cssi/SciSciGPT-SciSciNet huggingface dataset:
Statistical metrics for quality assessment of high density tiling array data

High-density tiling arrays are designed to blanket an entire genomic region of interest using tiled oligonucleotides at very high resolution and are widely used in various biological applications. Experiments are usually conducted in multiple stages, in which unwanted technical variations may be introduced. As tiling arrays become more popular and are adopted by many research labs, it is pressing to develop quality control tools as was done for expression microarrays. We propose a set of statistical quality metrics analogous to those in expression microarrays with application to tiling array data. We also develop a method to estimate the significance level of an observed quality measurement using randomization tests. These methods have been applied to multiple real data sets, including three independent ChIP-chip experiments and one transcriptom mapping study, and they have successfully identified good quality chips as well as outliers in each study.
Structures and thermochemistry of BHlFm(OH)n and several XYBO compounds at the G-2 level of theory

Abstract The heats of formation of BHlFm(OH)n, with l,m,n=0–3 and selected XYBO compounds with X,Y=H, OH, or F have been computed at the G aussian -2 level of theory. An rms deviation of 1.5 kcal/mol is found between the computed heats of formation and experiment for the following five BXYZ compounds with well known thermochemistry: BH3, BF3, B(OH)3, BHF2, and BF2(OH). Heats of formation are presented for 33 other species for which experimental thermochemistry is unavailable or unreliable.
Toward stochastic deep convective parameterization in general circulation models

[1] For the first time, a stochastic deep convective parameterization to represent variability arising from small-scale processes that are unresolved by traditional deterministic moist convective parameterizations is tested in a general circulation model. Two physical pathways of representing small-scale variability as a stochastic process are explored. First, the relationship between cloud-base mass flux Mb and large-scale convective available potential energy (CAPE) is posited to have a stochastic component (the CAPE-Mb scheme). Second, the vertical structure of heating is modified by a simple random process about the structure given by the traditional convective scheme (the VSH scheme). The CAPE-Mb scheme increases the overall variance of precipitation toward observations with a realistic spatial pattern. The VSH scheme has smaller impacts on precipitation variance but yields preferential enhancement at large spatial scales and low frequencies.
An object flow computer for database applications: design and performance evaluation

Abstract In the past two decades, a considerable amount of research exists which uses hardware, firmware, and novel architectures to achieve the needed efficiency in implementing database management functions. However, most of the past efforts have been directed toward developing database computers for supporting a relatively primitive data model, namely, the relational model. This paper presents the design and evaluation of an Object Flow Computer (OFC). OFC is designed to efficiently support the processing of object-oriented databases. OFC employs a vertically fragmented data storage structure and a two-phase parallel query processing strategy. A set of primitive operators is defined for OFC. Depending on the performance requirement, these operators can be implemented in software running on general-purpose processors or as functions in special-purpose coprocessors. A high-level database request can be decomposed into these primitive operators and executed in parallel. OFC combines a number of known database processing techniques such as query decomposition, pipelining mode of data processing, and data flow control strategy. The performance evaluation of the proposed two-phase query processing strategy and a comparison with the conventional query processing strategy are also presented.
The control of progression order in a captive herd of sable antelope (Hippotragus niger)

A small herd of captive sable antelope (Hippotragus niger) was observed repeatedly while progressing through a gate connecting a pasture to a corral. The ordinal position of each herd member was recorded during each progression. These data were analyzed quantitatively with respect to three models of progression order control and one of random ordering. An end point-control model, stating that the oldest female of a progression occupies the first position while the remainder of the animals randomly distribute themselves within the progression, accounts for the data. These results are related to both protection and resource learning theories of progression order. The terminology used in the study of leadership and ordinal progressions is discussed as well.
Bilingual creativity, multidimensional analysis, and world Englishes

Research in world English literatures has concentrated on qualitative measures of analysis in order to understand what is meant by ‘bilingual creativity.’ These measures demonstrate that there are differences in rhetorical and literary style within world English literatures both in the inner and outer circle. Using Biber's multidimensional analysis (1988) to examine a large corpus of world English literatures written in Indian, West African, Britain, Anglo-American and Mexican American varieties of English, this paper examines whether quantitative analyses can also be insightful and useful in the examination of world English literatures in expanding our understanding of what ‘bilingual creativity’ entails. The results of this study reveal that computational methods of analyzing texts both confirm former research comparing differences between texts written in different varieties of English and also shed new light on differences that exist between these varieties.
Leave means never having to say I quit.

It has been the author's experience as both clinician and supervisor, that when professional staff begin to experience burnout, a common reaction is to change jobs or even careers. The author suggests another alternative, that of the mental-health leave, or sabbatical, and comments on her personal experience with this concept.
A Meta-Analytic Investigation of the Relationship of State and Trait Anxiety to Performance on Figural and Verbal Creative Tasks:

Extensive research suggests when and how anxiety has debilitating or facilitating effects on routine cognitive tasks or motor tasks. However, research examining anxiety’s relation to performance on creative tasks such as divergent thinking and artistic tasks is less conclusive despite a rather substantial literature. The authors’ meta-analytic investigation of 59 independent samples finds that anxiety is significantly and negatively related to creative performance. In addition, the findings provide insights into factors such as task complexity, type of task (i.e., figural or verbal), and type of anxiety (i.e., state or trait) that moderate the relationship between anxiety and creativity—all of which are consistent with the idea that anxiety and creativity present competing cognitive demands. In addition to identifying gaps in the literature such as the need for research using a two-component model of anxiety in relation to creativity, the authors’ results have practical implications for those seeking to i...
Acute survivorship of the deep-sea coral Lophelia pertusa from the Gulf of Mexico under acidification, warming, and deoxygenation

Changing global climate due to anthropogenic emissions of CO2 are driving rapid changes in the physical and chemical environment of the oceans via warming, deoxygenation, and acidification. These changes may threaten the persistence of species and populations across a range of latitudes and depths, including species that support diverse biological communities that in turn provide ecological stability and support commercial interests. Worldwide, but particularly in the North Atlantic and deep Gulf of Mexico, Lophelia pertusa forms expansive reefs that support biological communities whose diversity rivals that of tropical coral reefs. In this study, L. pertusa colonies were collected from the Viosca Knoll region in the Gulf of Mexico (390 to 450 m depth), genotyped using microsatellite markers, and exposed to a series of treatments testing survivorship responses to acidification, warming, and deoxygenation. All coral nubbins survived the acidification scenarios tested, between pH of 7.67 and 7.90 and aragonite saturation states of 0.92 and 1.47. However, calcification generally declined with respect to pH, though a disparate response was evident where select individuals net calcified and others exhibited net dissolution near a saturation state of 1. Warming and deoxygenation both had negative effects on survivorship, with up to 100% mortality observed at temperatures above 14oC and oxygen concentrations of approximately 1.5 ml·l-1. These results suggest that, over the short-term, climate change and OA may negatively impact L. pertusa in the Gulf of Mexico, though the potential for acclimation and the effects of genetic background should be considered in future research.
Two-dimensional Heisenberg antiferromagnet with next-nearest-neighbor coupling.

We study the two-dimensional $S=\frac{1}{2}$ antiferromagnet with next-nearest-neighbor antiferromagnetic coupling using a sublattice-symmetric spin-wave theory and exact diagonalization. For sufficiently large frustration the theory predicts a transition to a disordered state with an energy gap and exponentially decaying correlations, rather than to a gapless spin-liquid state. Comparison with exact results on finite lattices up to 26 sites indicates that the theory overestimates the disordering effect of the next-nearest-neighbor coupling, implying that the long-range antiferromagnetic order is surprisingly robust.
Professional perspectives on physical activity screening practices: Shifting the paradigm

Context: This was a qualitative study with focus groups that included researchers and health care providers with expertise in exercise and physical activities with adults. Objective: The purpose of this study was to explore professional perspectives on current practices and beliefs about screening of older adults prior to having them initiate a structured or independent physical activity program appropriate for their physical ability and interests. Design and setting: This qualitative study included five different focus groups held at four national professional meetings based on a standard interview guide. Participants: Forty-two practitioners and researchers participated in these focus groups. These individuals were selected for participation based on their expertise in aging, primary care, exercise science, or behavioral science. Results: The focus groups revealed professional perspectives articulating advantages and disadvantages of pre-exercise screening. Four major themes were identified: (1) rationa...
Thermoelectric power of YBa2Cu3O7−δ superconductive thin films as a function of oxygen contents

Experimental correlations of thermoelectric power (TEP), oxygen deficiency (δ), and c -lattice constant in YBa 2 Cu 3 O 7−δ (YBCO) c -oriented, polycrystalline, thin-film, high-temperature oxide superconductors are presented. The TEP values in the normal state were observed to be positive for samples with oxygen deficiencies between 0.08 ≤ δ ≤ 1.00 and negative for 0.00 ≤ δ ≤ 0.08. Furthermore, the TEP magnitudes were highly sensitive to the amount of oxygen and were found to increase with increasing oxygen deficiency, ranging from values of −2 μ V/K to more than two orders of magnitude higher. In addition, relatively temperature-independent TEP values were observed for hole-conductive samples with low oxygen deficiencies (δ ≤ 0.30). The lattice constants (c) of the same samples were measured by XRD. These were found to increase with oxygen deficiency and to correlate systematically with the TEP values. We conclude that TEP is a reliable indicator of the oxygen content in YBCO materials.
Attitudes of String Teachers and Performers Toward Preparation for and Teaching of Private Lessons

The present study was designed to examine attitudes toward private lesson teaching of a cross-section of string instrument instructors (N = 1,617). The participant pool was drawn from the membership of the American String Teachers Association (ASTA). Results were similar in many ways to responses in previous studies also involving music faculty and music students. These groups indicated that they liked teaching, liked the challenges of teaching musicians, and believed preparation for teaching is important. Depending on the age of their students, they also enjoyed talking about pedagogical issues with students. Engaging the membership of organizations such as ASTA will be necessary if the profession is to find additional ways to provide educational opportunities for musicians interested in teaching.
Clinical Staging of Rectal Cancer

Initial accurate clinical staging of patients with rectal cancer is necessary in order to select optimal treatment and determine prognosis. Decision-making for the best possible treatment is predicated on achieving the highest rate of cure while maintaining acceptable quality of life and avoiding unnecessary morbidity. Surgical options and indications for combined modality therapy will differ significantly, however, depending on tumor stage. Staging is based on depth of invasion of the rectal wall by tumor (T-stage) and presence of lymph node involvement (N-stage). Digital rectal examination (DRE), computed tomography (CT), magnetic resonance imaging (MRI), and endorectal ultrasound (ERUS) have all been used in local staging of rectal cancer. In the hands of an experienced clinician, the currently available technology can satisfactorily determine T-stage; however, prediction of N-stage is less reliable. This review discusses and compares the indications for, and advantages and limitations of, the various diagnostic modalities used in clinical staging of rectal cancer, with emphasis on ERUS and MRI. These two modalities have shown a similar accuracy in overall tumor staging. MRI seems to be more accurate in assessment of T3 and T4 lesions, whereas ERUS may be more accurate in assessment of T1 and T2 lesions. ERUS is faster, portable, more accessible and less expensive. MRI provides a multiplanar and larger field of view, capable of encompassing the entire mesorectal fascia and assessing the possibility of obtaining a tumor-free circumferential resection margin. Both modalities show moderate accuracy in predicting nodal disease.
Expression of transforming growth factor-beta isoforms (beta 2 and beta 3) in the mouse uterus: analysis of the periimplantation period and effects of ovarian steroids.

Expression of beta-type transforming growth factor genes (TGF beta 2 and TGF beta 3) in the mouse uterus during the periimplantation period and in response to an acute exposure to 17 beta-estradiol (E2) and progesterone (P4) was studied using Northern blot hybridization and/or immunocytochemistry. Polyclonal antipeptide antibodies specific for TGF beta 2 or TGF beta 3 were employed for immunocytochemistry. In the preimplantation uterus [days (D) 1-4 of pregnancy; day 1 = vaginal plug], immunostaining for TGF beta 2 was observed in luminal and glandular epithelia as well as in myometrium and vascular smooth muscle. In the postimplantation period (D5-D8), TGF beta 2 immunostaining was also detected in decidual cells. In contrast, TGF beta 3 immunostaining was restricted to the myometrium and vascular smooth muscle throughout the periimplantation period (D1-D8). Antisense TGF beta 2 and TGF beta 3 RNA probes were employed for Northern blotting. Northern blot hybridization revealed four TGF beta 2 transcripts...
Generating Geometric Graphs Using Automorphisms

We outline an algorithm for generating nets, a “net” being a geometric graph embedded in a space on which some group acts transitively. We prove that any connected net in such a space can be generated by this process, which can also be regarded as a covering of the net by copies of a connected “transversal” subnet. This paper outlines some of the underlying theory supporting a crystal prediction and design program currently under development. The paper begins with some background in geometric group theory.
Racial and Ethnic Disparities in the Treatment of Cerebrovascular Diseases: Importance to the Practicing Neurosurgeon

In various surgical procedures, evidence for racial/ethnic disparities has continued to grow in recent years. Our purpose was to review the current literature regarding racial/ethnic disparities in the United States in the surgical treatment and outcome of three different cerebrovascular disease entities: carotid stenosis, intracranial aneurysm, and cerebral arteriovenous malformation (AVM). We conducted an electronic search of literature published between January 1, 1966 and December 10, 2005 using MEDLINE (OVID), EMBASE, CINAHL, and Science Citation Index (Web of Science), along with manual reference checking, resulting in 313 screened items. Main outcome measures examined were racial/ethnic differences in procedure utilization rates and perioperative stroke, death, and complications. Out of 3,624,581 articles indexed in MEDLINE pertaining to the treatment of these 3 cerebrovascular diseases, 141 (0.004%) articles pertained to minority groups and 33 (0.001%) articles met search criteria for inclusion in this review. Two additional articles were found in other searched databases. Carotid endarterectomy was the focus of 30 articles, and 5 articles pertained to craniotomy for treatment of intracranial aneurysms. No articles were found that examined racial differences in AVM treatment. Our systematic review found evidence of racial disparities in the surgical treatment of patients with carotid stenosis and aneurysmal subarachnoid hemorrhage. The data, however, is limited and confounded. Results of this comprehensive literature review suggest that racial disparities in cerebrovascular disease are understudied. Race-associated differences in neurosurgical outcomes must be documented and vigorously investigated to determine the basis of any observed differences and ensure that we are providing the best care possible to all of our patients.
Short-term costs and correlates of play in cheetahs

Abstract Costs and benefits of play were investigated by observing cheetah,Acinonyx jubatus, cubs in the wild. Cubs played either after resting or nursing, or while the family was moving; cubs were never injured during 2600 h of observation, and did not become separated from their mother during play; and mothers showed few signs of unease while cubs played. It is argued that energetic and indirect costs of play were insubstantial. Taking all these potential costs together, overall costs of play appeared low. Very young cubs showed high rates of locomotor play suggesting that play may have immediate rather than delayed benefits, possibly aiding cubs in escaping predation. Components of non-contact social play may be functionally or causally related to approaching prey, whereas components of object and contact play may be related to contacting prey. Litter-mates that stalked and crouched at other family members more frequently during play also stalked and crouched at prey more often, and those showing more frequent object play and contact social play showed higher rates of contacting live prey released for them by their mothers. Distances that cubs chased each other and their success in catching each other during play chases increased with age but the ability of cubs to remain concealed during play stalks and crouches did not improve, implying that only certain aspects of play might be suitable for rehearsing predatory skills.
Synthetic enhancement in gene interaction: a genetic tool come of age

Synthetic enhancement, in which one mutation exacerbates the severity of another, is a genetic interaction of increasing importance in biology. This review focuses on the logic of interpreting synthetic enhancement, and begins by comparing the phenomenon with genetic suppression.
Bacterial allergy and infection, chronic bronchopulmonary obstruction and their relationship to intractable bronchial asthma

Chronic bronchial asthma which has been unresponsive to good allergic and medical management may be improved considerably by detailed attention to often-overlooked important considerations. These are bacterial allergy and infection, careful elimination of foci of infection, the use of autogenous bacterial vaccines, the use of gamma globulin for IgG and IgA deficiency, and the use of bronchoscopy and lavage with acetylcysteine and a bronchodilator to liquefy and loosen the long-standing obstructive mucus plugs.
Acute respiratory failure associated with pulmonary cryptococcosis in non-aids patients.

Purpose To determine the incidence of acute respiratory failure (ARF) in non-AIDS patients with pulmonary cryptococcosis (PC). Design Retrospective cohort study. Setting University of Pittsburgh Medical Center, Pittsburgh, PA. Subjects All patients in whom PC without HIV infection was diagnosed between February 1989 and March 1999. Results Thirty-three patients with PC were identified, and 11 of those patients (33%) developed ARF and comprised the study group. Underlying diseases included solid-organ transplant recipients (seven patients; 64%) and other underlying medical conditions (four patients; 36%). The most common symptoms were cough, shortness of breath, and temperature elevation. Extrapulmonary involvement was seen in six patients (meningitis, four patients; peritonitis, one patient; laryngeal mass, one patient). Six of the 11 patients (55%) died. Conclusion ARF may develop in one third of non-AIDS patients with PC. This clinical syndrome is associated with the dissemination to extrapulmonary sites and high mortality rates. PC should be recognized as a possible cause of respiratory failure in non-AIDS patients.
Electron microprobe study of Mg distribution in Recent Mg calcites and recrystallized equivalents from the Pleistocene and Tertiary

ABSTRACT The effect of early freshwater diagenesis on Mg distributions in former Mg calcite cements was determined by electron microprobe analysis of two major groups of samples: 1) Mg calcites in Recent limestones not yet exposed to freshwater, and 2) Tertiary-Recent Mg calcites and recrystallized equivalents which have undergone freshwater exposure. Pristine Mg calcites are characterized by a uniform Mg concentration. In contrast, former Mg calcites from the Miocene of Enewetak Atoll, most of which are now radiaxial, prismatic calcites, have a much greater variation in Mg content, and traverses across the calcites reveal definite trends. Mg content of the calcite is inversely correlated with abundance of inclusions. Some of the cloudy growth layers are due to infestation by endolithic organi ms (fungi?). The small variation in Mg content in original Mg calcite cements is a valuable starting point to be aware of when interpreting Mg trends in recrystallized equivalents. Mg content can be related to inclusion abundance in recrystallized, former Mg calcites, but not in pristine Mg calcites. Therefore, Mg trends in altered materials most likely reflect dissolution/reprecipitation processes, not original Mg trends. A likely cause for the low Mg content associated with inclusion-rich growth layers is relatively high rates of dissolution and reprecipitation in these relatively permeable layers. In some cases, the increased permeability is the result of infestation by endoliths. Such organisms may cause the cloudiness observed in some other radiaxial calcites.
Non-uniform ultrasound speckle phase distribution applied to scatterer spacing estimation (medical imaging application)

When regularly spaced scatters exist in an insonated region, the speckle phase may not be uniformly distributed. A novel frequency sweeping technique for scatterer spacing estimation is proposed and applied to simulated and to experimental data. Parametric expressions of the phase statistics are proposed and tested and tested for the estimation. Changes in these parameters identify the mean scatterer spacing for even and for odd multiples of the 1/4 wavelength cases, when sweeping the receiver quadrature demodulation frequency. This technique has good tolerance for variations in scatter spacing, and has real-time implementation capability. >
Free probability on Hecke algebras and certain group C^{*}-algebras induced by Hecke algebras

In this paper, by establishing free-probabilistic models on the Hecke algebras \(\mathcal{H}\left(GL_{2}(\mathbb{Q}_{p})\right)\) induced by \(p\)-adic number fields \(\mathbb{Q}_{p}\), we construct free probability spaces for all primes \(p\). Hilbert-space representations are induced by such free-probabilistic structures. We study \(C^{*}\)-algebras induced by certain partial isometries realized under the representations.
Abstract 219: Cardiac Stress Testing Does Not Improve Patient Selection or Outcomes Among Patients Undergoing Abdominal Aortic Aneurysm Repair

Objectives: Cardiac stress testing (CST) is commonly used to help determine whether patients with abdominal aortic aneurysms (AAA) are candidates for an open vs. endovascular repair, although it is unknown whether use of CST achieves its goal of optimizing patient selection and postoperative outcomes. This study was designed to examine whether utilization of CST reduces adverse cardiac events and improves survival following AAA repair. Methods: We retrospectively identified 3,635 patients in the Vascular Quality Initiative (VQI) database (2010- 2012) with an AAA ≥ 5.0cm who were candidates for open or endovascular AAA repair. The Vascular Study Group Cardiac Risk Index (VSG-CRI) was used to stratify patient risk. We applied generalized estimating equations with inverse probability weighting to adjust for patient factors and hospital level CST utilization to evaluate the effect of CST on composite of 30-day major adverse cardiac events or mortality (MACE-M) following AAA repair. Analyses were restricted to hospitals with 20% to 80% CST utilization to facilitate adjustment of the utilization rate. Results: CST was utilized in 1627 (45%) patients during AAA workup, including 451 of 794 (57%) patients selected for open repair and 1176 of 2841 (41%) selected for endovascular repair. After inverse probability weighting, the use of CST was not associated with the probability of patients receiving open vs. endovascular repair (OR: 1.00; 95%CI: 0.77-1.32). As compared to patients without CST during AAA workup, adjusted analyses revealed that CST utilization was not associated with improved MACE or mortality outcomes following AAA repair. Among patients receiving CST, an abnormal CST was not significantly associated with selection of open vs. endovascular repair or with postoperative outcomes after adjustment for the VSG-CRI score. Similar results were found for patients with either low or high VSG-CRI scores. Conclusions: Utilization of CST during workup for AAA is not associated with selection of repair procedure and improved postoperative outcomes. Our results suggest that CST adds no value beyond known clinical risk factors in selecting patients for open or endovascular repair or in predicting post-operative events.
How We Deliver Our Desktop Support Services to Washington University in St. Louis the ITIL Way

The Solutions Center service desk at Washington University provides desktop and server application support for the administrative departments and one school, the Brown School of Social Work. As part of a Shared Services initiative, we will be rebalancing the IT resources across the university, which will provide opportunities to leverage existing areas of innovation. In particular, our team has undergone ITIL-based organization and service design strategies. This paper will review how we use ITIL's Service Design methodology to frame our desktop computer service. I will describe how the processes, people, partners, and products combine to create a highly functioning support desk that provides call center and desk side support to over 2200 customers across campus. Additionally, I will describe how we organize our call center and field tech staff to deliver this service to meet the following metrics: 1. 95% of calls answered on the first attempt. 2. Average 12 seconds in queue. 3. No longer than 20 minute call duration. 4. Field Tech will respond to desk side within 20 minutes. 5. No tickets not updated in more than three days. In our environment, we target one technician to 150 users. With over 2200 users, we use organizational structure and processes to provide great service to those customers. We maintain well-known processes for on-boarding new staff, hardware refresh cycles, imaging and desktop engineering. I. Processes: on boarding, scheduled harware refresh, software licensing, desktop engineering, security, dynamic call center, inventory, and checklists. II. Products (tools): Web Help Desk ticketing system, transactional surveys, remote desktop tools, asset database, desktop automation, knowledgebase. III. People: staff - with an understanding of their role in the organization, staff rotations, training, coaching, customers IV. Partners: external vendors - software and hardware, internal application development teams, broaden scope of contractor usage, work with other university help desks. This organizational structure and the implementation of ITIL-based processes has given us the ability to provide a robust, customer-focused service that can scale up to incorporate areas of the school that are ready to move to this model.
Integrin up-regulation as marker of neuroblastoma cell differentiation: correlation with neurite extension.

We have characterized the adhesion properties, integrin expression, and morphological changes due to extracellular matrix (ECM)-integrin interactions in a neuronal model. We showed that a modulation of some integrin heterodimers occurs during interferon-g (IFN-g) induced neuroblastoma (NB) cell differentiation. To better elucidate the possible implication and function of integrin receptors during neuronal maturation, we analyzed the changes in integrin expression in two human NB cell lines, LAN-5 and GI-LI-N, which represent different stages of neuronal differentiation. These models show opposite morphological maturation after interferon-g and tumor necrosis factor-a (IFN-g+TNF) treatment. While LAN-5 cells acquired the ability to extend long and branched neurites, GI-LI-N cells did not. Both cell lines showed enhanced expression of phenotypical and biochemical markers of neural maturation. Moreover, retinoic acid (RA) had different effects on the two NB cell lines: on LAN-5 cells it acts as a differentiation-promoting agent, while on GI-LI-N cells it has an antiproliferative effect, driving them to apoptosis. RT ‐ PCR experiments and immunoprecipitation assays showed a late but marked increase in the expression of a
Doubling the Cross-Linking Interface of a Rationally Designed Beta Roll Peptide for Calcium-Dependent Proteinaceous Hydrogel Formation

We have rationally engineered a stimulus-responsive cross-linking domain based on a repeats-in-toxin (RTX) peptide to enable calcium-dependent formation of supramolecular hydrogel networks. The peptide isolated from the RTX domain is intrinsically disordered in the absence of calcium. In calcium rich environments, the peptide binds Ca(2+) ions and folds into a beta roll (β-roll) secondary structure composed to two parallel β-sheet faces. Previously, we mutated one of the faces to contain solvent exposed leucine side chains which are localized only in the calcium-bound β-roll conformation. We demonstrated the ability of this mutant peptide to self-assemble into hydrogels in the presence of calcium with the aid of additional peptide-based cross-linking moieties. Here, we have expanded this approach by engineering both β-roll faces to contain leucine residues, thereby doubling the cross-linking interface for each monomeric building block. These leucine rich surfaces impart a hydrophobic driving force for self-assembly. Extensive characterization was performed on this double-faced mutant to ensure the retention of calcium affinity and subsequent structural rearrangement similar to that of the wild type domain. We genetically fused an α-helical leucine zipper capable of forming tetrameric coiled-coil bundles to the peptide and the resulting chimeric protein self-assembles into a hydrogel only in calcium rich environments. Since this new mutant peptide enables cross-linking on both surfaces simultaneously, a higher oligomerization state was achieved. To further investigate the cross-linking capability, we constructed concatemers of the β-roll with maltose binding protein (MBP), a monomeric globular protein, without the leucine zipper domains. These concatemers show a similar sol-gel transition in response to calcium. Several biophysical techniques were used to probe the structural and mechanical properties of the mutant β-roll domain and the resulting supramolecular networks including circular dichroism, fluorescence resonance energy transfer, bis-ANS binding, and microrheology. These results demonstrate that the engineered β-roll peptides can mediate calcium-dependent cross-linking for protein hydrogel formation without the need for any other cross-linking moieties.
A Solution Method for Navier-Stokes Equations Based on the Mean Value Theorem

An innovative and robust algorithm capable of solving a variety of complex fluid dynamics problems is developed. This so-called, Integro-Differential Scheme (IDS) is designed to overcome known limitations of well-established schemes. The IDS implements a smart approach in transforming 3-D computational flowfields of fluid dynamic problems into their 2-D counterparts, while preserving their physical attributes. The strength of IDS rests on the implementation of the mean value theorem to the integral form of the conservation laws. This process transforms the integral equations into a finite difference scheme that lends itself to efficient numerical implementation. Preliminary solutions generated by IDS demonstrated its accuracy in terms of its ability to capture complex flowfield behaviors. In this paper, the results obtained from the application of the IDS to three problems; namely, the hypersonic flat plate problem, the shock/boundary layer interaction problem, and the shock train problem are documented and discussed. In the three cases, the results showed very good agreement with the physical expectation of these problems. In an effort to validate the new algorithm, IDS solution to the shock/boundary layer interaction problem was compared to experimental data. The results obtained by IDS show excellent agreement with the experimental data. As one of the most challenging problems in computational fluid dynamics, the new solver is used to simulate the shock train problem. Even though, very coarse grid type is used in this simulation, the code was able to capture three shocks in the shock train.
Optimally Discriminative Choice Sets in Discrete Choice Models: Application to Data-Driven Test Design

Difficult test questions can be made easy by providing a set of possible answer options of which most are obviously wrong. In the education literature, a plethora of instructional guides exist for crafting a suitable set of wrong choices (distractors) in order to probe the students' understanding of the tested concept. The art of multiple-choice question design thus hinges on the question-maker's experience and knowledge of the potential misconceptions. In contrast, we advocate a data-driven approach, where correct and incorrect options are assembled directly from the students' own past submissions. Large-scale online classroom settings, such as massively open online courses (MOOCs), provide an opportunity to design optimal and adaptive multiple-choice questions that are maximally informative about the students' level of understanding of the material. We deploy a multinomial-logit discrete choice model for the setting of multiple choice testing, derive an optimization objective for selecting optimally discriminative option sets, and demonstrate the effectiveness of our approach via a user study.
Application of an Optimized Ultra-long Span Optical Transmission Technology for Project

When constructing electric power communication networks in western areas, the issue of long-span transmission must be considered. This paper introduces the design and construction of two ultra-long unrepeated SDH transmission channels in the "Xinganshi" project operated by Sichan electric power company. Applying remote pump amplifying, enhanced forward error correction and wavelength conversion, the project builds two SDH light paths—"220 k V Ganzi –220 k V Xidi"(361 km) and "220 k V Ganzi –220 k V Yulin"(348 km) at the speed of 2.5 Gbps, which offers experiences for comprehensive use of the remote pump in constructing electric power communication systems.
Improvement on Measure of Liquidity Demand in Payment System

In order to better control the risk of payment system,based on the existing measure method analysis of the liquidity requirements on the daytime in payment system,relaxing the assumption of no other risk and delayed payment,using the method of dynamic game,the results are found to determine whether a bank should adopt delay payment basis,we put forward a measure of the size of the payment system liquidity risk indicators.Certain theory reference is provided for the central bank when it formulates relevant daytime credit policy to balance liquielity risk and the efficiency of payment system.
Analysis of body composition changes of swine during growth and development.

This study was conducted to model the growth of carcass, viscera, and empty body components and component composition of pigs. Quantitative tissue and chemical composition of 319 swine, representative of barrows and gilts from five commercial genetic populations, was determined at eight stages of growth between 25 and 152 kg. After whole body grinding and carcass dissection, proximate analyses were performed to calculate concentrations of protein, lipid, moisture, and ash of carcass, viscera, empty body, carcass lean, and carcass fat. Linear and nonlinear equations were developed to investigate the growth patterns of each component. Nonlinear growth functions accounted for the greatest amount of variation in empty body protein, lipid, moisture, and ash mass. Differences (P < .05) existed between barrows and gilts for nearly all components investigated. Carcass lean and fat tissues significantly increased in lipid percentage and decreased in moisture percentage as live weight increased. There were significant changes in the ratio and composition of the tissues of barrows and gilts during growth. Nonlinear models fitted the data better than allometric equations for nearly all of the components investigated.
New Onset Partial Epilepsy in Adolescence

An 18-year-old right-handed neurologically normal woman has new onset focal epilepsy, presenting with a secondary generalized tonic-clonic seizure after a year-long history of episodes of deja vu associated with mild confusion lasting 1–2 min. She has a normal MRI, no risk factors for epilepsy, and an EEG that shows right temporal spikes. What is your decision pathway in terms of diagnostic and treatment approaches for her?
Scalpelloid and brachylepadomorph barnacles (Cirripedia, Thoracica) from the Upper Cretaceous Mt. Laurel Sand, Delaware

A diverse cirriped fauna, including the scalpelloids Cretiscalpellum homseyi n. sp., Arcoscalpellum withersi Collins, Arcoscalpellum bakeri Collins, Virgiscalpellum gabbi heintzi n. subsp., Virgiscalpellum sp., V. cf. V. gabbi apertus Collins, and the brachylepadomorph Brachylepas solida n. sp., occurs in the Upper Cretaceous Mt. Laurel Sand at the Biggs Farm locality on the Chesapeake and Delaware Canal, New Castle County, Delaware. This fauna represents the Maastrichtian Virgiscalpellum Zone originally identified in the Ripley and Prairie Bluff formations of the eastern Gulf Coast.
Motor-Based Monitoring During Minimally Invasive Lateral Spine Surgery

The minimally invasive lateral transpsoas approach to the spine requires navigation near important neurological bundles. Injury to these nerves can cause severe pain and neuropathy or permanent weakness along numerous myotomes. During the lateral dissection, motor monitoring is often used to ensure safe access to the spine. This chapter focuses on motor-based monitoring during this approach.
Synthesis and thiol–ene photopolymerization of (meth)allyl-terminated polysulfides

Thiol-terminated polysulfides (PS) are cured by mixing with an oxidant, resulting in limited shelf- and/or pot-life, depending on whether formulated as a one- or two-component system. Mixtures of thiol- and alkene-terminated polysulfides offer the potential for an on-demand curing process through thiol–ene photopolymerization. Thiol end groups of commercial polysulfides, PS-1 (1000 g/mol) and PS-2 (3000 g/mol), were converted to alkene by reaction with (meth)allyl bromide. Photopolymerizations were performed by irradiating films of equimolar thiol:ene mixtures at 320–500 nm (30 mW/cm2) in the presence of 5 wt % 2,2-dimethoxy-2-phenyl-acetophenone (DMPA). Reaction kinetics were measured using real-time FTIR by monitoring absorbances at 3075 cm−1 (alkene) or 2550 cm−1 (thiol). In the absence of any reactive diluent, mixtures of thiol and alkene polysulfides failed to gel notwithstanding high reaction conversion (>90%). Partial or total replacement of the thiol polysulfide component with pentaerythritol tetrakis(3-mercaptopropionate) (PETMP) yielded solid elastomeric films and ultimate reaction conversions of 80–96% after 5 min irradiation. Crosshatch adhesion measured on glass, aluminum, and steel was very poor (0B) for (meth)allyl PS-1/PETMP and poor (2B) for (meth)allyl PS-2/PETMP without adhesion promoters. (3-Mercaptopropyl)trimethoxysilane (1 wt %) significantly improved adhesion of (meth)allyl PS-2/PETMP on all substrates (4B) but yielded no improvement for (meth)allyl-terminated PS-1/PETMP. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017, 134, 45523.
Catching global interactions in vivo.

Histone proteins and transcription factors (TFs) play critical roles in gene transcription and development of multicellular organisms. Although antibody mediated protein isolation couple with mass spectrometry approach has been a standard method to identify TF interacting partners and characterize their functional molecular complexes, it becomes urge to develop a robust method to functional characterize how these transcription factors act during biological process in the post-human genome project era. Here, Dr. Zhao and his colleagues in the National Heart, Lung, and Blood Institute of NIH develop a sensitive and robust strategy to globally identify and characterize in vivo protein–protein interactions termed bait protein–protein interaction-sequencing (bPPI-seq) (Zhang et al. in Cell Res doi: 10.1038/cr.2017.112 , 2017). As a proof-of-principle, they demonstrated that genome-wide interacting partners of histone variant H2A.Z are mainly involved in transcriptional regulation which is distinct from the interacting proteins of canonical histone H2A. Thus, their results suggest that bPPI-seq can be widely used to globally characterize protein complexes especially transcription factor interacting partners and molecular networks formed.
On the Boundary-Field Equation Methods for Fluid-Structure Interactions

This paper is concerned with some recent developments in the combined boundary integral and field equation methods for fluid-structure interaction problems. Emphasis will be placed upon the variational formulations and mathematical foundations of various solution procedures.
Integrated in vivo multiomics analysis identifies p21-activated kinase signaling as a driver of colitis

Inflammatory bowel disease (IBD) is a chronic disorder of the gastrointestinal tract that has limited treatment options. To gain insight into the pathogenesis of chronic colonic inflammation (colitis), we performed a multiomics analysis that integrated RNA microarray, total protein mass spectrometry (MS), and phosphoprotein MS measurements from a mouse model of the disease. Because we collected all three types of data from individual samples, we tracked information flow from RNA to protein to phosphoprotein and identified signaling molecules that were coordinately or discordantly regulated and pathways that had complex regulation in vivo. For example, the genes encoding acute-phase proteins were expressed in the liver, but the proteins were detected by MS in the colon during inflammation. We also ascertained the types of data that best described particular facets of chronic inflammation. Using gene set enrichment analysis and trans-omics coexpression network analysis, we found that each data set provided a distinct viewpoint on the molecular pathogenesis of colitis. Combining human transcriptomic data with the mouse multiomics data implicated increased p21-activated kinase (Pak) signaling as a driver of colitis. Chemical inhibition of Pak1 and Pak2 with FRAX597 suppressed active colitis in mice. These studies provide translational insights into the mechanisms contributing to colitis and identify Pak as a potential therapeutic target in IBD.
The outcome of checkpoint inhibitor therapy in patients with cancer and solid organ transplant: A systematic review of the literature.

41Background: Solid organ transplant recipients have been excluded from Checkpoint inhibitors (CPI) clinical trials because of the concern of allo-immunity and possible organ rejection. Methods: We searched 5 databases through September 2017. Studies describing the use of CPI to treat cancer in solid organ transplant Patients (pts), and provided detailed description of each case were included. Results: Sixteen publications met inclusion criteria, reporting on 19 cases. Median age of pts was 59 (14-77) yrs and 74% were male. Cancer types included melanoma (n=11), cutaneous squamous cell carcinoma (ca) (n=3), non-small cell lung ca and hepatocellular ca (n=2 each), and duodenal ca (n=1). Median time to start CPI after organ transplant was 11 (1-25) yrs. Nivolumab (nivo) was used in 53%, ipilimumab (ipi) in 26%, and pembrolizumab (pem) in 21%. Most pts were maintained on low dose prednisone (≤ 10 mg), mTOR inhibitors, and other immunosuppressives prior to initiating CPI. Graft rejection occurred in 10 of 19 ...
Tunable Mechanical Metamaterials through Hybrid Kirigami Structures.

Inspired by the art of paper cutting, kirigami provides intriguing tools to create materials with unconventional mechanical and morphological responses. This behavior is appealing in multiple applications such as stretchable electronics and soft robotics and presents a tractable platform to study structure-property relationships in material systems. However, mechanical response is typically controlled through a single or fractal cut type patterned across an entire kirigami sheet, limiting deformation modes and tunability. Here we show how hybrid patterns of major and minor cuts creates new opportunities to introduce boundary conditions and non-prismatic beams to enable highly tunable mechanical responses. This hybrid approach reduces stiffness by a factor of ~30 while increasing ultimate strain by a factor of 2 (up to 750% strain) relative to single incision patterns. We present analytical models and generate general design criteria that is in excellent agreement with experimental data from nanoscopic to macroscopic systems. These hybrid kirigami materials create new opportunities for multifunctional materials and structures, which we demonstrate with stretchable kirigami conductors with nearly constant electrical resistance up to >400% strain and magnetoactive actuators with extremely rapid response (>10,000% strain s−1) and high, repeatable elongation (>300% strain).
Temporal Variability in Thermally Driven Cross-Shore Exchange: The Role of Semidiurnal Tides

AbstractWe examine temporal variability of thermally driven baroclinic cross-shore exchange in the context of a tropical fringing reef system focusing on the role of tidally driven alongshore flow....