cssi/SciSciGPT-SciSciNet huggingface dataset:
Diffusion MRI of uterine and ovarian masses: identifying the benign lesions

The purpose of the study was to assess the diagnostic performance of qualitative and quantitative diffusion-weighted imaging (DWI) in differentiating benign from malignant ovarian and uterine masses. Institutional review board approval was obtained for this HIPAA-compliant retrospective study, with waiver of informed consent. DWI MRIs of 222 women acquired over 1.5 years were evaluated. Reference standard was pathology or follow-up imaging. For qualitative assessment, two radiologists independently reviewed DWI and apparent diffusion coefficient (ADC) images for diffusion restriction. Differences were resolved by consensus. For quantitative assessment, a single reader measured ADC values. Readers were blinded to the reference standard. 222 lesions, 121 ovarian (99 benign and 22 malignant) and 101 uterine (54 benign and 47 malignant), were included. Final diagnosis was established with pathology in 129 (58%) or with imaging follow-up in 93 (42%). Mean (range) follow-up interval was 27 (13–48) months. Qualitative assessment yielded sensitivity (ratio, 95% CI), specificity, PPV and NPV of 100% (22/22, 85–100), 68% (68/99, 58–76), 41% (22/54, 27–54), and 100% (68/68, 94–100) for ovarian and 94% (44/47, 83–98), 91% (49/54, 80–96), 90% (44/49, 78–95) and 94% (49/52, 84–98) for uterine malignancies. ADC (mean ± SD) between benign ovarian [(1.11 ± 0.76) × 10−3 mm2/s] vs. malignant [(0.71 ± 0.26) × 10−3 mm2/s] lesions was significantly different (p < 0.001). ADC cutoff value of 1.55 × 10−3 mm2/s for ovarian lesions resulted in 99.9% confidence for the absence of malignancy. ADC (mean ± SD) of benign uterine [(0.64 ± 0.38) × 10−3 mm2/s] vs. malignant [(0.68 ± 0.19) × 10−3 mm2/s] lesions was not significantly different (P < 0.54). Quantitative and qualitative DWI assessment can be used to confidently characterize a subset of ovarian lesions as benign. With uterine lesions, although DWI is useful in differentiating benign from malignant lesions, the technique does not allow for definitive quantitative characterization.
X-ray crystallographic studies of the extracellular domain of the first plant ATP receptor, DORN1, and the orthologous protein from Camelina sativa.

Does not respond to nucleotides 1 (DORN1) has recently been identified as the first membrane-integral plant ATP receptor, which is required for ATP-induced calcium response, mitogen-activated protein kinase activation and defense responses in Arabidopsis thaliana. In order to understand DORN1-mediated ATP sensing and signal transduction, crystallization and preliminary X-ray studies were conducted on the extracellular domain of DORN1 (atDORN1-ECD) and that of an orthologous protein, Camelina sativa lectin receptor kinase I.9 (csLecRK-I.9-ECD or csI.9-ECD). A variety of deglycosylation strategies were employed to optimize the glycosylated recombinant atDORN1-ECD for crystallization. In addition, the glycosylated csI.9-ECD protein was crystallized at 291 K. X-ray diffraction data were collected at 4.6 A resolution from a single crystal. The crystal belonged to space group C222 or C2221, with unit-cell parameters a = 94.7, b = 191.5, c = 302.8 A. These preliminary studies have laid the foundation for structural determination of the DORN1 and I.9 receptor proteins, which will lead to a better understanding of the perception and function of extracellular ATP in plants.
Plastic Deformation of Polymer Blends as a Means to Achieve Stretchable Organic Transistors

Intrinsically stretchable semiconductors will facilitate the realization of seamlessly integrated stretchable electronics. However, to date demonstrations of intrinsically stretchable semiconductors have been limited. In this study, a new approach to achieve intrinsically stretchable semiconductors is introduced by blending a rigid high-performance donor-acceptor polymer semiconductor poly[4(4,4dihexadecyl4Hcyclopenta [1,2b:5,4b' ] dithiopen2yl) alt [1,2,5] thiadiazolo [3,4c] pyridine] (PCDTPT) with a ductile polymer semiconductor poly(3hexylthiophene) (P3HT). Under large tensile strains of up to 75%, the polymers are shown to orient in the direction of strain, and when the strain is reduced, the polymers reversibly deform. During cyclic strain, the local packing order of the polymers is shown to be remarkably stable. The saturated field effect charge mobility is shown to be consistently above 0.04 cm2 V-1s-1 for up to 100 strain cycles with strain ranging from 10% to 75% when the film is printed onto a rigid test bed. At the 75% strain state, the charge mobility is consistently above 0.15 cm2 V-1s-1. Ultimately, the polymer blend process introduced here results in an excellent combination of device performance and stretchability providing an effective approach to achieve intrinsically stretchable semiconductors.
Wetland Elevations at Sub-Centimeter Precision: Exploring the Use of Digital Barcode Leveling for Elevation Monitoring

Scientists investigating wetland soil vertical development have required a high precision, high accuracy technique to measure wetland surface elevation change over time. The Surface Elevation Table (SET), capable of millimeter-scale precision, has proven effective in supporting hypothesis-based inquiry into mechanisms of wetland vertical development. More recently, SET sampling stations have been established in many areas to monitor wetland elevation change in an effort to gauge wetland resilience to accelerated sea level rise. Unfortunately, each SET sampling station covers an area of about 1 m2, and the technique was not designed to monitor elevations across broad, hectare-sized spatial scales. The purpose of this study is to investigate an alternative method for obtaining repeated, high-precision measurements of wetland elevation and elevation change that could easily be extended to the hectare scale. This study compares the precision and accuracy of a novel digital barcode leveling technique to the now well-accepted SET for the purposes of measuring wetland surface elevation change. Results suggest that leveling can provide wetland elevations with similar vertical precision as the SET over much larger spatial scales and with an instrument that costs about the same as the SET.
Standard conjecture of Künneth type with torsion coefficients

A. Venkatesh raised the following question, in the context of torsion automorphic forms: can the mod p analogue of Grothendieck’s standard conjecture of Kunneth type be true (especially for compact Shimura varieties)? In the first theorem of this article, by using a topological obstruction involving Bockstein, we show that the answer is in the negative and exhibit various counterexamples, including compact Shimura varieties. It remains an open geometric question whether the conjecture can fail for varieties with torsion-free integral cohomology. Turning to the case of abelian varieties, we give upper bounds (in p) for possible failures, using endomorphisms, the Hodge–Lefschetz operators, and invariant theory. The Schottky problem enters into consideration, and we find that, for the Jacobians of curves, the question of Venkatesh has an affirmative answer for every prime number p.
A Method for Selecting Peer Deals in IT Service Contracts

To respond to requests for proposals from clients requiring complex Information technology (IT) services, IT service providers have to prepare a solution composed of the multiple services requested by the clients and price that solution. Then, each provider competes in a tender-kind of process trying to convince the client with their solution. Pricing these solutions/deals, using historical and market data, is a complex task that we studied in our previous works. In our prior pricing approaches, we used a simple algorithm for selecting similar historical and market deals to the one we are trying to price, before we mine the data of these deals to estimate the costs of that latter deal. However, there are multiple limitations to that algorithm that we overcome in the novel approach that we present in this paper. These limitations include missing on some similar deals due to the way we chose them. Our new approach involves an iterative algorithm that selects peer deals at different levels until a pre-specified number of deals is determined. We present a proof-of-concept implementation of our approach, using real-world data, to illustrate its efficiency.
Immunization documentation practices and vaccine-preventable disease surveillance capacity among institutions of higher education in Indiana.

Objective Complete and accurate documentation of immunization records and surveillance of disease transmission are critical to the public health response to outbreaks of communicable disease in institutions of higher education (IHEs). This study aims to describe immunization documentation practices and disease surveillance capacity among IHEs in Indiana in order to inform public health action. Methods IHEs in Indiana were identified and included in the study if they offered on-campus housing and had a dedicated student health center. Phone surveys were administered in September 2015 to each institution, inquiring about current immunization documentation policies and practices, disease surveillance capacity, and use of statewide electronic reporting systems. Additionally, IHE websites were searched to identify immunization documentation requirements for matriculating students. Results Surveys were completed for 33 of 38 eligible IHEs. Twenty-three (70%) IHEs reported that student immunization records are entered into an accessible electronic system or database. Matriculating student immunization requirements were identified for 32 institutions. Of these, 22 (69%) required a physician-signed proof of immunization. No IHEs reported documenting historical immunizations in the statewide electronic immunization system and three IHEs (9%) reported utilizing the state electronic disease surveillance program. Conclusions Immunization documentation practices vary among IHEs in Indiana and use of statewide immunization and disease reporting systems is minimal. Robust utilization of immunization and disease surveillance systems has been shown to improve public health response to communicable disease outbreaks. Improving mutual understanding of policy and practice between health departments and IHEs could improve the ability to respond to public health challenges.
Slide Esophagoplasty vs End-to-End Anastomosis for Recalcitrant Esophageal Stricture after Esophageal Atresia Repair

Background Anastomotic stricture is a common complication after esophageal atresia (EA) repair. Patients with a recalcitrant stricture may require surgical intervention. The technique of reanastomosis after stricture resection can affect patient outcomes. Study Design Patients with EA who underwent anastomotic stricture resection, from July 2010 to February 2017, were reviewed. After stricture resection, patients who had slide esophagoplasty performed were compared with those having conventional end-to-end anastomosis. Results Fifty patients underwent stricture repair surgery by slide esophagoplasty (n = 12) or end-to-end (n = 38) anastomosis technique at a median age of 14 months (interquartile range [IQR] 6 to 23 months). Significantly fewer patients required dilation therapy after slide esophagoplasty: 6 of 12 (50%) compared with 32 of 38 (84%) in the end-to-end group (p = 0.02). The number of dilation sessions was significantly lower in the slide group vs the end-to-end (p = 0.004) group, with a risk ratio confirming the approximately half the number of dilations for the slide approach (risk ratio 0.57, 95% CI 0.38 to 0.86). Steroid injection was combined with dilation in 3 of 12 (25%) vs 22 of 38 (58%) in the slide and end-to-end groups, respectively (p = 0.10). Stent placement was used in none of slide cases vs 8 of 38 (21%) in the end-to-end group (p = 0.17). Stricture incision was performed in 1 of 12 (8%) in the slide group and 11 of 38 (29%) in the end-to-end group (p = 0.25). There were leak complications in fewer patients after slide esophagoplasty compared with end-to-end anastomosis: 1 of 12 (8%) vs 8 of 38 (21%) (p = 0.43). Conclusions Slide esophagoplasty may be a useful technique of anastomotic configuration for selected patients with recalcitrant esophageal stricture, offering more favorable outcomes compared with end-to-end anastomosis.
Numerical investigation of driver lower extremity injuries in finite element frontal crash reconstruction

Objective: Lower extremity injuries are the most frequent Abbreviated Injury Scale (AIS) 2 injury for drivers in frontal crashes. The objective was to reconstruct 11 real-world motor vehicle crashe...
Abuse-deterrent opioid formulations: a key ingredient in the recipe to prevent opioid disasters?

The US Food and Drug Administration (FDA) is encouraging the innovation of long-acting opioid formulations that are manipulation-resistant. The purpose of this commentary is to assess the benefits and limitations of abuse-deterrent opioid formulations (ADFs) and discuss their role in mitigating the current opioid epidemic. ADFs have been created with chemical properties that make it difficult for people who non-medically use prescription drugs to crush and dissolve opioid tablets, as well as by combining opioids with antagonists such as naloxone or naltrexone, which are released only when the dosage form has been manipulated or the drug is taken by a non-intended route. Despite these and other technologies, consensus regarding the effectiveness of these formulations in preventing non-medical use is lacking given the difficulty in obtaining post-marketing data. Researchers also question if the creation of abuse-deterrent drugs will have a positive effect on those struggling with a severe opioid-use disorder, fearing that current opioid users will simply find a new - perhaps more dangerous - drug of choice. Abuse-deterrent opioids are still opioids, and although they may make manipulation more difficult than non-ADF formulations, they are not "abuse proof." The introduction of ADFs could provide a false sense of security among prescribers and dispensers, and we fear that ADFs may have a minimal impact on non-medical use of prescription opioids. Further epidemiological studies will be required to determine the large-scale impact of abuse-deterrent opioids in preventing opioid use disorder and its downstream consequences.
Clinical Vignette: Limbic Encephalitis Presenting as Bilateral Epilepsia Partialis Continua (P4.282)

Objective: To review the clinical presentation, MRI features, EEG characteristics and treatment response of a patient presenting with bilateral EPC secondary to limbic encephalitis Background: Epilepsia partialis continua (EPC) is defined as spontaneous regular or irregular clonic muscular twitching affecting a limited part of the body, sometimes aggravated by action or sensory stimuli, occurring for a minimum of one hour, and recurring at intervals of no more than ten seconds [1]. This rare clinical entity has been associated with various etiologies [2]. We present a unique case of bilateral EPC secondary to autoimmune encephalitis, principally involving the bilateral cingulate gyri. Design/Methods: Case report Results: A 34-year-old Jamaican woman presented with right leg weakness & intermittent jerking movements of both legs. This quickly progressed to bilateral leg weakness and continuous bilateral leg jerking. EEG revealed frequent midline electroclinical seizures. MRI showed focal cortical signal abnormality involving portions of the cingulate gyri and adjacent parahippocampal gyri. Seizures were resistant to levetiracetam, lacosamide, clobazam, phenytoin, valproate and midazolam infusion. High dose steroids, IVIG & plasma exchange were utilized for treatment of a potential autoimmune etiology. Extensive workup included following negative/normal studies: HIV, anti-TPO, Syphilis, Lyme, ACE; bacteria, viruses, fungi and TB in CSF; CT chest, abdomen/pelvis. Brain biopsy revealed a mononuclear infiltrate involving meninges and adjacent brain parenchyma, with no organisms. Paraneoplastic panel showed “nuclear non-neuronal specific antibodies” and the patient was started on rituximab, with noticeable clinical and electrographic improvement after the second dose. Six months after rituximab treatment, she has remained seizure free and her deficits continue to improve. Conclusions: This case represents a rare presentation of bilateral EPC in the context of an autoimmune encephalitis principally involving the bilateral cingulate gyri. We suggest that autoimmune encephalitides may present fulminantly with focal seizures that are resistant to traditional anti-seizure medications, and treatment with appropriate immunesuppressants is essential. Study Supported by: N/A Disclosure: Dr. Mandge has nothing to disclose. Dr. Castellano has nothing to disclose. Dr. McHugh has nothing to disclose. Dr Milstein has nothing to disclose. Dr. Boro has nothing to disclose.
Dynamics of Single Populations

This chapter develops the mathematics of discrete and continuous models for a single dynamic quantity. Separate sections introduce each type of model via simple examples and simulations, and two additional sections present the principal graphical methods: cobweb analysis for discrete equations and phase line analysis for continuous equations. The final section uses the graphical methods as motivation for the development of the linearized stability method. The examples and problem sets feature case studies for a variety of biological settings, including fishery models, insect population models, resource management, and lake eutrophication.
Catecholamine physiology in the ovine fetus. I. Gestational age variation in basal plasma concentrations.

Abstract Fifty-five ewes with chronically catheterized singleton gestations were studied to assess changes in basal concentrations of fetal catecholamines with increasing gestational age. All pregnancies were time dated, and measurements of catecholamines were conducted at least 5 days after placement of fetal catheters when fetal metabolic parameters had normalized. Plasma concentrations of catecholamines were measured by radioenzymatic assay. Additionally, fetal heart rate (FHR) and corrected mean blood pressure were analyzed in 32 of the fetuses for correlation with plasma levels of catecholamines. Multiple regression analysis revealed significant inverse correlations of fetal plasma concentrations of catecholamines with gestational age, as follows: norepinephrine (p
Right Hemisphere Contributions to Bilateral Force Control in Chronic Stroke: A Preliminary Report.

Abstract Background Bilateral motor control deficits poststroke may be lateralized by hemisphere damage. This preliminary study investigated bilateral force control between left and right hemisphere-damaged groups at baseline and after coupled bilateral movement training with neuromuscular stimulation. Methods Stroke participants (8 left hemisphere and 6 right hemisphere cerebrovascular accidents) performed a bilateral isometric force control task at 3 submaximal force levels (5%, 25%, and 50% of maximum voluntary contraction [MVC]) before and after training. Force accuracy, force variability, and interlimb force coordination were analyzed in 3-way mixed design ANOVAs (2 × 2 × 3; Group × Test Session × Force Level) with repeated measures on test session and force level. Results The findings indicated that force accuracy and variability at 50% of MVC in the right hemisphere-damaged group were more impaired than lower targeted force levels at baseline, and the impairment at the highest target level was improved after coupled bilateral movement training. However, these patterns were not observed in the left hemisphere-damaged group. Conclusions Current findings support a proposition that the right hemisphere presumably contributes to controlling bilateral force production.
Sacred Caves of the World: Illuminating the Darkness

Most religions of the world identify one or more caves as sacred using them as extraordinary sites for meditation, ritual, art, burial, and/or related purposes. These are extraordinary places as spaces at the interface between the natural and supernatural and also between geology and biology on the one hand and religion, culture, and history on the other. Sacred caves facilitate a holistic perspective and synthesis integrating the natural sciences, social sciences, and humanities, instead of the usual isolation or academic compartmentalization. This essay discusses a geographical comparison of a representative sample of sacred caves to reveal how different cultures and religions construct meaning for caves as sacred, the main similarities and differences among them and the distinctions between the sacred and the profane. It explores: what makes a cave sacred? Who uses sacred caves, where, when, how, and why? I draw on my field research on sacred caves in Thailand as well as an extensive literature survey. The anomalous and mysterious character of caves contributes to the sacredness of some, although historical, cultural, and/or religious factors may also be involved. Most are associated with Buddhism in Asia and the Maya in Central America. I also discuss prehistoric caves and sacred caves in indigenous, Abrahamic, and Asian religions. I conclude with comments on scientific research and conservation efforts and show caves which are also major tourist sites.
Role of dopamine D 2-like receptors and their modulation by adenosine receptor stimulation in the reinstatement of methamphetamine seeking

Previous work has demonstrated that dopamine and adenosine receptors are involved in drug-seeking behaviors, yet the pharmacological interactions between these receptors in methamphetamine (MA) seeking are not well characterized. The present studies examined the role of the dopamine D2-like receptors in MA seeking and identified the interactive effects of adenosine receptor stimulation. Adult male Sprague–Dawley rats were trained to lever press for MA in daily 2-h self-administration sessions on a fixed-ratio 1 schedule for 10 consecutive days. After 1 day of abstinence, lever pressing was extinguished in six daily extinction sessions. Treatments were administered systemically prior to a 2-h reinstatement test session. An increase in MA seeking was observed following the administration of the dopamine D2-like agonist, quinpirole, or the D3 receptor agonist, 7-OH-DPAT. Stimulation of D2 or D4 receptors was ineffective at inducing MA seeking. Quinpirole-induced MA seeking was inhibited by D3 receptor antagonism (SB-77011A or PG01037), an adenosine A1 agonist, CPA, and an adenosine A2A agonist, CGS 21680. MA seeking induced by a MA priming injection or D3 receptor stimulation was inhibited by a pretreatment with the adenosine A1 agonist, CPA, but not the adenosine A2A agonist, CGS 21680. These results demonstrate the sufficiency of dopamine D3 receptors to reinstate MA seeking that is inhibited when combined with adenosine A1 receptor stimulation.
Sentinel vascular access monitoring after endovascular intervention predicts access outcome.

Background and objectives:The vascular access pressure ratio test identifies dialysis vascular access dysfunction when three consecutive vascular access pressure ratios are >0.55. We tested whether...
Accelerating geostatistical seismic inversion using TensorFlow: A heterogeneous distributed deep learning framework

Abstract Geostatistical seismic inversion is one of emerging technologies in reservoir characterization and reservoir uncertainty quantification. However, the challenge of intensive computation often restricts its application in practical studies. To circumvent the computational limitation, in this work, we present a distributed parallel approach using TensorFlow to accelerate the geostatistical seismic inversion. The approach provides a general parallel scheme to efficiently take advantage of all the available computing resources, i.e. CPUs and GPUs: the computational workflow is expressed and organized as a Data Flow Graph, and the graph can be divided into several sub-graphs which are then mapped to multiple computing devices to concurrently evaluate the operations in them. The high-level interface and the feature of automatic differentiation provided by TensorFlow also makes it much easy for users to implement their algorithms in an efficient parallel manner, and allows employing programs on any computing platform almost without alteration. The proposed method was validated on a 3D seismic dataset consisting of 600 × 600 × 200 grid nodes. The results indicate that it is feasible to the practical application and the computational time can be largely reduced by using multiple GPUs.
Identifying volatile numeric expressions in numeric computing applications

Abstract The results of numerical computations with floating point numbers depend on the execution platform, which we define as the hardware and the tools (compilers, etc.) supporting that hardware. One reason for the dependence is that compilers have significant freedom in deciding how to evaluate a floating point expression, as such evaluation is not standardized (not even in standards such as IEEE-754). Another reason is that hardware may or may not provide specialized instructions like Fused Multiply Add (FMA), and if it does, the compiler can take advantage of FMA functionality in different ways. We call an expression volatile if, for some input, its value differs across platform parameters. Differences can become particularly large across heterogeneous parallel architectures. This undermines the software portability promised by programming standards such as OpenCL and significantly impacts reproducibility of results in general. In this paper, we present a technique that predicts bounds on the output of a program containing volatile expressions when executed on different platforms. Using randomly selected inputs, we compare the bounds to results from running the code across a variety of platforms including CPUs and GPUs. Our results show that the theoretical bounds are relatively tight (within an order of magnitude) and can help users pinpoint where results should be stabilized , for instance by restricting expression reordering.
Trends in urinary calculi composition from 2005 to 2015: a single tertiary center study

The goal of this study was to investigate recent changes in stone composition and patient demographics to identify factors influencing stone formation for the purpose of reducing the incidence of urolithiasis and preventing stone recurrence. This retrospective analysis includes patients who underwent percutaneous nephrolithotripsy or ureteroscopy at our institution from 2005 to 2015. Northwestern Medicine Enterprise Data Warehouse was used to retrieve demographic information and stone composition analyses. The composition of mixed stones containing uric acid (UA) and calcium oxalate monohydrate (COM) was analyzed further. Chi-squared tests were used for categorical variables and logistic regression was used to assess trends. From 2005 to 2015, 5268 stones were treated. COM was predominant in 42.2% and only 16.6% were pure. The male/female ratio decreased significantly from 1.8 to 1.08 and patient age increased (p < 0.001) with 45.6% of patients being 60 or older in 2015. Females formed more CO dihydrate (COD; p = 0.008) and struvite (p = 0.001) overall. The incidence of COM (p = 0.007) and UA (p < 0.001) rose significantly in men whereas both sexes saw a decrease in carbonate apatite (CA; p < 0.001). COM increased considerably from 12 to 75% amongst mixed stones with UA over the 11-year span. We concluded that stone formers have become older and more gender-equal. The increase in female patients parallels the increase in female obesity in the US. The rising predominance of COM, including when mixed with UA, and the scarcity of pure stones indicates it may be necessary to develop new approaches to managing and preventing urolithiasis.
Evolution of neutral oxygen during the epoch of reionization and its use in estimating the neutral hydrogen fraction

We use synthetic sightlines drawn through snapshots of the Technicolor Dawn simulations to explore how the statistics of neutral oxygen OI absorbers respond to hydrogen reionization. The ionization state of the circumgalactic medium (CGM) initially roughly tracks that of the intergalactic medium, but beginning at $z=8$ the CGM grows systematically more neutral owing to self-shielding. Weak absorbers trace diffuse gas that lies farther from halos, hence they are ionized first, whereas stronger systems are less sensitive to reionization. The overall OI covering fraction decreases slowly with time owing to competition between ongoing enrichment and gradual encroachment of ionization fronts into increasingly overdense gas. While the declining covering fraction is partially offset by continued formation of new halos, the ionization of the diffuse gas causes the predicted line-of-sight incidence rate of OI absorbers to decline abruptly at the overlap epoch, in qualitative agreement with observations. In comparison to the recently-observed equivalent width (EW) distribution at $z\approx6$, the simulations underproduce systems with $EW \geq 0.1 \unicode{x212B}$, although they reproduce weaker systems with $EW \geq 0.05 \unicode{x212B}$. By $z\approx5$, the incidence of $EW 10\%$
A Phylogenomic Approach to Clarifying the Relationship of Mesodinium within the Ciliophora: A Case Study in the Complexity of Mixed-Species Transcriptome Analyses

Recent high-throughput sequencing endeavors have yielded multigene/protein phylogenies that confidently resolve several inter- and intra-class relationships within the phylum Ciliophora. We leverage the massive sequencing efforts from the Marine Microbial Eukaryote Transcriptome Sequencing Project, other SRA submissions, and available genome data with our own sequencing efforts to determine the phylogenetic position of Mesodinium and to generate the most taxonomically rich phylogenomic ciliate tree to date. Regardless of the data mining strategy, the multiprotein data set, or the molecular models of evolution employed, we consistently recovered the same well-supported relationships among ciliate classes, confirming many of the higher-level relationships previously identified. Mesodinium always formed a monophyletic group with members of the Litostomatea, with mixotrophic species of Mesodinium-M. rubrum, M. major, and M. chamaeleon-being more closely related to each other than to the heterotrophic member, M. pulex. The well-supported position of Mesodinium as sister to other litostomes contrasts with previous molecular analyses including those from phylogenomic studies that exploited the same transcriptomic databases. These topological discrepancies illustrate the need for caution when mining mixed-species transcriptomes and indicate that identifying ciliate sequences among prey contamination-particularly for Mesodinium species where expression from stolen prey nuclei appears to dominate-requires thorough and iterative vetting with phylogenies that incorporate sequences from a large outgroup of prey.
Herpesvirus-infected Hofbauer cells activate endothelial cells through an IL-1β-dependent mechanism.

Abstract Introduction Placental viral infections are associated with fetal inflammation and adverse pregnancy outcomes. However, there have been limited studies on how placental macrophages in the villous and adjacent fetal umbilical endothelial cells respond to a viral insult. This study aimed to evaluate the communication between Hofbauer cells (HBCs) and human umbilical vein endothelial cells (HUVECs) during a viral infection. Methods HBCs were either uninfected or infected with the γ-herpesvirus, MHV-68, and the conditioned medium (CM) collected. HUVECs were exposed to HBC CM and the levels of the pro-neutrophilic response markers: IL-8; E-selectin; intercellular adhesion molecule 1 (ICAM-1); and vascular adhesion molecule 1 (VCAM-1) measured by ELISA and qPCR. The role of HBC-derived IL-1β was investigated using an IL-1β blocking antibody (Ab) or IL-1 receptor antagonist (IL-1Ra). Results MHV-68 infection of HBCs induced a significant increase in IL-1β secretion. CM from infected HBCs induced HUVEC expression of IL-8, E-selectin, VCAM-1, ICAM-1 mRNA, and secretion of IL-8. The HUVEC response to the CM of MHV-infected HBCs was inhibited by a neutralizing IL-1β Ab and by IL-1Ra. Discussion Virally-induced HBC IL-1β activates HUVECs to generate a pro-neutrophilic response. This novel cell-cell communication pathway may play an important role in the genesis of fetal inflammation associated with placental viral infection.
FEASIBILITY OF IVUS-DERIVED FFR AS A NOVEL TECHNIQUE TO ESTIMATE FUNCTIONAL SEVERITY OF CORONARY STENOSIS: SYSTEMATIC EVALUATION OF THE METHODS TO DETERMINE THE REFERENCE LUMEN AREA FOR AUTOMATED FFR CALCULATION

IVUS-derived FFR (IVUS-FFR) is a novel technique to estimate functional severity of coronary stenosis. Using a fluid dynamics algorithm, pressure loss (ΔP) across a stenosis is calculated as ΔP = FV + SV2, where V is the flow velocity, F and S are IVUS-defined coefficients: minimum lumen area (MLA
Optimizing the development and evaluation of complex interventions: lessons learned from the BetterBirth Program and associated trial.

Despite extensive efforts to develop and refine intervention packages, complex interventions often fail to produce the desired health impacts in full-scale evaluations. A recent example of this phenomenon is BetterBirth, a complex intervention designed to implement the World Health Organization’s Safe Childbirth Checklist and improve maternal and neonatal health. Using data from the BetterBirth Program and its associated trial as a case study, we identified lessons to assist in the development and evaluation of future complex interventions. BetterBirth was refined across three sequential development phases prior to being tested in a matched-pair, cluster randomized trial in Uttar Pradesh, India. We reviewed published and internal materials from all three development phases to identify barriers hindering the identification of an optimal intervention package and identified corresponding lessons learned. For each lesson, we describe its importance and provide an example motivated by the BetterBirth Program’s development to illustrate how it could be applied to future studies. We identified three lessons: (1) develop a robust theory of change (TOC); (2) define optimization outcomes, which are used to assess the effectiveness of the intervention across development phases, and corresponding criteria for success, which determine whether the intervention has been sufficiently optimized to warrant full-scale evaluation; and (3) create and capture variation in the implementation intensity of components. When applying these lessons to the BetterBirth intervention, we demonstrate how a TOC could have promoted more complete data collection. We propose an optimization outcome and related criteria for success and illustrate how they could have resulted in additional development phases prior to the full-scale trial. Finally, we show how variation in components’ implementation intensities could have been used to identify effective intervention components. These lessons learned can be applied during both early and advanced stages of complex intervention development and evaluation. By using examples from a real-world study to demonstrate the relevance of these lessons and illustrating how they can be applied in practice, we hope to encourage future researchers to collect and analyze data in a way that promotes more effective complex intervention development and evaluation. ClinicalTrials.gov, NCT02148952; registered on May 29, 2014
Comparison of the performance of aerosol sampling devices with aerosols containing Ebola virus

Previous laboratory studies of Ebola virus aerosols have used a variety of different sampling devices to collect viral material for analysis. However, sampling devices vary in their ability to coll...
Studying the SVC Control Strategy of the Ali Interconnection Project

The Ali Interconnection project will connect the isolated Ali grid and the main Tibet grid, and the transmission distance will be more than 1,000 kilometers. The system structure and the power support of the grid along the interconnection channel both are very weak, then the reactive power control and voltage control of which are very difficult, too. In order to improve the voltage control level of the Ali Interconnection project, some SVC reactive compensation devices are configured at both ends of the channel. Based on the data of Ali grid and Tibet main grid, the control strategies of these SVC devices are studied by digital-analog hybrid simulation. According to the simulation results, the suitable control parameters and strategies are given, which provides powerful technical support for the projects such as interconnection of weak grids or the new energy consumption.
Deep Learning Accelerated Determination of Hydride Locations in Metal Nanoclusters

Although the coordinates of the metal atoms can be accurately determined by X-ray crystallography, locations of hydrides in metal nanoclusters are challenging to determine. In principle, neutron crystallography can be employed to pinpoint the hydride positions, but it requires a large crystal and a neutron source, which prevents its routine use. Here, we present a deep-learning approach that can accelerate determination of hydride locations in single-crystal X-ray structure of metal nanoclusters of different sizes. We demonstrate the efficiency of our method in predicting the most probable hydride sites and their combinations to determine the total structure for two recently reported copper nanoclusters, [Cu25 H10 (SPhCl2 )18 ]3- and [Cu61 (St Bu)26 S6 Cl6 H14 ]+ whose hydride locations have not been determined by neutron diffraction. Our method can be generalized and applied to other metal systems, thereby eliminating a bottleneck in atomically precise metal hydride nanochemistry.
Emerging Human Ehrlichioses: Recently Recognized, Widely Distributed, Life-Threatening Tick-Borne Diseases

Phylogenetic analysis based on 16S rRNA gene homology places organisms currently designated Ehrlichia spp. within three different clusters. The theme of evolution for survival as obligately intracellular organisms within insects and ticks seems to characterize most of those bacteria well, except for those in the group containing Ehrlichia sennetsu and Neorickettsia helminthoeca. The etiologic organisms of human monocytotropic ehrlichiosis (HME) and human granulocytotropic ehrlichiosis (HGE) have surely been present on Earth for eons. The body of knowledge provided by veterinary scientists, including techniques to cultivate some of the Ehrlichia spp. as antigens for immunofluorescence serology and descriptions of their microscopic and ultrastructural appearance, facilitated the identification of the etiologic agent of HME as an Ehrlichia sp. Increasing numbers of commercial laboratories are offering serologic and PCR diagnostic assays for the diagnosis of the human ehrlichioses. A commercial laboratory with the most experience in the diagnosis of HME, demonstrated the presence of antibodies to E. chaffeensis in 1,136 serum specimens between October 1991 and May 1996. Cell culture recovery of the HGE agent in HL60 cells (a human myeloid cell line) has yielded more isolates than recovery of E. chaffeensis has in DH82 cells. HGE is treated successfully with doxycycline with the same doses as for HME. Based on cell culture antimicrobial susceptibility studies, rifampin, rifabutin, and selected fluoroquinolones show promise as alternative drugs that might prove useful in situations such as pregnancy.
Production of the antibiotic phenazine-1-carboxylic acid by fluorescent Pseudomonas species in the rhizosphere of wheat.

Pseudomonas fluorescens 2-79 and P. aureofaciens 30-84 produce the antibiotic phenazine-1-carboxylic acid and suppress take-all, an important root disease of wheat caused by Gaeumannomyces graminis var. tritici. To determine whether the antibiotic is produced in situ, wheat seeds were treated with strain 2-79 or 30-84 or with phenazine-nonproducing mutants or were left untreated and then were sown in natural or steamed soil in the field or growth chamber. The antibiotic was isolated only from roots of wheat colonized by strain 2-79 or 30-84 in both growth chamber and field studies. No antibiotic was recovered from the roots of seedlings grown from seeds treated with phenazine-nonproducing mutants or left untreated. In natural soils, comparable amounts of antibiotic (27 to 43 ng/g of root with adhering soil) were recovered from roots colonized by strain 2-79 whether or not the pathogen was present. Roots of plants grown in steamed soil yielded larger bacterial populations and more antibiotic than roots from natural soils. In steamed and natural soils, roots from which the antibiotic was recovered had significantly less disease than roots with no antibiotic, indicating that suppression of take-all is related directly to the presence of the antibiotic in the rhizosphere.
Choline may be an essential nutrient in malnourished patients with cirrhosis

Elemental diets designed for nutritional support in protein-calorie malnutrition are often deficient in choline, a nonessential nutrient. Previously, malnourished patients on these diets were found to be at risk of developing plasma choline deficiency. We have now estimated the prevalence of this deficiency by determining fasting plasma levels of choline among cirrhotic and noncirrhotic malnourished male subjects maintained on regular hospital mixed food or elemental parenteral and enteral formulas. Plasma choline concentrations (microM, average +/- SD) were as follows: (i) mixed foods, 11.3 +/- 4.3 for cirrhotic (n = 22) and 9.3 +/- 2.4 for noncirrhotic (n = 12) patients; (ii) parenteral formula, 5.3 +/- 1.6 for cirrhotic (n = 5) and 8.6 +/- 5.2 for noncirrhotic (n = 16) subjects; and (iii) enteral formula, 6.1 +/- 1.2 for cirrhotic (n = 5) and 11.7 +/- 1.9 for noncirrhotic (n = 4) subjects. The level for healthy normal subjects eating mixed foods was 12.0 +/- 2.2. The prevalence of plasma choline deficiency, i.e., plasma levels greater than or equal to 2 SD below the normal average, was as follows: parenteral formula, all cirrhotic and 10 of 16 noncirrhotic subjects; enteral formula, all cirrhotic and none of the noncirrhotic subjects. The reversibility of choline deficiency was examined in a longitudinal study of three phases involving 10 patients--5 with alcoholic cirrhosis (all on enteral formula); 5 noncirrhotic (1 on enteral and 4 on parenteral formula). During phase 1 (3-day equilibration period; ad libitum regular hospital diet), plasma choline levels were within the normal range for all subjects. During phase 2 (2 wk, choline depletion phase, elemental formulas), choline levels were subnormal in all cirrhotic subjects (5.1 +/- 2.0 microM) on enteral formula and all noncirrhotic patients on parenteral formula (5.9 +/- 1.3 microM). During phase 3 (2 wk, choline repletion phase, elemental formula + 6 g choline/day), the levels normalized in all patients (cirrhotic 11.4 +/- 3.1 microM and noncirrhotic 11.9 +/- 3.2 microM). Analyses of abdominal computed tomographic scans and plasma liver chemistries in the cirrhotic subjects during the three phases suggested a correlation between plasma choline deficiency and hepatic steatosis and abnormal liver enzyme levels in some patients. Therefore, choline may be an essential nutrient in malnourished cirrhotic patients and its deficiency may be associated with adverse hepatic effects.
Some insights into the stability of difference approximations for hyperbolic initial-boundary-value problems

This paper states a conjecture which relates Lax-Richmyer stability to the algebraic test of the stability theory of Gustafsson, Kreiss, and Sundstrom (1972), developed for difference approximations to initial boundary value problems where the matrix size J increases linearly with n as n goes to infinity. This corresponds to mesh refinement in both space and time for t = n x delta t = constant.
BEARING CAPACITY DETERMINATION BY LIMIT ANALYSIS

THE BEHAVIOR OF SPHERICAL SHELLS USED FOR THE FOUNDATION OF A WATER TOWER WAS INVESTIGATED. A CONCRETE MODEL WAS DESIGNED ON THE BASIS OF MEMBRANE ANALYSIS SUBJECTED TO UNIFORMLY DISTRIBUTED LOADING. THE SHELL FOUNDATION CONSISTED OF TWO SPHERICAL SHELLS; ONE WITH THE CAVITY FACING UPWARDS AND THE OTHER WITH THE CAVITY FACING DOWNWARDS. THESE TWO SHELLS WERE MONOLITHICALLY CONNECTED TO A RING BEAM. THE POSITION OF THE RING BEAM IS SUCH THAT THE HORIZONTAL COMPONENT OF THE DIRECT MERIDIONAL FORCE DEVELOPED BY THE TWO SHELLS AT THE RING BEAM BALANCE EACH OTHER. MEMBRANE ANALYSIS IS CONSIDERED AND EQUATIONS ARE PRESENTED. MAJOR STEPS IN THE DESIGN OF A FOOTING ARE OUTLINED. THE OVERALL DIMENSIONS OF THE PLAN AREA IS DETERMINED BY DIVIDING THE TOTAL LOAD BY THE SAFE BEARING CAPACITY. FACTORS INFLUENCING THE PRESENT INVESTIGATION ARE OUTLINED. DETAILS ARE GIVEN OF THE MODEL DESIGN. THE FOUNDATION BASE IS DESCRIBED IN DETAIL. A 200-TON HYDRAULIC JACK WAS USED FOR TESTING PURPOSES, AND THE APPLIED LOAD WAS INDICATED BY MEANS OF A PRESSURE GAGE. A LOADING DEVICE APPLIED FOUR POINT LOADS AT THE COLUMN POSITIONS ON THE RING BEAM. OBSERVATIONS MADE ARE RECORDED AND CONCLUSIONS DRAWN ON THE BASIS OF THE STUDY ARE PRESENTED.
Dynamic Models for Robust Optimization

This article discusses recent developments in robust optimization, with a focus on dynamic models. Traditional techniques such as stochastic programming and dynamic programming face dimensionality issues as the size of the problem increases; furthermore, probability distributions are often difficult to accurately estimate. After robust optimization emerged as a tractable modeling framework in static optimization, researchers investigated its applicability to dynamic decision making under uncertainty. We provide an overview and discussion of their findings. Keywords: recourse problem; closed-loop optimization; robust optimization; dynamic programming; stochastic programming