classified files present on a file system, we allow or prevent release of this information based on predefined policies. With this approach, we show that the unauthorized release of information can be prevented by using a system of accounting that is tied to access control policies. Users are given the authority to transfer files to a removable device according to their current access rights. As a proof of concept, our method demonstrates the value of using accounting as a means of preventing data loss or theft. Our approach can be applied to a variety of data types found on a file system including: executables, archived files, images, and even audio or video files.