bluuebunny/crossref_metadata_2025 huggingface dataset:
Is assignment‐deadline flexibility an appropriate accommodation?
Authors: Masinter Michael R.
Published: January 2019

A growing number of students have sought accommodation letters authorizing extended time for completion of future curricular assignments, or as it is sometimes known, assignment‐deadline flexibility, as an accommodation. These students do not seek after‐the‐fact extensions for last‐minute health crises, but instead seek advance accommodations available for use at their discretion.
Build deep relationships while also balancing student, family needs
Authors: Sutton Halley
Published: January 2019

Lisa Toft, M.Ed., C.A.G.S., is the director of the Disability Services and Programs department at the University of Southern California. She shared best practices for keeping students with disabilities front and center on your campus, and dealing with helicopter parents.
Top‐down pressure on a coastal ecosystem by harbor seals
Authors: Aarts Geert , Brasseur Sophie , Poos Jan Jaap , Schop Jessica , Kirkwood Roger , van Kooten Tobias , Mul Evert , Reijnders Peter , Rijnsdorp Adriaan D. , Tulp Ingrid
Published: January 2019

Historic hunting has led to severe reductions of many marine mammal species across the globe. After hunting ceased, some populations have recovered to pre‐exploitation levels and may have regained their prominent position as top predator in marine ecosystems. Also, the harbor seal population in the international Wadden Sea grew at an exponential rate following a ban on seal hunting in 1960s, and the current number ~38,000 is close to the historic population size. Here we estimate the impact of the harbor seal predation on the fish community in the Wadden Sea and nearby coastal waters. Fish remains in fecal samples and published estimates on the seal's daily energy requirement were used to estimate prey selection and the magnitude of seal consumption. Estimates on prey abundance were derived from demersal fish surveys, and fish growth was estimated using a Dynamic Energy Budget model. GPS tracking provided information on where seals most likely caught their prey. Harbor seals hauling‐out in the Dutch Wadden Sea fed predominantly on demersal fish, for example, flatfish species (flounder, sole, plaice, dab), but also on sandeel, cod, and whiting. Although harbor seals acquire the majority of prey further offshore in the adjacent North Sea, and only spend 14% of their diving time in the Wadden Sea, seal predation was still estimated to cause an average annual mortality of 43% of the remaining fish in the Wadden Sea and 60% in the nearby shallow coastal waters (<20 m). There were however large sources of uncertainty in the estimated impact of seals on fish, including the migration of fish between the North Sea and Wadden Sea, and catchability estimates of the fish survey sampling gear, particularly for sandeel and other pelagic fish species. Our estimate suggested a considerable top‐down pressure by harbor seals on demersal fish. However, predation by seals may also alleviate density‐dependent competition between the remaining fish, allowing for increased fish growth, and partly compensating for the reduction in fish numbers. This study shows that recovering coastal marine mammal populations could become an important component in the functioning of shallow coastal ecosystems.
Differential deployment of sanctioning mechanisms by male and female host trees in a gynodioecious fig–wasp mutualism
Authors: Zhang Xiao‐Wei , Dunn Derek W. , Wen Xiao‐Lan , Sun Bao‐Fa , Wang Rui‐Wu
Published: January 2019

In some insect nursery pollination mutualisms, plant hosts impose net costs to uncooperative “cheater” symbionts. These “sanctions” promote mutualism stability but their precise adaptive nature remains unclear. In fig–wasp mutualisms host trees (Ficus spp.) are only pollinated by female agaonid wasps whose larvae only use galled fig flowers as food. In actively pollinated systems, if wasps fail to pollinate, sanctions can result via fig abortion, killing all wasp offspring, or by increased offspring mortality within un‐aborted figs. These sanctions result from selective investment to pollinated inflorescences, a mechanism present in almost all angiosperms. To more fully understand how selective investment functions as sanctions requires the measurement of variation in their costs and benefits to both hosts and symbionts. Gynodioecious fig‐tree–fig‐wasp mutualisms are particularly suitable for this because pollen and wasps are produced only in the figs of “male” trees and seeds only in the figs of “female” trees. Male and female trees thus incur different net costs of pollen absence, and costs of sanctions to pollen‐free “cheater” wasps only occur in male trees. We used the actively pollinated host tree Ficus hispida and introduced into male and female figs either 1, 3, 5, 7, or 9 all pollen‐laden “cooperative” (P+) or all pollen‐free “cheater” (P−) wasps. Abortion in both male and female trees was highest in P− figs, with P− fig abortion higher in females (~90%) than in males (~40%). Fig abortion was negatively associated with foundress number mainly in P+ figs; in P− figs abortion was only weakly associated with the number of “cheater” wasps, especially in female figs. In un‐aborted male figs, wasp offspring mortality was higher in P− figs than in P+ figs, and in P− figs correlated positively with foundress (cheater) number. Increased offspring mortality was biased against female wasp offspring and likely resulted from reduced larval nutrition in unpollinated flowers. Variation in selective investment to P− figs thus reflects costs and benefits of pollen absence/presence to hosts, variation that translates directly to net costs to cheater wasps.
Jumping translocations: Short telomeres or pathogenic TP53 variants as underlying mechanism in acute myeloid leukemia and myelodysplastic syndrome?
Authors: Behrens Yvonne Lisa , Thomay Kathrin , Hagedorn Maike , Ebersold Juliane , Schmidt Gunnar , Lentes Jana , Davenport Claudia , Schlegelberger Brigitte , Göhring Gudrun
Published: January 2019

Chromosomal rearrangements involving one donor chromosome and two or more recipient chromosomes are called jumping translocations. To date only few cases of acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS) with jumping translocations have been described and the underlying mechanisms remain unclear. Here, we analyzed 11 AML and 5 MDS cases with jumping translocations. The cases were analyzed by karyotyping, FISH, telomere length measurement, and next‐generation sequencing with an AML/MDS gene panel. Cases with jumping translocations showed significantly (P < .01) shorter telomeres in comparison to healthy age‐matched controls. Additional neo‐telomeres were found in two cases. In total, eight cases showed recipient chromosomes with a breakpoint in the centromeric region all of them harboring a pathogenic variant in the TP53 gene (n = 6) and/or a loss of TP53 (n = 5). By contrast, no pathogenic variant or loss of TP53 was identified in the six cases showing recipient chromosomes with a breakpoint in the telomeric region. In conclusion, our results divide the cohort of AML and MDS cases with jumping translocations into two groups: the first group with a telomeric breakpoint of the recipient chromosome is characterized by short telomeres and a possibly telomere‐based mechanism of chromosomal instability formation. The second group with a centromeric breakpoint of the recipient chromosome is defined by mutation and/or loss of TP53. We, therefore, assume that both critically short telomeres as well as pathogenic variants of TP53 influence jumping translocation formation.
Trends in the risk and burden of second primary malignancy among survivors of smoking‐related cancers in the United States
Authors: Adjei Boakye Eric , Buchanan Paula , Hinyard Leslie , Osazuwa‐Peters Nosayaba , Simpson Matthew C. , Schootman Mario , Piccirillo Jay F.
Published: January 2019

While there are a growing number of cancer survivors, this population is at increased risk of developing second primary malignancies (SPMs). We described the incidence, most common tumor sites, and trends in burden of SPM among survivors of the most commonly diagnosed smoking‐related cancers. The current study was a population‐based study of patients diagnosed with a primary malignancy from the top 10 smoking‐related cancer sites between 2000 and 2014 from Surveillance, Epidemiology, and End Results data. SPM risks were quantified using standardized incidence ratios (SIRs) and excess absolute risks (EARs) per 10,000 person‐years at risk (PYR). Trends in the burden of SPM were assessed using Joinpoint regression models. A cohort of 1,608,607 patients was identified, 119,980 (7.5%) of whom developed SPM (76% of the SPMs were smoking‐related). The overall SIR of developing second primary malignancies was 1.51 (95% CI, 1.50–1.52) and the EAR was 73.3 cases per 10,000 PYR compared to the general population. Survivors of head and neck cancer had the highest risk of developing a SPM (SIR = 2.06) and urinary bladder cancer had the highest excess burden (EAR = 151.4 per 10,000 PYR). The excess burden of SPM for all smoking‐related cancers decreased between 2000 and 2003 (annual percentage change [APC] = −13.7%; p = 0.007) but increased slightly between 2003 and 2014 (APC = 1.6%, p = 0.032). We show that 1‐in‐12 survivors of smoking‐related cancers developed an SPM. With the significant increase in the burden of SPM from smoking‐related cancers in the last decade, clinicians should be cognizant of long‐term smoking‐related cancer risks among these patients as part of their survivorship care plans.
Immunogenomic analysis reveals LGALS1 contributes to the immune heterogeneity and immunosuppression in glioma
Authors: Chen Qun , Han Bo , Meng Xiangqi , Duan Chunbin , Yang Changxiao , Wu Zhenyu , Magafurov Dinislam , Zhao Shihong , Safin Shamil , Jiang Chuanlu , Cai Jinquan
Published: January 2019

Mutualistic and dynamic communication between tumour cells and the surrounding microenvironment accelerates the initiation, progression, chemoresistance and immune evasion of glioblastoma (GBM). However, the immunosuppressive mechanisms of GBM has not been thoroughly elucidated to date. We enrolled six microenvironmental signatures to identify glioma microenvironmental genes. The functional enrichment analysis such as ssGSEA, ESTIMATE algorithm, Gene Ontology, Pathway analysis is conducted to discover the potential function of microenvironmental genes. In vivo and in vitro experiments are used to verify the immunologic function of LGALS1 in GBM. We screen eight glioma microenvironmental genes from glioma databases, and discover a key immunosuppressive gene (LGALS1 encoding Galectin‐1) exhibiting obviously prognostic significance among glioma microenvironmental genes. Gliomas with different LGALS1 expression have specific genomic variation spectrums. Immunosuppression is a predominate characteristic in GBMs with high expression of LGALS1. Knockdown of LGALS1 remodels the GBM immunosuppressive microenvironment by down regulating M2 macrophages and myeloid‐derived suppressor cells (MDSCs), and inhibiting immunosuppressive cytokines. Our results thus implied an important role of microenvironmental regulation in glioma malignancy and provided evidences of LGALS1 contributing to immunosuppressive environment in glioma and that targeting LGALS1 could remodel immunosuppressive microenvironment of glioma.
Characterization of the epithelial membrane protein 3 interaction network reveals a potential functional link to mitogenic signal transduction regulation
Authors: Christians Arne , Poisel Eric , Hartmann Christian , von Deimling Andreas , Pusch Stefan
Published: January 2019

Epithelial Membrane Protein 3 (EMP3), a 4‐transmembrane glycoprotein, first gained attention as a putative tumor suppressor. Accumulating evidence, however, points to a more tumor promotive function of EMP3. The biological function of EMP3 remains largely unclear. To elucidate more of EMP3’s interaction network, we performed a Yeast‐Two‐Hybrid (Y2H) screening, followed by validation of candidate interactors by Biomolecular Fluorescence Complementation (BiFC) and Proximity Ligation Assay (PLA). Furthermore, we generated stable EMP3 knockdown cell lines and measured cell proliferation, migration and sensitivity to apoptosis induction as well as the expression and activation levels of important signal pathway components. The Y2H screening yielded 10 novel interactions of EMP3, eight of which could also be detected by BiFC and PLA interaction assays. All newly discovered interaction partners are involved in signaling or trafficking regulation. Most notably, FLOT1 and HTATIP2 have well described roles in the regulation of EGFR signaling. In addition, knockdown of EMP3 resulted in reduced levels of p‐AKT, p‐ERK and p‐EGFR, attenuated cell proliferation and migration and sensitized cells to apoptosis induction by TRAIL and Staurosporine. Based on these observations we hypothesize that EMP3 might be involved in the regulation of receptor‐tyrosine‐kinase mediated mitogenic signaling.
Saudi women's identities on Facebook: Context collapse, judgement, and the imagined audience
Authors: Alsaggaf Rania M.
Published: January 2019

As social networking sites present opportunities to construct identities, they also present challenges. This article explores women's experiences with Facebook in the Saudi context by looking at how their self‐presentation strategies and audience management might constitute a unique use of Facebook. The study utilises a mix of qualitative methods of research and extends Goffman's dramaturgical approach to consider more complex settings wherein the self is monitored and regulated, contexts “collapse,” the self is judged, and judgement by others is imagined. The findings reveal that different aspects of women's identities are constructed, gendered, and tightly managed as they address multiple audiences, with networks being formed in a way that has relatively narrowly defined boundaries.
Subventricular zone neural precursor cell responses after traumatic brain injury and binge alcohol in male rats
Authors: Ton Son T. , Tsai Shih‐Yen , Vaagenes Ian C. , Glavin Kelly , Wu Joanna , Hsu Jonathan , Flink Hannah M. , Nockels Daniel , O’Brien Timothy E. , Kartje Gwendolyn L.
Published: January 2019

Traumatic brain injury (TBI) is a major cause of disability worldwide. Additionally, many TBI patients are intoxicated with alcohol at the time of injury, but the impact of acute intoxication on recovery from brain injury is not well understood. We have previously found that binge alcohol prior to TBI impairs spontaneous functional sensorimotor recovery. However, whether alcohol administration in this setting affects reactive neurogenesis after TBI is not known. This study, therefore, sought to determine the short‐ and long‐term effects of pre‐TBI binge alcohol on neural precursor cell responses in the subventricular zone (SVZ) following brain injury in male rats. We found that TBI alone significantly increased proliferation in the SVZ as early as 24 hr after injury. Surprisingly, binge alcohol alone also significantly increased proliferation in the SVZ after 24 hr. However, a combined binge alcohol and TBI regimen resulted in decreased TBI‐induced proliferation in the SVZ at 24 hr and 1 week post‐TBI. Furthermore, at 6 weeks after TBI, binge alcohol administered at the time of TBI significantly decreased the TBI‐induced neuroblast response in the SVZ and the rostral migratory stream (RMS). The results from this study suggest that pre‐TBI binge alcohol negatively impacts reparative processes in the brain by decreasing short‐term neural precursor cell proliferative responses as well as long‐term neuroblasts in the SVZ and RMS.
Suppression of Δlon phenotypes in Escherichia coli by N‐terminal DnaK peptides
Authors: Kumaran Nagarajan , Munavar M. Hussain
Published: January 2019

Δlon mutant of Escherichia coli becomes hypersensitive to DNA damaging agents and over‐produce capsule due to stabilization of the Lon substrates, namely, SulA and RcsA, respectively. These phenotypes were earlier found to be suppressed in Δlon ssrA::cat/pUC4 K and Δlon faa (DnaJ, G232D) strains, called as “Alp” strains. We observed that a plasmid carrying an E. coli chromosomal fragment harboring few genes, a heat shock gene htpY and a portion of dnaK capable of encoding truncated N‐terminal ATPase domain (244 aa) could suppress lon mutant phenotypes. Deletion of htpY did not affect the efficiency of suppression. Clones expressing DnaK′ (244 aa) peptide alone could suppress both Δlon phenotypes in copy number dependent manner. Inactivation of clpQ did not affect the MMSR phenotype of Δlon strain carrying dnaK′ clones indicating that ClpYQ protease does not degrade SulA. We hypothesize that the high levels of defective DnaK′‐DnaJ chaperone complex formed in these strains might lead to aggregation of SulA and RcsA and, thereby the suppression of Δlon phenotypes. Systematic deletion analysis of dnaK′ revealed that, ∼220 aa N‐terminal DnaK peptide is required for suppression of cps‐lac over‐expression and ∼169 aa peptide is enough for the suppression of MMSS phenotype of Δlon mutant.
Simultaneous influence of the Southern Hemisphere annular mode on the atmospheric circulation of the Northern Hemisphere during the boreal winter
Authors: Shi Ning , Tian Pingyu , Zhang Leying
Published: January 2019

This study has discovered a significant linear relationship between the Southern Hemisphere (SH) annular mode (SAM) and the mid‐latitude Northern Hemisphere (NH) circulation in February using two reanalysis data sets. Significant positive height anomalies corresponding to the positive SAM appear over the mid‐latitude region of the NH, and significant positive surface air temperature anomalies prevail over Western Europe and Northeast Asia. The realistic vorticity forcing associated with the SAM is applied in a dry linear baroclinic model, and the results demonstrate that the SAM in February can induce height anomalies with the same sign at 300 hPa over the mid‐latitudes of the NH and that these anomalies have amplitudes as large as 22% of their counterparts in the SH. Further numerical experiments show that the positive height response over the mid‐latitudes of the NH mainly comes from the influence of the realistic positive vorticity over the mid‐latitudes of the SH and that the vorticity forcing over the southern Indian Ocean seems to be the most effective at exciting the NH circulation anomalies. The numerical experiments also demonstrate that the transient eddy feedback forcing contributes to the formation of mid‐latitude NH circulation anomalies, especially over Northeast Asia. The maintenance of the negative vorticity anomalies over Europe is further diagnosed through vorticity budget analysis. In December, however, the significant vorticity anomalies associated with the SAM are not limited to the middle and high latitudes of the SH but also appear over the subtropics of the SH (approximately 30°S). The numerical experiments show that cancellation occurs between the responses to the subtropical vorticity forcing and the mid‐latitude vorticity forcing, thereby accounting for the independence of the NH circulation from the December SAM variability.
Regional scale analysis of trends in rainfall using nonparametric methods and wavelet transforms over a semi‐arid region in India
Authors: Pal Lalit , Ojha Chandra Shekhar P. , Chandniha Surendra K. , Kumar Amit
Published: January 2019

Space‐time variability of rainfall at local scale is affected by several regional factors such as aerosol concentration, greenhouse gases, land cover changes, etc., along with large scale atmospheric circulations. Predictive ability of regional circulation models can be significantly improved and efficient management of water resources can be assured by identifying dominant variables controlling spatiotemporal variations in rainfall among aforementioned factors. The present study aims to investigate dominant climate system(s) controlling trends in rainfall over Chhattisgarh state (a semi‐arid region) in India over the period of 115 years (1901–2015). Discrete wavelet transform in conjunction with Mann–Kendall test is applied to the rainfall data series at different time scales (monthly, seasonal, annual, pre‐monsoon, monsoon, post‐monsoon and winter) in order to identify the long term trends and dominant periodic components influencing the trend. In the results, negative trends are found to exist in all rainfall time series at majority of districts (except for annual and monsoon rainfall at Bijapur and Sukma district). In addition, analysis of trend in actual evapotranspiration and soil moisture in the region does not exhibits the effect of anthropogenic variables (such as land cover change, irrigation projects, etc.) on the rainfall as significant negative trend are also observed in soil moisture for majority of districts. Overall, 2‐year and 4‐year periodic components have been detected to be dominating the trends in most of the rainfall time series (annual, monsoon, post‐monsoon and winter). On comparing the identified dominating components with the existing climate systems (Atlantic multidecadal oscillations, Indian ocean dipole, Madden‐Julian oscillations, Inter‐Tropical Convergence Zone, etc.), El Niño‐Southern Oscillations has been recognized as predominant climate circulation influencing the rainfall trends over the study region. The study outcomes are expected to improve the regional precipitation forecasts and should be useful in various hydro‐meteorological analyses and decision making at regional scale.
Chronic opioid use in patients undergoing treatment for oropharyngeal cancer
Authors: Silver Natalie , Dourado Justin , Hitchcock Kathryn , Fullerton Amy , Fredenburg Kristianna , Dziegielewski Peter , Danan Deepa , Tighe Patrick , Morris Chris , Amdur Robert , Mendenhall William , Fillingim Roger B.
Published: January 2019

Objectives/Hypothesis

Head and neck cancer pain is a prevalent problem, and the current opioid crisis has highlighted concerns raised in chronic pain management. This study assessed the characteristics of opioid use in patients undergoing treatment for oropharynx cancer and identified risk factors associated with chronic opioid use.

Study Design

Retrospective cohort study.

Methods

A study was conducted of 198 eligible patients who underwent radiotherapy as part of their treatment for oropharynx cancer at a single institution from 2012 to 2017. p16/human papillomavirus (HPV) status was determined by pathology report review. Opioid use was recorded. Statistical analysis was performed to assess risk factors for chronic opioid use and effect on overall survival.

Results

The average age was 62 years, and the mean follow‐up was 38 months. Eighty‐three percent of patients had stage III/IV disease, and 73% received chemoradiotherapy. Sixty‐nine percent were HPV/p16 positive. Fifty‐seven (29%) patients had preexisting chronic pain conditions. Chronic opioid use was observed in 53% of the patients. Age ≤ 62 years (P < .0001), history of depression (P = .0356), p16 negative status (P = .0097), opioid use at pretreatment visit (P = .0021), and presence of a preexisting chronic pain condition at time of diagnosis (P = .0181) were associated with chronic opioid use using univariate analysis. On multivariate analysis, T stage and anxiety/depression were associated with chronic opioid use. Overall survival was worse for patients who had chronic opioid use, but was not significant when recurrence was taken into consideration.

Conclusions

More than 50% of the patients treated for oropharynx squamous cell carcinoma in this cohort were chronic opioid users after treatment. Identifying patients at greatest risk for chronic opioid use prior to treatment may help with long‐term pain management in this patient population.

Level of Evidence

4

Laryngoscope, 129:2087–2093, 2019
Patient‐reported outcomes use during orthopaedic surgery clinic visits improves the patient experience
Authors: Bernstein David N. , Fear Kathleen , Mesfin Addisu , Hammert Warren C. , Mitten David J. , Rubery Paul T. , Baumhauer Judith F.
Published: January 2019

Objectives

The Patient‐Reported Outcomes Measurement Information System (PROMIS) is growing in popularity as healthcare shifts towards a value‐based system. However, it remains unclear if PROMIS use improves the patient experience. The aim of the present study was to determine if PROMIS use as part of routine orthopaedic clinical care is associated with improved patient experience, as measured by the Clinician and Group Consumer Assessment of Healthcare Providers and Systems (CGCAHPS) survey.

Methods

All patient visits to an orthopaedic surgery clinic at a single academic medical centre between February 2015 and September 2016 were reviewed. Accounting for known patient factors that have an impact on clinic visit satisfaction, CGCAHPS scores were compared between patients who had PROMIS used as part of their routine care and those who had not had PROMIS used as part of their routine care. A p‐value of <0.05 was considered significant.

Results

A total of 8,607 patient visits fitted our inclusion criteria. Of these, surgeons elected not to use PROMIS in 8,422 patient encounters, leaving 185 patient visits in which PROMIS was actively used. When PROMIS was used, patients were significantly more likely to feel that the provider had spent enough time with them, to recommend this provider office to another patient and to rate the provider significantly higher on a scale from 0 to 10. Although not significant, a trend was found between use of PROMIS and whether a patient felt that a provider explained health information in way that the patient understood.

Conclusions

PROMIS use in an orthopaedic clinic visit can have a positive impact on the patient experience, which is currently part of a number of alternative payment models.
Visualization of particles arrangement during filling stage of polyamide 6 – metal insert injection molding
Authors: Bula Karol , Szymańska Justyna , Sterzyński Tomasz , Piasecki Adam , Wróblewski Roman
Published: January 2019

An isotactic polypropylene filled with talc and mica particles was used for visualization of molten polymer flow lines during filling of mold cavity with metal insert. The talc particles orientation in polypropylene matrix was followed by scanning electron microscopy. For the quantification of platelet particles orientation in molten polymer flow localized near metal wall, the Herman's function was applied. An existence of regions with well oriented, randomly organized talc particles depending on the shape and cross‐section of the channels, was found and reported. The domain with the most disorganized platelet particles was detected in the region where polymer streamed around the sharp corner of the metal insert. Such a kind of disarranged region could be the weakest part of the whole injection molded polymeric element. POLYM. ENG. SCI., 59:E271–E278, 2019. © 2019 Society of Plastics Engineers
Context Matters! Looking Beyond Platform Structure to Understand Citizen Deliberation on Brazil'sPortal e‐Democracia
Authors: Mitozo Isabele , Marques Francisco Paulo Jamil
Published: January 2019

This article analyzes the participatory design of the Portal e‐Democracia, sponsored by the Brazilian Chamber of Deputies. More specifically, it examines how citizens took part in the online discussions about the Brazilian laws on the Budget Guidelines, the 2013 Annual Budgeting, and the Political Reform debates of 2013 and 2015. We hypothesize that discussion forums with identical structures can nevertheless host debates with very diverse characteristics. The methodological approach considers a quantitative content analysis, using descriptive statistics and correspondence analysis to examine how the forums’ features were related to their structure, in terms of user identification, openness and freedom of speech, agenda, and moderation. We also examine the quality of public debate in these arenas by considering the interactions with regard behaviors of justification, reciprocity, and respect. We find that, even though the space for debating was structurally the same, every forum had some particular characteristics concerning the discussions. This leads us to consider the issue at stake and the sociopolitical context as variables that are more important for characterizing the debate than structure per se.
Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information
Authors: Khare Shruti , Bhasin Munmun , Sahoo Anusmita , Varadarajan Raghavan
Published: January 2019

Structure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r ~ 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.
Expressional activation and functional roles of human endogenous retroviruses in cancers
Authors: Zhang Mengwen , Liang Jessie Qiaoyi , Zheng Shu
Published: January 2019

Human endogenous retroviruses (HERVs) are widely believed to be remnants of ancestral germ line infections by exogenous retroviruses. Although HERVs are deemed as “nonfunctional DNAs” due to loss of most of their viral protein coding capacity during evolution as part of the human genome, cumulative evidences are showing the expressional activation and potential roles of HERVs in diseases especially cancers. Work by other researchers and us has observed the dysregulation of HERVs in cancers, identified new HERV‐related genes, and revealed their potential importance in cancer development. Here, we summarized the current knowledge on the mechanisms of the expressional activation and functional roles of HERVs, with a focus on the H family HERV (HERV‐H), in carcinogenesis. HERV expression is regulated by external chemical or physical substances and exogenous virus infection, as well as host factors such as epigenetic DNA methylation, transcription factors, cytokines, and small RNAs. Diverse roles of HERVs have been proposed by acting in the forms of noncoding RNAs, proteins, and transcriptional regulators during carcinogenesis. However, much remains to be learnt about the contributions of HERVs to human cancers. More investigation is warranted to elucidate the functions of these “fossil remnants” yet important viral DNAs in the human genome.
Ligand‐Exchange of Low‐Temperature Synthesized CsPbBr3 Perovskite toward High‐Efficiency Light‐Emitting Diodes
Authors: Ye Fanghao , Zhang Huijun , Li Wei , Yan Yu , Cai Jinlong , Gurney Robert S. , Pearson Andrew J. , Liu Dan , Wang Tao
Published: January 2019

CsPbX3 perovskite nanocrystals (NCs) are promising light‐emitting materials that have gained significant attention over the past few years. The synthesis of CsPbX3 NCs is usually performed in an inert environment under high temperature conditions; however, this requirement hinders commercial development. Low‐temperature preparation of CsPbX3 NCs with rationally designed surface ligands is crucial to the performance and stability of CsPbX3 light‐emitting diodes (LEDs). In this work, short‐chain ligand‐anchored CsPbBr3 NCs in ambient conditions at room temperature are synthesized and a ligand‐exchange strategy is employed, using longer‐chain acid/amine ligand pairs, resulting in the dramatic improvement of performance and stability of CsPbBr3 NCs LEDs. It is found that CsPbBr3 NCs anchored by oleic acid and oleylamine complex ligands result in the best LED performance, with the maximum luminance of 5033 Cd m−2, current efficiency of 18.6 Cd A−1, external quantum efficiency of 5.4%, turn‐on voltage of 3.2 V, and the best thermal stability under ambient conditions.
C/N Vacancy Co‐Enhanced Visible‐Light‐Driven Hydrogen Evolution of g‐C3N4 Nanosheets Through Controlled He+ Ion Irradiation
Authors: Wang Xuening , Wu Liang , Wang Zhaowu , Wu Hengyi , Zhou Xuemei , Ma Hongyu , Zhong Huizhou , Xing Zhuo , Cai Guangxu , Jiang Changzhong , Ren Feng
Published: January 2019

Graphitic carbon nitride (g‐C3N4) is reported to be a promising metal‐free semiconductor for photocatalytic water splitting. However, the performance of g‐C3N4 is substantially limited by its insufficient visible‐light absorption and low photogenerated charge carrier separation efficiency. In this work, an innovative method (ion irradiation) to efficiently introduce both defined C‐ and N‐vacancies (VC and VN) simultaneously into g‐C3N4 nanosheets are explored. Unlike traditional chemical methods, by controlling He+ ion fluence, tunable vacancy concentrations are able to be obtained in g‐C3N4. Defect‐engineered g‐C3N4 shows highly improved performance under optimized conditions, the defective g‐C3N4 exhibits a significantly higher (2.7‐fold) hydrogen evolution rate of 1271 µmol g−1 h−1 than that of the g‐C3N4 nanosheets under visible light (λ > 420 nm) illumination. Meanwhile, the defective g‐C3N4 exhibits a significantly enhanced (threefold) photocurrent density as photoanodes for photoelectrochemical (PEC) water splitting. Further characterizations show that the enhanced visible light absorption and an extended charge carrier lifetime, can be ascribed to the presence of C‐ and N‐ vacancies. These experimental results are in line with density functional theory (DFT) calculations. Therefore, the present work shows that defect‐engineering on g‐C3N4 using ion irradiation technique, is an effective, controllable, and defined approach to improve the photocatalytic and PEC water splitting performance of g‐C3N4.
Second‐order feedback and climatic effects determine the dynamics of a small rodent population in a temperate forest of South America
Authors: Murúa Roberto , González Luz A. , Lima Mauricio
Published: January 2019

The multiannual cyclic fluctuations exhibited by arvicoline rodents in the Northern Hemisphere have attracted the attention of population ecologists. However, despite the abundant information on small rodent dynamics in South America, there are no studies reporting cyclic population dynamics. Here, we report evidence of cyclic population dynamics in a South American small rodent, the longhaired field mouse (Abrothrix longipilis) from southern temperate forests in Chile. The time‐series analyses showed that longhaired field mice dynamics are better represented by a second‐order autoregressive model characterized by 3‐year cyclic dynamics. The 3‐year cycles are clearly shown in the autocorrelation factor (ACF) pattern and in the dominant frequency of the spectral analysis. In addition, we determined nonlinear effects of the Antarctic Oscillation Index (AAOI). The results shown here pointed out that we need the integration of studies about cyclic small rodent populations from the different continents and beyond the Northern Hemisphere to resolve the enigma underlying the cyclic population dynamics exhibited by many small rodent species.
On the geometry and regularity of invariant sets of piecewise-affine automorphisms on the Euclidean space
Authors: GÜNTÜRK C. SİNAN , THAO NGUYEN T.
Published: January 2019

In this paper, we derive geometric and analytic properties of invariant sets, including orbit closures, of a large class of piecewise-affine maps $T$ on $\mathbb{R}^{d}$. We assume that (i) $T$ consists of finitely many affine maps defined on a Borel measurable partition of $\mathbb{R}^{d}$, (ii) there is a lattice $\mathscr{L}\subset \mathbb{R}^{d}$ that contains all of the mutual differences of the translation vectors of these affine maps, and (iii) all of the affine maps have the same linear part that is an automorphism of $\mathscr{L}$. We prove that finite-volume invariant sets of such piecewise-affine maps always consist of translational tiles relative to this lattice, up to some multiplicity. When the partition is Jordan measurable, we show that closures of bounded orbits of $T$ are invariant and yield Jordan measurable tiles, again up to some multiplicity. In the latter case, we show that compact $T$-invariant sets also consist of Jordan measurable tiles. We then utilize these results to quantify the rate of convergence of ergodic averages for $T$ in the case of bounded single tiles.
Prandtl–Batchelor theorem for flows with quasiperiodic time dependence
Authors: Arbabi Hassan , Mezić Igor
Published: January 2019

The classical Prandtl–Batchelor theorem (Prandtl, Proc. Intl Mathematical Congress, Heidelberg, 1904, pp. 484–491; Batchelor, J. Fluid Mech., vol. 1 (02), 1956, pp. 177–190) states that in the regions of steady 2D flow where viscous forces are small and streamlines are closed, the vorticity is constant. In this paper, we extend this theorem to recirculating flows with quasiperiodic time dependence using ergodic and geometric analysis of Lagrangian dynamics. In particular, we show that 2D quasiperiodic viscous flows, in the limit of zero viscosity, cannot converge to recirculating inviscid flows with non-uniform vorticity distribution. A corollary of this result is that if the vorticity contours form a family of closed curves in a quasiperiodic viscous flow, then at the limit of zero viscosity, vorticity is constant in the area enclosed by those curves at all times.
Writing against Mourning: Memory in Assia Djebar’s Franco-graphie
Authors: El Guabli Brahim
Published: January 2019

In this article, I provide a new reading of Djebar’s Le Blanc de l’Algérie as being antimourning. I argue that in the face of institutionalized amnesia and excessive commemoration, Djebar’s refusal to mourn her dead friends institutes a politics of antimourning that seeks to reckon with the larger memory and history of silenced political murders in Algeria. Rejection of mourning enables remembering and empowers feminist engagements with the past. Rather than being another al-Khansā’—the Arab dirge poet who composed elegies for her slain brother, Ṣakhr—Djebar sees herself in Polybe’s footsteps. In offering this new argument, I aim to steer scholarly conversations to antimourning as a condition for healing in postcolonial contexts. Conscious of the centrality of language in Djebar’s writings and in her larger Maghrebi context, I have developed the undertheorized concept of Franco-graphie, which I propose opens up a new space to conceptualize violence and amnesia in writings that emerge from postcolonial, multilingual contexts, and their contested legacies.
From Impasse to Operative
Authors: Vadde Aarthi
Published: January 2019

Aarthi Vadde is an associate professor of English at Duke University. She is author ofChimeras of Form: Modernist Internationalism beyond Europe, 1914–2016, which was the winner of the 2018 Harry Levin Prize awarded by the ACLA. She is at work on a second monograph tentatively titledThe Amateur Spirit: Contemporary Literature in the Sharing Economyand is co-editing a collection entitledThe Critic as Amateur.
Spatiotemporal evolution of paludification associated with autogenic and allogenic factors in the black spruce–moss boreal forest of Québec, Canada
Authors: Le Stum-Boivin Éloïse , Magnan Gabriel , Garneau Michelle , Fenton Nicole J. , Grondin Pierre , Bergeron Yves
Published: January 2019

Paludification is the most common process of peatland formation in boreal regions. In this study, we investigated the autogenic (e.g., topography) and allogenic (fire and climate) factors triggering paludification in different geomorphological contexts (glaciolacustrine silty-clayey and fluvioglacial deposits) within the Québec black spruce (Picea mariana)–moss boreal forest. Paleoecological analyses were conducted along three toposequences varying from a forest on mineral soil to forested and semi-open peatlands. Plant macrofossil and charcoal analyses were performed on basal peat sections (≤50 cm) and thick forest humus (<40 cm) to reconstruct local vegetation dynamics and fire history involved in the paludification process. Results show that primary paludification started in small topographic depressions after land emergence ca. 8000 cal yr BP within rich fens. Lateral peatland expansion and secondary paludification into adjacent forests occurred between ca. 5100 and 2300 cal yr BP and resulted from low-severity fires during a climatic deterioration. Fires that reduced or eliminated entirely the organic layer promoted the establishment ofSphagnumin microdepressions. Paludification resulted in the decline of some coniferous species such asAbies balsameaandPinus banksiana. The paleoecological approach along toposequences allowed us to understand the spatiotemporal dynamics of paludification and its impacts on the vegetation dynamics over the Holocene.
Petrogenesis and tectonic implications of Late Mesoproterozoic A1- and A2-type felsic lavas from the Huili Group, southwestern Yangtze Block
Authors: Wang Dong-Bing , Wang Bao-Di , Yin Fu-Guang , Sun Zhi-Ming , Liao Shi-Yong , Tang Yuan , Luo Liang , Liu Zheng
Published: January 2019

This paper presents new LA-ICP-MS zircon U–Pb chronology, whole-rock geochemical and zircon Hf isotopic data for the felsic lavas of the Huili Group from the southwestern Yangtze Block. LA-ICP-MS zircon U–Pb dating shows that these rocks were emplaced in Late Mesoproterozoic time (∼1028 to 1019 Ma). Relative to typical I-type and S-type granitoids, all the samples are characterized by low Sr and Eu, and high high-field-strength element contents, highTFeO/MgO, enriched rare earth element compositions and negative Eu anomalies, indicating that they share the geochemical signatures of A-type granitoid. They can be further divided into two groups: Group I and Group II. Group I are A1-type felsic rocks and were produced by fractional crystallization of alkaline basaltic magmas. The Group II felsic lavas belong to the A2-type and were derived by partial melting of a crustal source with mixing of mantle-derived magmas. Both Group I and Group II felsic lavas may erupt in a continental back-arc setting. The coexistence of A1- and A2-type rocks in the southwestern Yangtze Block suggests that they can occur in the same tectonic setting.
The Concile National of 1811: Napoleon, Gallicanism and the Failure of Neo-Conciliarism
Authors: CAIANI AMBROGIO A.
Published: January 2019

Theconcile nationalof 1811 was one of the greatest flashpoints in the struggle that pitted the Napoleonic Empire against the papacy. This episode, which deserves to be situated within more recent historiographical trends, reveals much about the nature of Napoleonic imperialism and the Church's distrust for the power of the state. This article puts forward the view that the failure of theconcile nationalwas not strategic but tactical. Several bishops were frustrated with the pope's recalcitrance over episcopal investiture and fearful of schism. But their initial openness to neo-conciliarism turned to hostility when confronted with the state's intolerance.
Southern right whales in the South-western Atlantic Ocean: proposed criteria to identify suitable areas of use in poorly known reproductive grounds
Authors: Figueiredo Giovanna Corrêa e , Goya Samara Cazzoli y , Santos Marcos César de Oliveira
Published: January 2019

Urbanization and intense vessel traffic in coastal areas are obstacles for right whales when selecting breeding and calving grounds. Human activities might be the main cause for the recently observed drop in right whale sightings along the south-eastern coast of Brazil. Information concerning the biology and the activities that can potentially affect the presence of individuals along the coast are essential for management purposes, as well as for the recovery of the species stocks after a period of whaling pressure. This study correlated the occurrence of right whales in the northern limit of the breeding ground in the South-western Atlantic Ocean with local geomorphology, degree of urbanization and oceanographic features to better identify suitable areas for use by these whales. The study area was divided into 14 sub-areas based on local coastal geomorphology and discharge of large rivers. The following five ranking criteria were applied to each sub-area: presence of whaling stations and whaling activity in the past; presence and activity of ports; protection from swell, coastal slope and composition of the bottom substrate. The sub-areas that offered conditions conducive to the presence of right whales received higher scores. The proposed criteria were validated by overlapping the ranking scores with the records of right whales sighted in each sub-area. In south-eastern Brazil, protected areas with sandy bottom and gentle slope were associated with more sightings of female-calf pairs. The criteria can be used as a primary diagnostic indicating suitable sub-areas for right whales in poorly known breeding grounds.
Comparison of an in-house developed monitor unit double-check program for 3D conformal radiation therapy and treatment planning system verification
Authors: Slassi Noureddine , Ouabi Hmad , El Khayati Naïma
Published: January 2019

Aim

The treatment planning system (TPS) plays a key role in radiotherapy treatments; it is responsible for the accurate determination of the monitor unit (MU) needed to be delivered to treat a patient with cancer. The main goal of radiotherapy is to sterilise the tumour; however, any imprecise dose delivered could lead to deadly consequences. The TPS has a quality assurance tool, an independent program to double check the MU, evaluate patient plan correctness and search for any potential error.

Materials and methods

In this work, a comparison was carried out between a MU calculated by TPS and an independent in-house-developed monitor unit calculation program (MUCP). The program, written in Cplusplus (C++ Object-Oriented), requires a database of several measured quantities and uses a recently developed physically based method for field equivalence calculation. The ROOT CERN data analysis library has been used to establish fit functions, to extend MUCP use to a variety of photon beams. This study presents a new approach to checking MU correctness calculated by the TPS for a water-like tissue equivalent medium, using our MUCP, as the majority of previous studies on the MU independent checks were based on the Clarkson method. To evaluate each irradiated region, four calculation points corresponding to relative depths under the water phantom were tested for several symmetric, asymmetric, irregular symmetric and asymmetric field cases. A comparison of MU for each radiation fields from readings of the TPS and the MUCP was undertaken.

Results

A satisfactory agreement has been obtained and within the required standards (3%). Additional experimental measurements of dose deposited in a water phantom showed a deviation of <1·6%.

Findings

The MUCP is a useful tool for basic and complex MU verification for 3D conformal radiation therapy plans.