cssi/SciSciGPT-SciSciNet huggingface dataset:
Dying on Dialysis: The Case for a Dignified Withdrawal

Acceleration of comorbid illness in patients undergoing long-term maintenance hemodialysis may be manifested by clinical deterioration that is subtle and not immediately life-threatening. Nonetheless, it is emotionally debilitating for patients and families in addition to being medically and ethically challenging for treating nephrologists. A marked decline in clinical status warrants review of the balance of benefits to burdens dialysis is providing to a given patient and should trigger conversation about the option of withdrawal using an individualized patient-centered, rather than disease-oriented, approach. This paper presents a rationale for and an objective approach to initiating and managing dialysis withdrawal for patients who wish to withdraw because of unsatisfactory quality of life and those (many with significant cognitive impairment) for whom withdrawal is deemed appropriate because the burdens of continuing treatment substantially outweigh the benefits.
Does use of the calendar in surveys reduce heaping

This study examines heaping of reported durations of three postpartum variables in five countries based on two methods of data collection in retrospective surveys. Two Demographic and Health Surveys were conducted for each of the countries, one that used a five-year month-by-month calendar to record the durations and a subsequent survey in which duration information was collected from simple questions in the body of the questionnaire. Heaping indexes were calculated for breastfeeding, amenorrhea, and abstinence at six, 12, 18, and 24 months postpartum. Use of the calendar was associated with a significant reduction in the proportion of heaped responses for both breastfeeding and amenorrhea, and the effect increased for longer durations. To obtain more accurate information about these variables, the authors recommend the use of the calendar.
Investment Behavior and the Negative Side of Emotion

Can dysfunction in neural systems subserving emotion lead, under certain circumstances, to more advantageous decisions? To answer this question, we investigated how normal participants, patients with stable focal lesions in brain regions related to emotion (target patients), and patients with stable focal lesions in brain regions unrelated to emotion (control patients) made 20 rounds of investment decisions. Target patients made more advantageous decisions and ultimately earned more money from their investments than the normal participants and control patients. When normal participants and control patients either won or lost money on an investment round, they adopted a conservative strategy and became more reluctant to invest on the subsequent round; these results suggest that they were more affected than target patients by the outcomes of decisions made in the previous rounds.
Radar Observations of Convective System Variability in Relationship to African Easterly Waves during the 2006 AMMA Special Observing Period

Abstract A radar-based analysis of the structure, motion, and rainfall variability of westward-propagating squall-line mesoscale convective systems (SLMCSs) in Niamey, Niger, during the African Monsoon Multidisciplinary Activities (AMMA) 2006 special observing period is combined with an analysis of 700-mb (hPa) winds and relative vorticity to study the relationship between SLMCSs and African easterly waves (AEWs). Radar results show that SLMCSs were the most important rainmakers in Niamey and accounted for about 90% of the rainfall despite being present less than 17% of the time. Analysis of the 700-mb synoptic-scale flow revealed that during the 2006 West African monsoon season the African easterly jet vacillated between about 10° and 15°N on time scales of 1–2 weeks. AEWs followed the jet as it vacillated north and south, thereby producing two preferred paths for AEWs propagating past Niamey’s longitude, a northern track along 8°–16°N and a southern track along 2°–6°N. It was found that Niamey SLMCSs oc...
Technical considerations in mandibular ridge reconstruction with collagen/hydroxylapatite implants.

A surgical technique for placement of a collagen-hydroxylapatite implant to augment severely atrophic mandibles is described.
44-GHz monolithic plane-wave amplifiers

A Plane Wave Amplifier is an array of small power amplifiers that accept input signals via input antennas and radiate amplified output signals from an output antenna. Such array amplifiers promise a method of efficient power at EHF. This concept has been experimentally explored in the 40-50 GHz band and gain over acceptable bandwidths has been measured. >
Family-focused interventions.

The importance of recognizing and including families in caring for critically ill patients has been well documented in the literature. During the past two decades critical care units have moved away from limiting family encounters to encouraging family visits and interactions. This change has been due in part to family needs research indicating consistently that families need to be close to their critically ill family members; however, being in close proximity to their family members does not automatically reduce their feelings of helplessness and high levels of stress and anxiety. Benefits of caring for the family as well as the critically ill family member include decreasing concerns of the ill family member if they know their family is receiving care, allowing the family to be more supportive of the ill member, less disruption likely for the family system, and less anxiety communicated to the ill family member by the family [1]. A wide variety of interventions have been suggested to reduce stress experienced by patients and family members [2–5]. Sleep disturbances and the inability to relax are often symptoms related to stress. The use of complementary and alternative therapies (CAT) has been shown to promote sleep and relaxation and reduce levels of stress. This article examines the role of families in providing CAT to their critically ill family members as well as being possible recipients of CAT.
Defining the Utility of Clinically Acceptable Variations in Evidence-based Practice Guidelines for Evaluation of Quality Improvement Activities

This study examines the utility of systematically accounting for acceptable physician variations in guideline application. The results argue against assuming that even seemingly noncontentious guideline protocol offer a threshold of variation similar to conventional Continuous Quality Improvement (CQI) assessment standards. Findings also suggest that health service organizations can derive greater benefits from expending the resources necessary to standardize guidelines if compliance with both the medical review criteria, and the guidelines as originally constructed, is monitored as part of the evaluation activity.
The Cyclin-dependent Kinase Inhibitor Dacapo Promotes Genomic Stability during Premeiotic S Phase

The proper execution of premeiotic S phase is essential to both the maintenance of genomic integrity and accurate chromosome segregation during the meiotic divisions. However, the regulation of pre...
Guidance and control of saturn launch vehicles.

Navigation, guidance and control modes and problems of Saturn launch vehicles used for Apollo missions
Fuzzy composite programming to combine remote sensing and crop models for decision support in precision crop management

Abstract Precision crop management is by definition a multi-objective decision-making process that must incorporate a diversity of data, opinion, preference and objective. This paper details an approach to decision making that allows users to express individual or corporate values and preferences; highlights the degree of imprecision associated with each input; highlights the degree of imprecision associated with each alternative; facilitates structuring of the decision process; reduces several levels of complex information into a single chart; allows examination of trade-off between alternatives and interests; and forces examination of inter-relationships between interest. The addition of using remote sensing data provides an efficient method to describe spatial variability in terms that can be related to a crop model, making the decision-making approach feasible for precision farming applications. The crop model provides information that can be used by the decision model, and the remote sensing data is used to fine tune the calibration of the crop model, maximizing the accuracy of its results.
Nitrification in the Upper Mississippi River: patterns, controls, and contribution to the NO3− budget

We measured nitrification rates in sediment samples collected from a variety of aquatic habitats in Navigation Pool 8 of the Upper Mississippi River (UMR) 7 times between May 2000 and October 2001. We also conducted nutrient-enrichment experiments and analyzed vertical profiles of sediment to determine factors regulating nitrification. Nitrification rates were relatively high com- pared to other ecosystems (ranging from 0-8.25 m gNc m 22 h21) and exhibited significant temporal and spatial patterns. Nitrification rates were greatest during the summer and spring compared to autumn and winter (ANOVA, p , 0.05) and were greater in contiguous backwater and impounded habitats compared to main and side-channel habitats (p , 0.05). Regression analysis indicated that nitrification rates were weakly (r2 5 0.18, p , 0.0001) related to temperature and exchangeable NH4 1 of the sediment. However, nutrient-enrichment experiments showed that NH4 1 availability did not limit nitrification in 3 sediment types with variable organic matter. Vertical profiles of sediment cores demonstrated that oxygen concentration and nitrification had similar patterns suggesting that nitri- fication may be limited by oxygen penetration into sediments. We conclude that temperature and sediment NH4 1 can be useful for predicting broad-scale temporal and spatial nitrification patterns, respectively, but oxygen penetration into the sediments likely regulates nitrification rates in much of the UMR. Overall, we estimated that nitrification produces 6982 mt N/y of NO3 2 or 7% of the total annual NO3 2 budget.
Salvage of exposed arteriovenous hemodialysis fistulas.

Abstract Arteriovenous fistulas constructed with an interposed segment of expanded polytetrafluoroethylene (PTFE) have been used successfully for long-term hemodialysis, but ultimately these fistulas may fail because of graft thrombosis, infection, or pseudoaneurysm. A PTFE graft may become exposed from skin necrosis at an area of repeated puncture for hemodialysis or from wound breakdown at a site of thrombectomy. Removal of an exposed PTFE graft has heretofore been considered inevitable, especially if a suture line is involved, because of the risk of hemorrhage and infection. We describe coverage of an exposed graft by a simple full-thickness skin flap that is locally rotated and report the successful salvage of five fistulas by this technique. Thus the concept that an exposed graft is infected and must be removed may not always be correct. (J VASC SURG 1985;2:610-2.)
The impact of combined radiation and chemotherapy on outcome in uterine papillary serous carcinoma compared to chemotherapy alone

Objective To investigate the impact of pelvic radiation on survival in patients with uterine serous carcinoma (USC) who received adjuvant chemotherapy.
Sorption of amiodarone to polyvinyl chloride infusion bags and administration sets.

The loss of amiodarone from i.v. admixtures to flexible polyvinyl chloride (PVC) infusion bags and i.v. administration sets was studied. Admixtures containing amiodarone hydrochloride 600 micrograms/mL and either 5% dextrose injection or 0.9% sodium chloride injection were stored at room temperature in glass bottles (both with and without contact of the drug solution with the rubber bottle closure), in flexible PVC bags, or in rigid PVC bottles. After 120 hours, the contents of each flexible PVC bag were emptied and replaced by methanol, which was allowed to remain in the bag for an additional 120 hours and was then analyzed for amiodarone content. To determine availability of amiodarone after infusion through a 1.8-m PVC i.v. administration set, solutions stored in glass containers were run through the set at 0.5 mL/min for 90 minutes. Samples of drug solutions were collected at appropriate intervals and analyzed by a stability-indicating high-performance liquid chromatography (HPLC) assay. Admixtures containing 0.9% sodium chloride injection were not stable; visual incompatibility was evident after 24 hours of storage in glass bottles, and no further testing was performed. In admixtures containing 5% dextrose injection that were stored in 50-mL flexible PVC bags, 60% of the initial amiodarone concentration remained after 120 hours; approximately half of the lost drug was recovered with the methanol. In effluent collected from the PVC administration set, 82% of the initial amiodarone concentration remained. Amiodarone concentrations did not decrease appreciably, after storage in glass or rigid PVC bottles, indicating that drug loss was probably affected by the plasticizer, di-2-ethylhexyl phthalate.(ABSTRACT TRUNCATED AT 250 WORDS)
Mentoring Beyond Homophobia: Reauthoring for Cultural Competence

Using the narrative paradigm for teaching about cultural competence in the context of prejudice, this paper presents a conceptual framework for helping students reach beyond homophobia and heterosexist bias to integrate the ethics of the profession into their practices with lesbian, gay, bisexual, and transgender populations. Drawing from the theoretical writings of Michael White’s narrative approach to therapeutic practice, the model organizes around the constructs of mentorship, story deconstruction, and “reauthoring.” Designed to reach out to undergraduate students through examining prejudice (homophobia) and the concept of privilege as a derivative of power (heterosexism), this pedagogical approach uses the structures of dialogue in the form of a reauthoring journal and parallel self-examination as the tools for mentorship.
Neuromorphic controllers

The feasibility of utilizing neural networks for the design of learning controllers is investigated. The design of both regulators and trackers for such controllers is considered. The relationship of these learning controllers to conventional adaptive controllers is investigated. This enables a learning methodology that guarantees the stability of the training process under mild conditions to be developed for these networks, with minimal information about the plant dynamics required. >
Best Intentions, Worst Results: Grounding Ethics Students in the Realities of Organizational Context

tions cannot be justified purely on economic grounds. Marilyn immediately turned her insights into action. She wrote a letter to the governor, complaining about conflicts of interest among some industrial commission members he had appointed. She joined campus protests against one of her university's suppliers of athletic gear on the grounds that they had violated worker rights. Marilyn's civic activism strengthened her ethical voice, and all was going well until she began expressing that voice in her workplace. She held a part-time job at a hi-tech company planning trade shows, and when she started criticizing some company policies on ethics grounds, her boss defended them and rejected her complaints. Finally, when Marilyn thought that sales personnel were systematically lying to customers about delivery schedules, she reported the matter up the chain of command as an ethics problem. A subsequent investigation turned up insufficient evidence, and Marilyn's hours were cut back, forcing her to look for another part-time job. Marilyn had a disconf irming experience that is in one sense similar to those faced by any novice attempting to apply academic ideas in a realworld setting. Yet, there are two things that make applying ethics different from applying other business concepts. First, ethics is potentially central to the development of the self (Baumeister & Exline, 1999). In ancient times, ethics and character were inseparable. The Greeks conceived of ethical behavior as an expression of personal virtue rather than the application of principles. While this viewpoint is rarely at the center of ethics teaching today (for how that might be done, see Hartman, 2006, in this journal), it reminds us that moral development parallels the development of the self. And, while not all people define their sense of self in moral terms (Aquino & Reed, 2002), ethics is a subject that touches more raw nerves, stirs more emotions, and surfaces more strongly held opinions than any other in the business curriculum. Marilyn's business ethics course did not merely expose her to knowledge; it gave her a means of actuating her nascent moral self. So, when she took that knowledge into the workplace and experienced failure, it was a much more serious blow than if she had discovered that an action
Metabolic Pathway Determination and Flux Analysis in Nonmodel Microorganisms Through 13 C-Isotope Labeling

C-isotope labeling is a commonly used technique for determining and quantifying pathways in microorganisms under various growth conditions. The experimental protocol consists of feeding the cell with a composition-defined substrate and measuring isotopic labeling patterns in the synthesized metabolites (often the amino acids). Not only can the labeling information be cross-referenced with genomic information to identify the novel pathways, but it can also be used to decipher absolute carbon fluxes through the metabolic network of interest. This technique can be widely used for functional characterization of nonmodel microbial species, and thus we provide a (13)C-pathway and flux analysis protocol. The five key procedures are: (1) growing cells using labeled substrates, (2) measuring extracellular metabolite and biomass component, (3) analyzing isotopic labeling patterns in amino acids and central metabolites using gas chromatography-mass spectrometry, (4) tracing (13)C carbon transitions in metabolites and discovering new pathways, and (5) estimating flux distributions based on isotopomer constraints. This protocol provides complementary information to the recently published protocol for (13)C-based metabolic flux analysis of the model species Escherichia coli (Nat Protoc 4:878-892, 2009).
The etiology of nasopharyngeal cancer and its management.

In dealing with the nasopharyngeal cancer problem, we find a fascinating pathologic entity, which acts in a varied fashion depending on the ethnic origin of the patient with a possible genetic basis for its etiology. More recently we have become aware of the possible etiology, i.e., the role of the Epstein-Barr virus in cancer of the nasopharynx. The earlier the diagnosis is made, in view of the present radiotherapeutic advances, the greater the possibility of increasing the cure rate in this disease.
Changes in the Accuracy of Newcomers’ Perceptions of Supermarket Locations

The purpose of this study was to determine the accuracy of newcomers' perceptions of the location of retail outlets during the critical early period when store patronage patterns of long duration are being established. A related purpose was to assess the rate at which newcomers acquired cognitive maps of retail outlets. We expected that within two months, the accuracy of newcomers' cognitive maps would approach the accuracy of cognitive maps of long term residents in the same area.
Switch-like Transitions Insulate Network Motifs to Modularize Biological Networks

Cellular decisions are made by complex networks that are difficult to analyze. Although it is common to analyze smaller sub-networks known as network motifs, it is unclear whether this is valid, because these motifs are embedded in complex larger networks. Here, we address the general question of modularity by examining the S. cerevisiae pheromone response. We demonstrate that the feedforward motif controlling the cell-cycle inhibitor Far1 is insulated from cell-cycle dynamics by the positive feedback switch that drives reentry to the cell cycle. Before cells switch on positive feedback, the feedforward motif model predicts the behavior of the larger network. Conversely, after the switch, the feedforward motif is dismantled and has no discernable effect on the cell cycle. When insulation is broken, the feedforward motif no longer predicts network behavior. This work illustrates how, despite the interconnectivity of networks, the activity of motifs can be insulated by switches that generate well-defined cellular states.
The Radiation Entropy in Laser Cooling Process

The laser cooling of atoms has made great progress beyond the Doppler limit I and even beyond the recoil limit by using the polarization gradients (the atomic sisyphus effect)2 and velocity-selective coherent population trapping (VSCPT)3.
Food Yields and Nutrient Analyses of the Three Sisters: A Haudenosaunee Cropping System

Scholars have studied The Three Sisters, a traditional cropping system of the Haudenosaunee (Iroquois), from multiple perspectives. However, there is no research examining food yields, defined as the quantities of energy and protein produced per unit land area, from the cropping system within Iroquoia. This article compares food yields and other nutrient contributions from the Three Sisters, comprised of interplanted maize, bean and pumpkin, with monocultures of these same crops. The Three Sisters yields more energy (12.25 x 106 kcal/ha) and more protein (349 kg/ha) than any of the crop monocultures or mixtures of monocultures planted to the same area. The Three Sisters supplies 13.42 people/ha/yr. with energy and 15.86 people/ha/yr. with protein. Nutrient contents of the crops are further enhanced by nixtamalization, a traditional processing technique where maize is cooked in a high alkaline solution. This process increases calcium, protein quality, and niacin in maize.
The transient behavior of the Volt/Var control of photovoltaic systems for solar irradiation variations

Nowadays, photovoltaic (PV) systems supply reactive power in limited or planned situations with mutual agreements so that they can minimize an increase in over- and under-voltages. However, since PV systems depend on weather conditions, including solar irradiation, they have, in nature, intermittency in their output. Therefore, the objective of this study is to analyze the effect of ramp events of solar irradiation on the generation output of PV systems in the transient state. For this purpose, this study (a) models a distribution system that includes a PV system (e.g., a PV array, a DC bus and capacitor model, a controller, and a static generator) in DIgSILENT of Power Factory, (b) generates a ramp event of solar irradiation as input data to the PV system, and (c) examines the transient behavior of the PV system at the electromagnetic transient mode of DIgSILENT. Finally, the effect of reactive power control for the ramp event on over- and under-voltages will be addressed.
Algorithmic bosses, robotic colleagues: toward human-centered algorithmic workplaces

We already know algorithms can make our lives and our work more efficient, but how can we go beyond that to create trustworthy, fair, and enjoyable workplaces in which workers can find meaning and continuously learn?
The Effector Domain Region of the Vibrio vulnificus MARTX Toxin Confers Biphasic Epithelial Barrier Disruption and Is Essential for Systemic Spread from the Intestine.

Vibrio vulnificus causes highly lethal bacterial infections in which the Multifunctional Autoprocessing Repeats-in-Toxins (MARTX) toxin product of the rtxA1 gene is a key virulence factor. MARTX toxins are secreted proteins up to 5208 amino acids in size. Conserved MARTX N- and C-terminal repeat regions work in concert to form pores in eukaryotic cell membranes, through which the toxin’s central region of modular effector domains is translocated. Upon inositol hexakisphosphate-induced activation of the of the MARTX cysteine protease domain (CPD) in the eukaryotic cytosol, effector domains are released from the holotoxin by autoproteolytic activity. We previously reported that the native MARTX toxin effector domain repertoire is dispensable for epithelial cellular necrosis in vitro, but essential for cell rounding and apoptosis prior to necrotic cell death. Here we use an intragastric mouse model to demonstrate that the effector domain region is required for bacterial virulence during intragastric infection. The MARTX effector domain region is essential for bacterial dissemination from the intestine, but dissemination occurs in the absence of overt intestinal tissue pathology. We employ an in vitro model of V. vulnificus interaction with polarized colonic epithelial cells to show that the MARTX effector domain region induces rapid intestinal barrier dysfunction and increased paracellular permeability prior to onset of cell lysis. Together, these results negate the inherent assumption that observations of necrosis in vitro directly predict bacterial virulence, and indicate a paradigm shift in our conceptual understanding of MARTX toxin function during intestinal infection. Results implicate the MARTX effector domain region in mediating early bacterial dissemination from the intestine to distal organs–a key step in V. vulnificus foodborne pathogenesis–even before onset of overt intestinal pathology.
Neurobiology of obsessive compulsive disorder.

Two aspects of the neurobiology of obsessive compulsive disorder (OCD) are explored in this article. The results of several neuropharmacologic studies that implicate serotonin in the treatment and possibly in the pathophysiology of OCD are described. Neuroimaging studies that provide an early look at brain regions that might mediate specific aspects of the obsessive compulsive syndrome are discussed. These two neurobiologic approaches to OCD appear promising, but additional studies will be necessary to permit a full interpretation of early results.
Three Edaphic-Endemic Ceanothus (Rhamnaceae) New to Science

North America is home to approximately 55 species of Ceanothus (Rhamnaceae), more than 30 of them endemic to the biodiversity hotspot known as the California Floristic Province. Although several species of Ceanothus are widespread in North America, most of the species are micro-endemics, known from a small number of occurrences and generally associated with special ecological conditions. As botanical exploration of North America continues, it is expected that more such micro-endemics will be discovered. However, field work is not the only way in which additional Ceanothus diversity will come to light; the strongly variable morphology of Ceanothus means that specimens are difficult to identify, and many biological entities that probably deserve taxonomic recognition are already represented in herbaria but have not yet been recognized as new. We here describe three new taxa of Ceanothus, two initially noted among existing collections, and another discovered during botanical exploration in San Diego County. All three are edaphic micro-endemics found only in the southern California Floristic Province, California. These include 1) Ceanothus foliosus var. viejasensis D. O. Burge&Rebman, restricted to gabbro-derived soils on ViejasMountain in SanDiego County, 2) Ceanothus pendletonensis D. O. Burge, Rebman, &M. R. Mulligan, found on granodiorite-derived soils of the central Santa Margarita Mountains in San Diego County, and 3) Ceanothus thyrsiflorus var. obispoensis D. O. Burge, endemic to rhyolite-derived soils near Hollister Peak in San Luis Obispo County.
Monetary policy transparency in a forward-looking market: Evidence from the United States

Abstract Because unsatisfactory measures of the monetary policy transparency were used, the existing literature found mixed empirical results for the relationship between the monetary policy transparency and risk/volatility. This paper extends the literature by using a recently developed monetary transparency index [Kia’s (2011) index] which is dynamic and continuous. Furthermore, the existing literature ignores the fact that market participants can be forward looking and, therefore, not policy invariant. This study also finds that the agents in the market are not policy invariant and the more transparent the monetary policy is the less risky and volatile the money market will be.
Impact of a change in surveillance definition on performance assessment of a catheter-associated urinary tract infection prevention program at a tertiary care medical center.

Background In January 2015, the Centers for Disease Control and Prevention (CDC)/National Health Safety Network (NHSN) changed the definition of catheter-associated urinary tract infection (CAUTI). We evaluated the outcomes of a robust CAUTI prevention program when we performed surveillance using the old definition (before 2015) versus the new definition (after 2015). This is the first study to evaluate how the change in CDC/NHSN definitions affected the outcomes of a CAUTI reduction program. Methods Baseline was from January 2012 to September 2014; the intervention period was from October 2014 to February 2016. Staff nurses were trained to be liaisons of infection prevention (Link Nurses) with clearly defined CAUTI prevention goals and with ongoing monthly activities. CAUTI incidence per 1000 catheter days was compared between the baseline and intervention periods, using the 2 definitions. Results With the new definition, CAUTIs decreased by 33%, from 2.69 to 1.81 cases per 1000 catheter days (incidence rate ratio [IRR] = 0.67; 95% confidence interval [CI]: 0.48-0.93; P Conclusion We aggressively targeted CAUTI prevention, but a reduction was observed only with the new definition. Our findings stress the importance of having a reasonably accurate surveillance definition to monitor infection prevention initiatives.
Leveraging known genomic variants to improve detection of variants, especially close-by Indels.

Motivation The detection of genomic variants has great significance in genomics, bioinformatics, biomedical research and its applications. However, despite a lot of effort, Indels and structural variants are still under-characterized compared to SNPs. Current approaches based on next-generation sequencing data usually require large numbers of reads (high coverage) to be able to detect such types of variants accurately. However Indels, especially those close to each other, are still hard to detect accurately. Results We introduce a novel approach that leverages known variant information, e.g. provided by dbSNP, dbVar, ExAC or the 1000 Genomes Project, to improve sensitivity of detecting variants, especially close-by Indels. In our approach, the standard reference genome and the known variants are combined to build a meta-reference, which is expected to be probabilistically closer to the subject genomes than the standard reference. An alignment algorithm, which can take into account known variant information, is developed to accurately align reads to the meta-reference. This strategy resulted in accurate alignment and variant calling even with low coverage data. We showed that compared to popular methods such as GATK and SAMtools, our method significantly improves the sensitivity of detecting variants, especially Indels that are close to each other. In particular, our method was able to call these close-by Indels at a 15-20% higher sensitivity than other methods at low coverage, and still get 1-5% higher sensitivity at high coverage, at competitive precision. These results were validated using simulated data with variant profiles extracted from the 1000 Genomes Project data, and real data from the Illumina Platinum Genomes Project and ExAC database. Our finding suggests that by incorporating known variant information in an appropriate manner, sensitive variant calling is possible at a low cost. Availability and implementation Implementation can be found in our public code repository https://github.com/namsyvo/IVC. Supplementary information Supplementary data are available at Bioinformatics online.
Self-reported chemotherapy-related cognitive impairment compared with cognitive complaints following menopause.

Objective Cancer-related cognitive impairment (CRCI) is commonly reported following the administration of cancer treatment. Current longitudinal studies, primarily in women with breast cancer, suggest that up to 35% to 60% of patients exhibit persistent CRCI (pCRCI) following completion of chemotherapy. Complaints of subjective cognitive decline (SCD) are also commonly reported by women during and following the menopause transition in noncancer patients. Although the majority of evidence for cognitive difficulties in cancer patients and survivors is attributed to chemotherapy, there is growing evidence to suggest that menopausal status can also influence cognitive function in cancer patients. Methods Given that menopausal status may be contributing to pCRCI, we compared a group of primarily postmenopausal women with pCRCI to 2 groups of postmenopausal women: women who endorse menopause-associated SCD (maSCD+) and women who do not (maSCD-) to explore the similarities/differences between maSCD and pCRCI and the potential role of menopause in pCRCI. Results Persistent CRCI participants report more severe SCD symptoms than women after natural menopause, despite being on average 2.5-year postchemotherapy, supporting previous findings that CRCI can persist for months to years after completing treatment. Persistent CRCI participants not only endorsed greater SCD but also exhibited objective performance differences. In addition, pCRCI participants endorsed significantly greater menopausal symptoms compared with either maSCD group. Results were not related to menopausal status prior to chemotherapy or current endocrine therapy use. Conclusions These results suggest that while menopausal symptoms may contribute to SCD experienced by cancer patients after chemotherapy, they do not fully account for pCRCI.
Recombination and the Standard Model in Amorphous Hydrogenated Silicon (a-Si:H) : An Essay

Non-radiative photocarrier recombination in amorphous hydrogenated silicon (a-Si:H) is reviewed. Primary emphasis is given to undoped material in the room temperature regime and to the effects upon photocarrier processes of the D center observed in electron spin resonance. The measurements summarized include electron spin resonance, transient and steady-state photoconductivity, spin-dependent photoconductivity, and surface photo-voltage. Three principal issues are addressed: (i) Is the electron recombination process due to tunneling or to free-to-bound transitions? (ii) Is there an important electron trap, and is the D 0 such a trap? (iii) Is electron capture by the D 0 center and hole capture by the D 0 center and hole capture by the D− the dominant recombination channel?
Soil moisture patterns and hydraulic properties associated with alternative biomass cropping systems across a landscape gradient

Predicting the hydrologic consequences of biomass cropping systems requires an understanding of how different crops and management practices affect soil hydraulic properties across space and time. To inform such predictions, I investigated the impacts of five biomass cropping systems on the hydraulic properties of soils across a landscape gradient in wet, dry, and average rainfall years. I used data from 2010 – 2012 on monthly volumetric soil moisture content and data from 2009 – 2013 on changes in saturated hydraulic conductivity to measure significant differences in mean soil moisture content among five cropping systems across five landscape positions. My results suggest moisture content was most broadly controlled by the amount of rainfall within a year, but there were also significant differences with landscape positions, cropping systems, cropping system by landscape position, and soil clay content; biomass yield was not a significant predictor of soil moisture. I also found a significant change in saturated hydraulic conductivity among cropping systems from 2009 to 2013, and different saturated conductivity among cropping systems at different landscape positions in 2013. Differences in hydraulic conductivity among cropping systems were commonly found at floodplain and footslope positions; there were very few significant differences among cropping systems at the summit, shoulder, and backslope positions. Changes over time within cropping systems are attributed to conversion to either perennial cropping systems or to no-till soil management in annual systems. My results support the hypothesis that different biomass cropping systems will have different hydrological impacts depending on landscape position. This knowledge can be used to parameterize or improve physically-based hydrologic models of biomass production and understand the potential environmental impacts bioenergy crop production.
Hormonal Control of Reproductionin the Male

This chapter describes the physiology of male reproductive organs, biochemistry, and mechanisms of action and regulation of testosterone hormone in male. The testes serve the dual function of producing sperm and hormones. Sperms are formed and developed within the seminiferous tubules through the process, spermatogenesis. Testosterone is the principal testicular hormone produced by the interstitial Leydig cells that plays an important role in sperm production and development of secondary sexual characteristics. Testicular function is driven by the pituitary, through the secretion of two gonadotropic hormones: follicle-stimulating hormone (FSH) and luteinizing hormone (LH) and secretion of these hormones by the pituitary gland are driven by the central nervous system through its secretion of the gonadotropin-releasing hormone (GnRH). Without them, the testes lose spermatogenic and steroidogenic capacities and either atrophy or fail to mature. Differentiation of the testes from the ambipotential gonadal primordia depends upon the transient expression of a single gene on the Y chromosome and anomalies of sexual differentiation result from inactivating mutations in genes that are critical for normal sexual differentiation. Clearly, the onset of reproductive capacity is influenced by, and must be coordinated with, the metabolic factors and attainment of physical size. However, the genetic, developmental, and nutritional factors that are integrated to signal the readiness for reproductive development and function are still not clear.
CRT-200.12 Increased Procedural Success With Parallel Wire Technique and Crosser CTO Recanalization Device in Very Long Lower-Extremity Chronic Total Arterial Occlusions

Chronic total occlusions (CTOs) remain the Achilles’ heel of vascular interventions, present in up to 40% of patients with severe lower-extremity arterial vascular disease. Despite alternative access options, very long CTOs are particularly challenging. The Crosser CTO Recanalization Device (CRD
Inhibitors of cellular kinases with broad-spectrum antiviral activity for hemorrhagic fever viruses

Host cell kinases are important for the replication of a number of hemorrhagic fever viruses. We tested a panel of kinase inhibitors for their ability to block the replication of multiple hemorrhagic fever viruses. OSU-03012 inhibited the replication of Lassa, Ebola, Marburg and Nipah viruses, whereas BIBX 1382 dihydrochloride inhibited Lassa, Ebola and Marburg viruses. BIBX 1382 blocked both Lassa and Ebola virus glycoprotein-dependent cell entry. These compounds may be used as tools to understand conserved virus-host interactions, and implicate host cell kinases that may be targets for broad spectrum therapeutic intervention.
Molecular Mechanisms of Vascular Calcification in Chronic Kidney Disease: The Link between Bone and the Vasculature

Vascular calcification is highly prevalent in patients with chronic kidney disease (CKD) and increases mortality in those patients. Impaired calcium and phosphate homeostasis, increased oxidative stress, and loss of calcification inhibitors have been linked to vascular calcification in CKD. Additionally, impaired bone may perturb serum calcium/phosphate and their key regulator, parathyroid hormone, thus contributing to increased vascular calcification in CKD. Therapeutic approaches for CKD, such as phosphate binders and bisphosphonates, have been shown to ameliorate bone loss as well as vascular calcification. The precise mechanisms responsible for vascular calcification in CKD and the contribution of bone metabolism to vascular calcification have not been elucidated. This review discusses the role of systemic uremic factors and impaired bone metabolism in the pathogenesis of vascular calcification in CKD. The regulation of the key osteogenic transcription factor Runt-related transcription factor 2 (Runx2) and the emerging role of Runx2-dependent receptor activator of nuclear factor kappa-B ligand (RANKL) in vascular calcification of CKD are emphasized.
Protective measurement of open quantum systems

We study protective quantum measurements in the presence of an environment and decoherence. We consider the model of a protectively measured qubit that also interacts with a spin environment during the measurement. We investigate how the coupling to the environment affects the two characteristic properties of a protective measurement, namely, (i) the ability to leave the state of the system approximately unchanged and (ii) the transfer of information about expectation values to the apparatus pointer. We find that even when the interaction with the environment is weak enough not to lead to appreciable decoherence of the initial qubit state, it causes a significant broadening of the probability distribution for the position of the apparatus pointer at the conclusion of the measurement. This washing out of the pointer position crucially diminishes the accuracy with which the desired expectation values can be measured from a readout of the pointer. We additionally show that even when the coupling to the environment is chosen such that the state of the system is immune to decoherence, the environment may still detrimentally affect the pointer readout.
Ribonucleoprotein Immunoprecipitation (RIP) Analysis

RNAs and RNA-binding proteins (RBPs) can interact dynamically in ribonucleoprotein (RNP) complexes that play important roles in controlling gene expression programs. One of the powerful ways to investigate changes in the association of RNAs with an RBP of interest is by immunoprecipitation (IP) analysis of native RNPs. RIP (RNP immunoprecipitation) analysis enables the rapid identification of endogenous RNAs bound to an RBP and to monitor time-dependent changes in this association, as well as changes in response to different metabolic and stress conditions. The protocol is based on the use of an antibody, typically an anti-RBP antibody, to immunoprecipitate the RNP complex. The RNA within the immunoprecipitated complex can then be isolated and further studied using different approaches such as PCR, microarray, Northern blot, and sequencing analyses. Among other advantages, RIP analysis (i) measures RNP associations in many samples relatively quickly, (ii) can be adapted easily to different endogenous RBPs, and (iii) provides extensive information at low cost. Among its limitations, RIP analysis does not inform on the specific sites of interaction of an RBP with a given target RNAs, although recent adaptations of RIP have been developed to overcome this problem. Here we provide an optimized protocol for RIP analysis that can be used to study RNA-protein interactions relevant to many areas of biology.
Epithelial–Neuronal Communication in the Colon: Implications for Visceral Pain

Visceral hypersensitivity and pain result, at least in part, from increased excitability of primary afferents that innervate the colon. In addition to intrinsic changes in these neurons, emerging evidence indicates that changes in lining epithelial cells may also contribute to increased excitability. Here we review recent studies on how colon epithelial cells communicate directly with colon afferents. Specifically, anatomical studies revealed specialized synaptic connections between epithelial cells and nerve fibers and studies using optogenetic activation of the epithelium showed initiation of pain-like responses. We review the possible mechanisms of epithelial–neuronal communication and provide an overview of the possible neurotransmitters and receptors involved. Understanding the biology of this interface and how it changes in pathological conditions may provide new treatments for visceral pain conditions.
Molecular biomarkers in the neurological ICU: is there a role?

Purpose of review The aim of the article is to summarize recent advances in the field of molecular biomarkers in neurocritical care. Recent findings Advances in ultrasensitive immunoassay technology have made it possible to measure brain-derived proteins that are present at subfemtomolar concentrations in blood. These assays have made it possible to measure neurofilament light chain (NfL) in serum or plasma, and early studies indicate that NfL is a promising prognostic and pharmacodynamic biomarker across a broad range of neurologic disorders, including cardiac arrest and traumatic brain injury. However, as acquired brain injury is a complex and heterogeneous disorder, it is likely that assays of panels of biomarkers will ultimately be needed to maximally impact practice. Micro-RNAs are a novel but exciting class of molecules that also show potential to provide clinically actionable information. Summary Although not yet ready for adoption into routine clinical practice, several molecular biomarkers are on the cusp of clinical validation. The availability of such tests likely will revolutionize the practice of neurocritical care.
Venous Thoracic Outlet Syndrome in a Young Student

Abstract Background Venous thoracic outlet syndrome (VTOS) results from compression and thrombosis of the axillosubclavian vein. In primary effort thrombosis, a subtype of VTOS, chronic repetitive compression injury of the axillosubclavian vein leads to scarring, stenosis, and eventually, thrombosis. This is a rare manifestation of an upper extremity deep vein thrombosis. Case Report A 23-year-old male student without significant past medical history presented to our Emergency Department with a complaint of intermittent swelling and discoloration of his upper right arm. His symptoms had been present for the past year and had worsened over the past few weeks. Swelling was associated with overhead use of the arm. There is no family history of clotting disorders. A computed tomography angiogram of the chest with upper extremity runoff showed findings consistent with VTOS. The patient was discharged with an urgent referral to Vascular Surgery. Within 2 weeks, he underwent multiple surgical procedures and was initiated on anticoagulation. Why Should an Emergency Physician Be Aware of This? VTOS usually presents in patients who do not have commonly recognized prothrombotic risk factors. Emergency physicians should include this diagnosis in their differential because good functional outcomes rely on early diagnosis and prompt initiation of treatment. In addition, emergency physicians must refer these patients to vascular surgeons, as most will require surgical management.