cssi/SciSciGPT-SciSciNet huggingface dataset:
Geological and hydrological visualization models for Digital Earth representation

This paper presents techniques and interactive models for multi-dimensional analyses and geospatial visualization in virtual globes based on three application examples: (1) earthquakes around the world, (2) groundwater well levels in Texas, and (3) geothermal subsurface heat indexes in Texas.While studies are known that represent multi-dimensional geospatial data points, we develop and suggest multi-dimensional models for virtual globes using KML and KMZ (compressed KML files) with a complete and static time series data set. The benefit of this approach for the user is the ability to view and analyze time-based correlations interactively over the entire time span in one instance, which is not possible with animated (dynamic) models.The methods embedded in our models include: (a) depth layered cueing within subsurface Earth visualization for a better orientation when maneuvering below the ground, (b) a technique with Ternary Visual Shape Logic (TVSL) as a quick indicator of change over time, and (c) different visual representations of multiple dimensions for the addressed case study examples. The models can be applied to a variety of problems in different disciplines, especially to support decision-making processes. Display Omitted Earthquakes, groundwater wells, and geothermal energy are examined.Integration of multiple visualization techniques into KML.Efficient memory use of KML data structures.The models are interactive and open access.The models can be used on any modern computer system and smartphone devices.
Cathodic Control of Intergranular Corrosion Propagation in Al-Mg Alloys Under Thin Film Conditions

Many studies have been conducted to investigate the role of metallurgical and electrochemical factors on intergranular corrosion (IGC) of Al-Mg alloys. However, the majority of these studies have been conducted under full immersion conditions, whereas most of the marine infrastructure using these alloys are exposed to atmospheric conditions. Hence, there is a need to extend the existing full immersion corrosion framework to atmospheric and/or thin film conditions. The work presented here investigates the cathodic control of IGC propagation in AA5xxx in thin film electrolyte conditions.
The effects of resynchronization of estrus using a progestin-based system

Improved synchronization systems facilitate fixed-time AI (FTAI) in beef heifers. However, after FTAI 30 to 50% of heifers are not pregnant. The objectives were to (1) characterize return to estrus patterns after initial FTAI, (2) determine the effectiveness of an FTAI resynchronization protocol, and (3) evaluate the economic costs of resynchronization. Estrus was synchronized in crossbred heifers (n = 176) using the 5-d CO-Synch + CIDR with FTAI at 72 h (d 0). Estrus was detected with HeatWatch (d −8 to 37). Similar numbers of heifers identified as estrus or nonestrus at initial AI were randomly assigned to resynchronization (RS) or natural service (NSV) rebreeding treatments. The RS treatment was diagnosed for pregnancy on d 29, and nonpregnant heifers were resynchronized using 5-d CO-Synch + CIDR with FTAI at 72 h. Pregnant RS heifers received no further treatment. The NSV heifers were exposed to fertile bulls from d 14 to 66. Of heifers not pregnant to initial AI, 24.7 and 48.2% were in estrus from d 5 to 11 and d 14 to 25, respectively. Total AI pregnancies tended to be greater (P = 0.07) for RS (69.7%) than NSV (56.5%) groups. Overall pregnancy rate was greater (P < 0.01) for NSV (89.4%) than for RS (69.7%). Not accounting for genetic merit of AI calves, cost per pregnancy was $24 greater for RS than NSV because of more nonpregnant RS heifers. Distribution of return estrus is highly variable. Resynchronization protocols incorporating pregnancy detection may not be biologically or economically effective in commercial beef heifers.
Development of the embedded LSI technology in PALAP/spl trade/

We are developing the embedded LSI technology in PALAP/spl trade/; PWB developed by DENSO CORP.; made from plural patterned thermoplastic resin films and fabricated with one time hot press process. To understand the behavior of the resin, via, copper land, LSI and so on during press process, a new strong coupling analysis system was developed. Using this system, we analyzed the velocity of resin around the LSI, when embedding the LSI. As a result, it was cleared that the resin under the LSI flowed toward the clearance, and the velocity sharply increased at peripheral position of the LSI. Practically, via under the LSI radially moved from the LSI central part according to the velocity distribution. It is not concerned with the positional relationship between the LSI bump and via that the clearance is different from each other at the left right of the LSI, because the LSI moves with the resin at the same timing and velocity.
Supporting Upper-Level Undergraduate Students in Building a Systems Perspective in a Botany Course.

AbstractUndergraduate biology majors require biological literacy about the critical and dynamic relationships between plants and ecosystems and the effect human-made processes have on these systems. To support students in understanding systems relationships, we redesigned an undergraduate botany course using an ecological framework and embedded systems modelling to support students in understanding the criticality of plant processes to the global carbon cycle. The class meetings included lectures, opportunities to develop systems models identifying the relationships between plant processes and other systems, reflections on their systems understanding and open-floor discussions about assigned primary and secondary readings that explored the relationships between plant systems, abiotic and biotic processes and global carbon cycling in their systems models. We used the systems models students developed at the beginning and end of the course to examine how their systems understanding grew. Our results suggest...
Factors Affecting Nutritional Status of the Elderly

A complete assessment of nutritional status includes determination of dietary intake, anthropometric measurements, biochemical measurements, and clinical assessment. The state of the art in assessing nutrition status through each of these parameters has been reviewed recently by Kohrs and Czajka-Narins (1986). In interpreting data on the elderly, the advantages and limitations of the methods for dietary intake and anthropometric measurement need to be taken into consideration as well as the limitations of the current biochemical methods.
Single-staged resections and 3D reconstructions of the nasion, glabella, medial orbital wall, and frontal sinus and bone: Long-term outcome and review of the literature.

BACKGROUND Aesthetic facial appearance following neurosurgical ablation of frontal fossa tumors is a primary concern for patients and neurosurgeons alike. Craniofacial reconstruction procedures have drastically evolved since the development of three-dimensional computed tomography imaging and computer-assisted programming. Traditionally, two-stage approaches for resection and reconstruction were used; however, these two-stage approaches have many complications including cerebrospinal fluid leaks, necrosis, and pneumocephalus. CASE DESCRIPTION We present two successful cases of single-stage osteoma resection and craniofacial reconstruction in a 26-year-old female and 65-year-old male. The biopolymer implants were preselected and contoured based on imaging prior to surgery. The ideal selection of appropriate flaps for reconstruction was imperative. The flaps were well vascularized and included a pedicle for easy translocation. Using a titanium mesh biopolymer implant for reconstruction in conjunction with a forehead flap proved advantageous, and the benefits of single-stage approaches were apparent. The patients recovered quickly after the surgery with complete resection of the osteoma and good aesthetic appearance. The flap adhered to the biopolymer implant, and the cosmetic appearance years after surgery remained decent. The gap between the bone and implant was less than 2 mm. The patients are highly satisfied with the symmetrical appearance of the reconstruction. CONCLUSIONS Advances in technology are allowing neurosurgeons unprecedented opportunities to design complex yet feasible single-stage craniofacial reconstructions that improve a patient's quality of life by enhancing facial contours, aesthetics, and symmetry.
Gα13 negatively controls osteoclastogenesis through inhibition of the Akt-GSK3β-NFATc1 signalling pathway.

Many positive signalling pathways of osteoclastogenesis have been characterized, but negative signalling pathways are less well studied. Here we show by microarray and RNAi that guanine nucleotide-binding protein subunit α13 (Gα13) is a negative regulator of osteoclastogenesis. Osteoclast-lineage-specific Gna13 conditional knockout mice have a severe osteoporosis phenotype. Gna13-deficiency triggers a drastic increase in both osteoclast number and activity (hyper-activation), mechanistically through decreased RhoA activity and enhanced Akt/GSK3β/NFATc1 signalling. Consistently, Akt inhibition or RhoA activation rescues hyper-activation of Gna13-deficient osteoclasts, and RhoA inhibition mimics the osteoclast hyperactivation resulting from Gna13-deficiency. Notably, Gα13 gain-of-function inhibits Akt activation and osteoclastogenesis, and protects mice from pathological bone loss in disease models. Collectively, we reveal that Gα13 is a master endogenous negative switch for osteoclastogenesis through regulation of the RhoA/Akt/GSK3β/NFATc1 signalling pathway, and that manipulating Gα13 activity might be a therapeutic strategy for bone diseases. Osteoclasts are bone resorptive cells and an attractive target to treat diseases characterized by excessive bone loss, but little is known about osteoclast inhibition. Here the authors identify Gα13 as an intracellular inhibitor of osteoclastogenesis that can prevent bone loss in mice via Akt activation and inhibition of RhoA signalling.
Safety impacts of bicycle infrastructure: A critical review.

Abstract Problem and method This paper takes a critical look at the present state of bicycle infrastructure treatment safety research, highlighting data needs. Safety literature relating to 22 bicycle treatments is examined, including findings, study methodologies, and data sources used in the studies. Some preliminary conclusions related to research efficacy are drawn from the available data and findings in the research. Results and discussion While the current body of bicycle safety literature points toward some defensible conclusions regarding the safety and effectiveness of certain bicycle treatments, such as bike lanes and removal of on-street parking, the vast majority treatments are still in need of rigorous research. Fundamental questions arise regarding appropriate exposure measures, crash measures, and crash data sources. Practical applications This research will aid transportation departments with regard to decisions about bicycle infrastructure and guide future research efforts toward understanding safety impacts of bicycle infrastructure.
The Prospects for a Color Revolution in Russia

From 1998 to 2005, six elections took place in postcommunist Europe and Eurasia that led to the defeat of authoritarian incumbents or their anointed successors, the empowerment of opposition forces, and, thereafter, the introduction of democratic reforms. Because Putin's regime closely resembles those regimes that were successfully challenged by these dramatic changes in politics, Russia is a logical candidate for such a “color revolution,” as these electoral turnovers have been termed. Moreover, the color revolutions have demonstrated an ability to spread among countries, including several that border Russia. However, the case for a color revolution in Russia is mixed. On the one hand, the many costs of personalized rule make Putin's Russia vulnerable. On the other hand, Putin has been extraordinarily effective at home and abroad in preempting the possibility of an opposition victory in Russian presidential and parliamentary elections.
Comorbidities and Biological Correlates of Conduct Disorder

Chronic antisocial syndromes in adulthood are preceded by antisocial behavior in childhood and adolescence (Robins, 1966, 1978). The near-universality of this sequence is codified in the DSM-IV (American Psychiatric Association, 1994) definition of Antisocial Personality Disorder (APD), in the diagnostic criterion requiring that Conduct Disorder (CD) originated before the age of 15 years. Unlike the diagnostic category of APD, psychopathy is measured dimensionally, and it has no essential diagnostic requirements even when dimension score cutpoints are applied to make a categorical distinction. Documentation of youthful onset can only raise the dimensional score by affecting the two (of a total of 20) items from the Hare Psychopathy Checklist-Revised PCL-R (Hare, 1991) that refer to antisocial behavior during the developmental period—early behavior problems and juvenile delinquency. Yet, developmental origin is just as axiomatic for psychopathy as for APD (Hare, 1970).
Epigallocatechin gallate induces phosphorylation of epidermal growth factor receptor via activation of p38 MAPK in colon cancer cells.

616 We previously reported that (-)-Epigallocatechin Gallate (EGCG) inhibits epidermal growth factor (EGF) binding to the EGF receptor (EGFR) and the subsequent dimerization of the EGFR by altering plasma membrane organization, and that this is associated with loss of ordered domains, so called “lipid rafts” in the plasma membrane (Adachi S et al., Cancer Res. 2007 67:6493-501). Since lipid rafts are thought to play a role in endocytosis, we next examined the effects of EGCG on cellular localization of the EGFR in SW480 colon cancer cells and found that EGCG caused internalization of EGFRs and that these internalized EGFRs can recycle back to the cell surface. To further examine the mechanism of this we focused on p38 MAPK, a stress-inducible kinase believed to negatively regulate tumorigenesis, because it was recently reported that Cisplatin and UV can induce internalization of EGFR via activation of p38 MAPK. We first found that EGCG can strongly induce phosphorylation of p38 MAPK (Thr180/Tyr182) in a time- and dose-dependent manner. EGFR underwent a gel mobility shift upon treatment with EGCG and this was canceled by the p38 MAPK inhibitor SB202190, indicating that EGCG might cause phosphorylation of the EGFR at serine or threonine, residues, sites phosphorylated by p38 MAPK. We also found that longer exposure to 50 μM EGCG for 12 hours can lead to degradation of the EGFR and IGF-1R, while exposure to 50 μM EGCG caused degradation of HER-2 within 1 hour. The degradation of these RTKs by treatment with EGCG was not blocked by SB202190 even though the internalization of EGFR by Cisplatin was blocked by this inhibitor. Interestingly, phosphorylation of p38 MAPK was seen by EGCG as well as cisplatin in SW480 cells, but cisplatin had much less effect than EGCG in CCD841 normal colon epithelial cells. Taken together, these results indicate that relatively high concentrations of EGCG can induce degradation of EGFR, IGF-1R and HER-2 but this is unlikely to be due to activation of the p38 MAPK pathway, even though EGCG activated this pathway. The pathway of internalization of the EGFR induced by EGCG appears to be different from that of Cisplatin-induced internalization of the EGFR. However, it is still of interest to further examine the function of p38 MAPK in anti-cancer effects of EGCG.
Community-Owned Transport

It is easy to imagine that we are in a transformative time for mobility, with increasingly connected vehicles, renewed investments in rail and bus rapid transit, expanding e-hail taxi platforms, an...
Tracheal stenosis by innominate artery compression in infants: surgical treatment in 35 cases

This is a report on 35 cases of innominate artery compression of the trachea and its surgical correction by means of aortotruncopexy. Diagnostic procedures of choice were tracheoscopy and magnetic resonance imaging, which offers representative images of inspiration and expiration, shows the anatomical relations between aortic arch and trachea and reveals the extent of tracheal compression. Surgical treatment is indicated if narrowing of the tracheal lumen exceeds 70%. By fixation of the aortic arch and the proximal innominate artery to the back of the sternum, tracheal compression is relieved. There was no unsuccessful operation in the 35 children. One late death occurred from cardiac failure, unrelated to tracheal compression.
Time and Sequence Integrated Runtime Anomaly Detection for Embedded Systems

Network-connected embedded systems grow on a large scale as a critical part of Internet of Things, and these systems are under the risk of increasing malware. Anomaly-based detection methods can detect malware in embedded systems effectively and provide the advantage of detecting zero-day exploits relative to signature-based detection methods, but existing approaches incur significant performance overheads and are susceptible to mimicry attacks. In this article, we present a formal runtime security model that defines the normal system behavior including execution sequence and execution timing. The anomaly detection method in this article utilizes on-chip hardware to non-intrusively monitor system execution through trace port of the processor and detect malicious activity at runtime. We further analyze the properties of the timing distribution for control flow events, and select subset of monitoring targets by three selection metrics to meet hardware constraint. The designed detection method is evaluated by a network-connected pacemaker benchmark prototyped in FPGA and simulated in SystemC, with several mimicry attacks implemented at different levels. The resulting detection rate and false positive rate considering constraints on the number of monitored events supported in the on-chip hardware demonstrate good performance of our approach.
Algorithmic identification of discrepancies between published ratios and their reported confidence intervals and P-values.

Motivation Studies, mostly from the operations/management literature, have shown that the rate of human error increases with task complexity. What is not known is how many errors make it into the published literature, given that they must slip by peer-review. By identifying paired, dependent values within text for reported calculations of varying complexity, we can identify discrepancies, quantify error rates and identify mitigating factors. Results We extracted statistical ratios from MEDLINE abstracts (hazard ratio, odds ratio, relative risk), their 95% CIs, and their P-values. We re-calculated the ratios and P-values using the reported CIs. For comparison, we also extracted percent-ratio pairs, one of the simplest calculation tasks. Over 486 000 published values were found and analyzed for discrepancies, allowing for rounding and significant figures. Per reported item, discrepancies were less frequent in percent-ratio calculations (2.7%) than in ratio-CI and P-value calculations (5.6-7.5%), and smaller discrepancies were more frequent than large ones. Systematic discrepancies (multiple incorrect calculations of the same type) were higher for more complex tasks (14.3%) than simple ones (6.7%). Discrepancy rates decreased with increasing journal impact factor (JIF) and increasing number of authors, but with diminishing returns and JIF accounting for most of the effect. Approximately 87% of the 81 937 extracted P-values were ≤ 0.05. Conclusion Using a simple, yet accurate, approach to identifying paired values within text, we offer the first quantitative evaluation of published error frequencies within these types of calculations. Contact jonathan-wren@omrf.org or jdwren@gmail.com. Supplementary information Supplementary data are available at Bioinformatics online.
Effect of Biomolecules on the Nanostructure and Nanomechanical Property of Calcium-Silicate-Hydrate.

Inspired by nature, this paper investigates the effect of biomolecules, such as amino acids and proteins, on the nanostructure and mechanical stiffness of calcium-silicate-hydrate (C-S-H). Amino acids with distinct functional groups, and proteins with different structures and compositions were used in the synthesis of the C-S-H nanocomposite. The atomic structure was examined using X-ray diffraction (XRD) and Fourier transform infrared spectroscopy (FTIR). The morphology was investigated using scanning electron microscopy (SEM) and atomic force microscopy (AFM). AFM nanoindentation was used to evaluate the Young’s modulus of the modified C-S-H. Positively charged, H-bond forming and hydrophobic amino acids were shown to influence the atomic structure of C-S-H. The effect of negatively charged amino acid on atomic structure was more pronounced at higher C/S ratio. A noticeable increase in silicate polymerization of C-S-H modified with proteins at high C/S ratio was observed. The microscopic examination demonstrated a globular morphology for all samples except for C-S-H modified with hemoglobin, which showed a platelet morphology. The Young’s modulus of C-S-H with amino acids and proteins showed a general reduction compared to that of the control C-S-H.
Hybrid stimulation enhances torque as a function of muscle fusion in human paralyzed and non-paralyzed skeletal muscle.

ObjectiveAfter spinal cord injury (SCI), hybrid stimulation patterns that interpose paired-pulse doublets over a constant-frequency background may enhance the metabolic “work” (muscle torque) perfo...
Carbachol acts through protein kinase C to modulate cholecystokinin receptors on pancreatic acini

Cholecystokinin (CCK) and cholinergic agonists are both major stimulants of pancreatic enzyme secretion and both utilize a common calcium-phosphoinositide-mediated receptor coupling system. In this...
Virtual Worlds, the IRB and a User's Bill of Rights

Virtual worlds provide a vibrant and exciting new venue for the conduct of social research. New social phenomena have emerged in the context of these worlds as individuals and groups use the worlds’ social communication tools to overcome limitations of time and distance. Yet these worlds also pose some novel ethical problems for social researchers who wish to conduct their work in these contexts. The present paper discusses ethical dimensions of research in virtual worlds in order to uncover some of these novel problems. The paper reports and analyzes a case study in which the author participated in a virtual world research study. The paper discusses a preliminary version of a virtual world subject’s bill of rights that can serve as the basis for further discussion among social researchers. The paper concludes with recommendations for virtual worlds researchers on strategies for working with their institutional review boards (human subjects ethics review) to obtain approval for their research proposals.
Effects of cigarette nicotine content and smoking pace on subsequent craving and smoking.

Abstract Rationale. The relative contribution of sensory and pharmacological variables in regulating craving and smoking remains unclear. Rapid smoking procedures and denicotinized cigarettes can be used to further disentangle these factors, and to explore the relationship between craving and smoking. Objective. The present study examined the role of nicotine and sensory cues in mediating craving and smoking, and the relationship between craving and smoking. Methods. Participants (n=15) engaged in one session each of rapid smoking (up to nine cigarettes with puffs taken every 6 s) and normal paced smoking with nicotinized and denicotinized cigarettes (total of four sessions). During the next 3 h, craving and withdrawal assessments and smoking opportunities were scheduled every 15 min. Plasma nicotine levels were measured at baseline, immediately and 15 min after the smoking interventions, and subsequently at the time when the participant first chose to smoke. Results. Craving ratings were equally suppressed immediately after all conditions. After self-paced conditions, both types of cigarettes produced equivalent effects on latency to smoke. Latency to smoke was significantly longer after rapid smoking of nicotinized cigarettes compared to all other conditions. Finally, changes in craving were associated with choices to smoke. Conclusions. The sensory cues associated with smoking suppressed craving ratings regardless of the smoking pace or nicotine content. Only at high doses did nicotine levels play an additional role in acutely suppressing smoking behavior. Small elevations in craving ratings were associated with choices to smoke.
The Goals, Development, and use of Trauma Registries and Trauma Data Sources in Decision Making in Injury

Trauma is the leading killer of Americans under the age of 40 years and the fourth most common cause of death for all Americans. Its impact has not been studied adequately or understood completely. Rational decisions in the care and treatment of trauma patients, the prevention of injury, and the reduction of trauma's annual $177 billion costs can only be made with adequate information on the. effectiveness of prevention and treatment measures. This information includes current and accurate data on who is at risk, what types of injuries are sustained, how they are treated, the severity of their consequences, and their outcomes. The availability of this information enables local and national agencies and hospitals to establish priorities, characterize high-risk groups, target prevention and treatment measures within each community, and evaluate the effectiveness of injurycontrol interventions. The value of hospital trauma registries as a major research tool is recognized increasingly because of their role in improving the care of the trauma patient and bringing about better resource utilization.
Molecular Organization and the Fluid Nature of the Mitochondrial Energy Transducing Membrane

The inner or energy transducing membrane of the mitochondrion is the site of various metabolic activities, including the sequential transfer of electrons along a chain of respiratory proteins and the coupling of the free energy derived from such transfer to the phosphorylation of ADP. Electron transfer between the heme protein components of the membrane is rapid and can be expected to require protein-protein interactions equal to the half times of their oxidations, for example, as rapid as 2 msec in the case of the oxidation of cytochrome c by cytochrome c oxidase (Chance et al., 1967). Interactions between other redox components in the membrane, however, may be somewhat slower as indicated by delays in the transfer of reducing equivalents, as for example between the b cytochromes and cytochrome c l and between the flavoproteins and b cytochromes. Of interest in this regard are the reported delays in the rate and half time of ATP synthesis coupled to the rapid half time oxidation of cytochrome c oxidase (Lemasters and Hackenbrock, 1975; Thayer and Hinkle, 1975). Irrespective of such delays, the sequential and rapid events inherent in electron transfer and energy transduction generally tend to support the inference that the proteins in the energy transducing membrane of the mitochondrion are stabilized in a continuous, rigid protein-protein lattice (Fleisher et al., 1967; Sjostrand and Barajas, 1970; Capaldi and Green, 1972). In classical agreement, the specific proteins of the respiratory chain have been assumed to be ordered with a recurring lateral intermolecular spacing throughout the plane of the membrane (Klingenberg, 1968; Lehninger, 1970). Further, these notions are supported by the fact that the energy transducing membrane is endowed with an unusually high protein content (75%) compared to various other membranes of eukaryote cells.
Supporting mixed-datatype matrix multiplication within the BLIS framework

We approach the problem of implementing mixed-datatype support within the general matrix multiplication (GEMM) operation of the BLIS framework, whereby each matrix operand A, B, and C may be stored as single- or double-precision real or complex values. Another factor of complexity, whereby the computation is allowed to take place in a precision different from the storage precisions of either A or B, is also included in the discussion. We first break the problem into mostly orthogonal dimensions, considering the mixing of domains separately from mixing precisions. Support for all combinations of matrix operands stored in either the real or complex domain is mapped out by enumerating the cases and describing an implementation approach for each. Supporting all combinations of storage and computation precisions is handled by typecasting the matrices at key stages of the computation---during packing and/or accumulation, as needed. Several optional optimizations are also documented. Performance results gathered on a 56-core Marvell ThunderX2 and a 52-core Intel Xeon Platinum demonstrate that high performance is mostly preserved, with modest slowdowns incurred from unavoidable typecast instructions. The mixed-datatype implementation confirms that combinatoric intractability is avoided, with the framework relying on only two assembly microkernels to implement 128 datatype combinations.
Determining sufficient sequencing depth in RNA-Seq differential expression studies

RNA-Seq studies require a sufficient read depth to detect biologically important genes. Sequencing below this threshold will reduce statistical power while sequencing above will provide only marginal improvements in power and incur unnecessary sequencing costs. Although existing methodologies can help assess whether there is sufficient read depth, they are unable to guide how many additional reads should be sequenced to reach this threshold. We provide a new method called superSeq that models the relationship between statistical power and read depth. We apply the superSeq framework to 393 RNA-Seq experiments (1,021 total contrasts) in the Expression Atlas and find the model accurately predicts the increase in statistical power gained by increasing the read depth. Based on our analysis, we find that most published studies (> 70%) are undersequenced, i.e., their statistical power can be improved by increasing the sequencing read depth. In addition, the extent of saturation is highly dependent on statistical methodology: only 9.5%, 29.5%, and 26.6% of contrasts are saturated when using DESeq2, edgeR, and limma, respectively. Finally, we also find that there is no clear minimum per-transcript read depth to guarantee saturation for an entire technology. Therefore, our framework not only delineates key differences among methods and their impact on determining saturation, but will also be needed even as technology improves and the read depth of experiments increases. Researchers can thus use superSeq to calculate the read depth to achieve required statistical power while avoiding unnecessary sequencing costs.
Small Numbers from Tunneling between Brane Throats

In generic string compactifications with branes, the regions of space in the vicinity of brane horizons, or brane throats, support effective potential barriers. raised by the background gravitational fields. A familiar example is the AdS brane throats in the Randall-Sundrum model. The barriers obstruct the interaction of observers inside different throats, whose communication is effectively described by tunneling through the barriers. Consequently the interactions between different throats are exponentially weak, This provides for a new mechanism for explaining small numbers in Nature. We review the applications to the hierarchy problem where supersymmetry breaking scale is reduced by tunneling, long-lived cold dark matter particles which decay into hot CFT, and consider the implications for holography. We finally discuss the important interplay between the tunneling suppression and our recent conjecture that blaholes stuck on a brane in AdS D + 1 should be interpreted as duals of quantum-corrected D-dimensional black holes. rather than classical ones, of a CFT coupled to gravity.
Phlegmasia cerulea dolens associated with acute coronavirus disease 2019 pneumonia despite supratherapeutic warfarin anticoagulation.

Abstract Patients with acute coronavirus disease 2019 (COVID-19) respiratory infection are associated with concomitant thromboembolic complications and a hypercoagulable state. Although these mechanisms are not completely understood, unique alterations in the serum markers for hemostasis and thrombosis have been detected. A high index of suspicion is required by vascular surgeons for patients presenting with this novel virus. We present the case of a 51-year-old man with acute COVID-19 pneumonia who developed phlegmasia cerulea dolens despite chronic warfarin therapy and a supratherapeutic international normalized ratio.
Learning-Enabled Robotic Assistive Support: Understanding Older Adult Opinions and Comparing Them to Younger Adult Opinions.

Background As older adults age, they may require assistance completing activities of daily living (ADLs). Robotic assistance can offset healthcare costs and allow older adults to preserve their autonomy. Younger adults are often involved in the design and purchase of these robotic technologies, and must take into account the needs and expectations of the target population (i.e., older adults) to create a robot that the end-user will adopt. Research aim/questions This study evaluated the opinions of both younger and older adults regarding the design and performance of the Robot Activity Support (RAS) system. It is important to understand points of agreement and divergence between these populations' perspectives so that effective robotic aids are created for older adults. Methods Fifty-two younger and older adults completed three scripted tasks with the RAS robot in a smart home environment. Each participant made task errors to cue the robot to offer help via three prompt modalities (guide to the object, video of forgotten step, and video of the full task). After interacting with the robot, participants completed questionnaires to evaluate their opinions of and satisfaction with the robot. Results There were no differences between younger and older adults' perceptions of the robot across a variety of factors (e.g., likability, cognitive demand), with both age groups expressing generally neutral opinions. Both groups rated the Full Video prompt as least helpful, effective, and liked. Participants recommended the robot's response accuracy, movement speed, alerting style and system flexibility be improved. Younger adults overestimated how much older adults would want a robot like this. Conclusions This study underscores the importance of testing technology with the end-user, as older adults were less interested in having a similar robot in their home than younger counterparts expected. Future studies will show if older adults' opinions can be improved after making the recommended changes.
Universal Intrinsic Dynamics and Freezing of Water in Small Nanotubes

Although it is well known that confinement alters the freezing point of water, the mechanism by which this occurs, particularly in small nanotubes, is still under active research. It was recently c...
Atherogenic Dyslipidemia After Liver Transplantation: Mechanisms and Clinical Implications

Cardiovascular disease (CVD), particularly atherosclerosis-associated CVD, is a major cause of long-term mortality after liver transplantation (LT). The liver is central in lipid homeostasis, and changes associated with insulin resistance, weight gain, adipose tissue inflammation, and development of nonalcoholic fatty liver disease (NAFLD) after LT promote atherogenesis. These factors synergistically alter lipid homeostasis, thereby leading to the production of proatherogenic lipoproteins, which contribute to the heighted risk of CVD-associated events observed in LT recipients. Although the exact mechanism promoting this shift of a proatherogenic lipoprotein profile is currently not known, the choice of immunosuppression and preexisting metabolic risk factors (ie, NAFLD) are likely contributors. This shift in proatherogenic lipoprotein subparticles presents clinical challenges as the traditional lipid profile employed in clinical practice may not fully capture this atherogenic risk. This review focuses on lipoprotein metabolism and atherogenesis in LT recipients.
Fostering Mathematical Creativity Through Problem Posing and Three-Act Tasks:

The National Association for Gifted Children and The National Council of Teachers of Mathematics both call for problem posing. This article illustrates the strategies used during a series of three ...
The Steady Wave Potential of a Unit Source, at the Centerplane

The paper is concerned with the linearized wave disturbance trailing downstream from a unit source in steady rectilinear motion at or below the free surface of a quiescent sea, at the "centerplane," that is, at the vertical plane of symmetry containing the source and parallel to its direction of motion.
Data fusion and distributed robotic perception

This thesis explores data fusion and distributed robotic perception through a series of theoretical developments, analyses and experiments. First, a GSF with component extended Kalman filters (EKF) is proposed as an approach to localize an autonomous vehicle in an urban environment with limited GPS availability. The GSF is used because of its ability to represent the posterior distribution of the vehicle pose with better efficiency (fewer terms, less computational complexity) than a corresponding bootstrap particle filter with various numbers of particles due to the interaction with measurement hypothesis tests. A series of in-depth empirical studies are performed using 37 minutes of recorded data from Cornell University’s autonomous vehicle driven in an urban environment, including a 32 minute GPS blackout. Second, a distributed grid-based terrain mapping algorithm using Gaussian Mixture Models is developed for use in tree connected and arbitrary connected sensor networks. The distributed data fusion rules are developed that operates directly on the sufficient statistics summarizing the grid-cell height and uncertainty. The distributed grid-based terrain mapping algorithms is demonstrated in an experimental environment involving 8 autonomous robots operating in an indoor environment for 120 seconds. Third, an algorithm to segment 3D points in dense range maps generated from the fusion of a single optical camera and a multiple emitter/detector laser range finder is presented. The algorithm is demonstrated on data collected with the Cornell University DARPA Urban Challenge vehicle. Finally, two information theoretic procedures for fusing multiple distributions with unknown correlation are developed. The first approach developed is Entropy Weighted Chernoff fusion; this fusion procedure biases the WEP fusion weight towards the distribution with the lowest entropy. An information loss for the WEP conservative fusion rule is introduced and an approximation derived by computing the Kullback-Leibler divergence between the Naive Bayes and WEP fused distributions. The approximation is minimized for the second fusion approach: Minimum-Information-Loss fusion; the procedure generates the least conservative fused distribution in the family of WEP results. Experimental results include the fusion of multiple occupancy grid maps over an optimally connected sensor network, demonstrating consistent map estimates.
On the mechanism of 5-enolpyruvylshikimate 3-phosphate synthetase.

The enzymic synthesis of 5-enolpyruvylshikimate 3-phosphate (ES-3-P) from enolpyruvate phosphate (labeled with 18O in the C-O-P oxygen) and shikimate 3-phosphate occurred with C-O cleavage of the pyruvate ester. ES-3-P formed in a D2O reaction medium showed incorporation of approximately 1.3 atoms of deuterium, and consisted of 39% d2 molecules, 53% d1, and 8% d0. Enolpyruvate phosphate isolated from the same reaction mixture had 0.72 atom of deuterium with a similar d2:d1 ratio. In both compounds, the nuclear magnetic resonances of the vinyl methylene protons were diminished equally in intensity. ES-3-P formed in a tritiated medium contained 0.42 atom of 3H in the vinyl methylene hydrogens. A reversible addition-elimination mechanism is proposed in which protonation of carbon 3 of enolpyruvate phosphate is associated with a nucleophilic attack on carbon 2 by the 5-hydroxyl group of shikimate 3-phosphate. A methyl group of unrestricted rotation is formed in the resulting postulated intermediate. Elimination of orthophosphate then yields ES-3-P, and elimination of shikimate 3-phosphate yields enolpyruvate phosphate. A procedure was developed for preparing enolpyruvate phosphate with 18O in the C-O-P oxygen. The isolation of shikimate 3-phosphate was improved. ES-3-P synthetase from Salmonella was purified 80-fold by a simple procedure.
Aerosol-Cloud-Radiation Interactions in Atmospheric Forecast Models

Abstract : The long-term goal of this project is to gain a deep understanding of the role of atmospheric aerosols in affecting transmission of radiation through the atmosphere and in influencing cloud properties. The scientific objectives of this project are to identify the specific manner in which atmospheric aerosols determine cloud properties and to represent these interactions in atmospheric models. The technological objectives are to develop state-of-the-art instruments for aircraft sampling of aerosols that advance the long-term goals of the project.
Chaos and Deviation from Uniform Distribution: Eigenfunction Computation; Applied Modular Arithmetic

In the first part of this talk we focus on computational tools of quantum chaos—a classical numerical task of high accuracy computations of eigenvalues and eigenfunctions of Schrodinger and Laplace operators in multidimensional domains. These computations are only tools of the analysis of “chaos” in quantum systems which can be primitively described as the deviation from regular and/or simple statistical behavior. We focus on several practical methods of spectral analysis, needed for high accuracy of eigenvalues and eigenstates calculations. In the second part of the talk we look at a completely different number-theoretic task—a construction of very regular, but still random, finite structures for new generation of computer chips and verification of chip designs.
Subject-Specific Multiscale Modeling to Investigate Effects of Transcranial Magnetic Stimulation

Objective Transcranial magnetic stimulation (TMS) is an effective intervention in noninvasive neuromodulation used to treat a number of neurophysiological disorders. Predicting the spatial extent to which neural tissue is affected by TMS remains a challenge. The goal of this study was to develop a computational model to predict specific locations of neural tissue that are activated during TMS. Using this approach, we assessed the effects of changing TMS coil orientation and waveform. Materials and Methods We integrated novel techniques to develop a subject-specific computational model, which contains three main components: 1) a figure-8 coil (Magstim, Magstim Company Limited, Carmarthenshire, UK); 2) an electromagnetic, time-dependent, nonhomogeneous, finite element model of the whole head; and 3) an adaptation of a previously published pyramidal cell neuron model. We then used our modeling approach to quantify the spatial extent of affected neural tissue for changes in TMS coil rotation and waveform. Results We found that our model shows more detailed predictions than previously published models, which underestimate the spatial extent of neural activation. Our results suggest that fortuitous sites of neural activation occur for all tested coil orientations. Additionally, our model predictions show that excitability of individual neural elements changes with a coil rotation of ±15°. Conclusions Our results indicate that the extent of neuromodulation is more widespread than previous published models suggest. Additionally, both specific locations in cortex and the extent of stimulation in cortex depend on coil orientation to within ±15° at a minimum. Lastly, through computational means, we are able to provide insight into the effects of TMS at a cellular level, which is currently unachievable by imaging modalities.
Euler’s Conception of the Derivative

This describes perfectly the situation of the authors of the preceding article. They are attempting to understand how Euler uses differentials in later volumes without having understood his explanation in the first volume of what he is using differentials for. As a result, they have, as Euler foretold, come to entertain strange ideas about the concept of the infinite. Their strange ideas derive, however, from 20th century notions of set theory and nonstandard analysis that are far stranger than anything Euler could have imagined. The authors cite H. J. M. Bos’s article Differentials and Derivatives in Leibniz’s Calculus [Bos 1974], but they appear to have read it no more carefully than they read mine [Edwards 2007], because Bos’s descriptions of Euler’s ideas concur with those in my paper, not with those being advanced by the authors. Bos writes on page 66:
Genetic analysis of a region of the Bordetella pertussis chromosome encoding filamentous hemagglutinin and the pleiotropic regulatory locus vir.

The vir locus of Bordetella pertussis apparently encodes a trans-acting positive regulator that is required for the coordinate expression of genes associated with virulence: pertussis toxin, filamentous hemagglutinin (FHA), hemolysin, and adenylate cyclase toxin. DNA clones of vir and of genes required for the synthesis of some of the factors under vir control were obtained with DNA probes from the chromosomal DNA surrounding sites of Tn5 insertion mutations that inactivated those genes. Two vir clones were found which also contained genes required for the proper expression of FHA in B. pertussis. The plasmids which contained both the fha and vir genes expressed immunologically reactive FHA in Escherichia coli, as detected by colony blots, whereas plasmids which contained only fha or vir were negative in this assay. The regulation of FHA production in E. coli, as in B. pertussis, was temperature dependent and inhibited by high concentrations of either magnesium ions or nicotinic acid, indicating that the sequences cloned in E. coli contained the information required to preserve the physiological responses seen in B. pertussis. Further characterization of the vir-fha clones by Tn5 mutagenesis in E. coli and by the return of cloned sequences to B. pertussis in trans and to the B. pertussis chromosome led to the localization of the vir locus, the structural gene for FHA, and genes that are possibly required for the synthesis and export of FHA. Images
α,β‐Diphenylcinnamonitrile

α,β-Diphenylcinnamonitrile product: α,β-Diphenylcinnamonitrile Keywords: condensation, carbonyl-active methylene condensations; benzyl cyanide, purification of; ammonia; bath, cooling, dry ice and trichloroethylene; tower, soda-lime
Leg intramuscular pressures during locomotion in humans

To assess the usefulness of intramuscular pressure (IMP) measurement for studying muscle function during gait, IMP was recorded in the soleus and tibialis anterior muscles of 10 volunteers during treadmill walking and running by using transducer-tipped catheters. Soleus IMP exhibited single peaks during late-stance phase of walking [181 +/- 69 (SE) mmHg] and running (269 +/- 95 mmHg). Tibialis anterior IMP showed a biphasic response, with the largest peak (90 +/- 15 mmHg during walking and 151 +/- 25 mmHg during running) occurring shortly after heel strike. IMP magnitude increased with gait speed in both muscles. Linear regression of soleus IMP against ankle joint torque obtained by a dynamometer produced linear relationships (n = 2, r = 0.97 for both). Application of these relationships to IMP data yielded estimated peak soleus moment contributions of 0.95-1.65 N . m/kg during walking, and 1.43-2.70 N . m/kg during running. Phasic elevations of IMP during exercise are probably generated by local muscle tissue deformations due to muscle force development. Thus profiles of IMP provide a direct, reproducible index of muscle function during locomotion in humans.