bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Psychopharmacology Algorithm Project at the Harvard South Shore Program: An Update on Unipolar Nonpsychotic Depression
Authors: Giakoumatos Christoforos Iraklis , Osser David 
Published: January 2019

Abstract

Background
The Psychopharmacology Algorithm Project at the Harvard South Shore Program presents evidence-based recommendations considering efficacy, tolerability, safety, and cost. Two previous algorithms for unipolar nonpsychotic depression were published in 1993 and 1998. New studies over the last 20 years suggest that another update is needed.

Methods
The references reviewed for the previous algorithms were reevaluated, and a new literature search was conducted to identify studies that would either support or alter the previous recommendations. Other guidelines and algorithms were consulted. We considered exceptions to the main algorithm, as for pregnant women and patients with anxious distress, mixed features, or common medical and psychiatric comorbidities.

Summary
For inpatients with severe melancholic depression and acute safety concerns, electroconvulsive therapy (or ketamine if ECT refused or ineffective) may be the first-line treatment. In the absence of an urgent indication, we recommend trialing venlafaxine, mirtazapine, or a tricyclic antidepressant. These may be augmented if necessary with lithium or T3 (triiodothyronine). For inpatients with non-melancholic depression and most depressed outpatients, sertraline, escitalopram, and bupropion are reasonable first choices. If no response, the prescriber (in collaboration with the patient) has many choices for the second trial in this algorithm because there is no clear preference based on evidence, and there are many individual patient considerations to take into account. If no response to the second medication trial, the patient is considered to have a medication treatment–resistant depression. If the patient meets criteria for the atypical features specifier, a monoamine oxidase inhibitor could be considered. If not, reconsider (for the third trial) some of the same options suggested for the second trial. Some other choices can also considered at this stage. If the patient has comorbidities such as chronic pain, obsessive-compulsive disorder, attention-deficit/hyperactivity disorder, or posttraumatic stress disorder, the depression could be secondary; evidence-based treatments for those disorders would then be recommended.
Tenofovir and telbivudine combination therapy rapidly decreases viral loads in immune-tolerant chronic hepatitis B patients awaiting assisted reproduction: an open-label, randomized, controlled study
Authors: Wu Zhi-xian , Chen Feng-sui , Zhou Xiao-ling , Huang Qian , Zhang Shi-an , Wu Hai-cong , Cai Li-rong , Zeng Zhi-yu , Li Ying-hui , Li Dong-liang 
Published: January 2019

Background
Immune-tolerant chronic hepatitis B (CHB) patients awaiting assisted reproduction (AR) are required to initiate antiviral therapy because of laboratory safety concerns. The antiviral therapy in this group has not been well assessed. We sought to explore the efficacy and safety of the combination therapy (COM) of tenofovir (TDF) and telbivudine (LdT).

Patients and methods
In this open-label, randomized, controlled study, we enrolled and randomized hepatitis B virus e-antigen (HBeAg)-positive CHB patients awaiting AR into the study COM group and the control (TDF) group. The COM group received combination therapy of TDF and LdT, and the TDF group received a single treatment of TDF. The patients were followed up for at least 48 weeks. The primary endpoint was the proportion of patients with undetectable HBV DNA level at week 12.

Results
A total of 121 patients were recruited into the COM group (n=60) and the TDF group (n=61). The percentages of patients with undetectable HBV DNA levels were 90.0% (54/60) in the COM group and 67.2% (41/61) (P=0.002) in the TDF group at week 12; the percentages were 96.6% (58/60) in the COM group and 85.2% (52/61) in the TDF group at week 48 (P=0.028), respectively. HBeAg seroconversion occurred in 5/60 (8.3%) patients in the COM group and 2/61 (3.3%) patients in the TDF group at week 48 (P=0.233).

Conclusion
TDF and LdT combination therapy shows a rapid antivirological response in immune-tolerant CHB patients awaiting AR, which provide an alternative for this group at AR centers. However, the HBeAg seroconversion rate is unsatisfactory in the short term.
Prognostic predictors for patients with hepatocellular carcinoma receiving adjuvant transcatheter arterial chemoembolization
Authors: Gu Jingxian , Zhang Xing , Cui Ruixia , Zhang Jia , Wang Zhixin , Jia Yifan , Miao Runchen , Dong Yanyan , Ma Xiaohua , Fan Haining , Wang Haijiu , Ren Li , Li Yiming , Niu Wenquan , Zhang Jingyao , Qu Kai , Liu Chang 
Published: January 2019

Objectives
We aimed to confirm the clinical effectiveness of postoperative adjuvant transcatheter arterial chemoembolization (PA-TACE) in patients with hepatocellular carcinoma after liver resection, and further identify the patients who could benefit most from PA-TACE.

Patients and methods
Propensity score matching at a ratio of 1 : 2 was used between hepatectomy patients with and without receiving PA-TACE. Kaplan–Meier analysis was performed to compare overall survival and recurrence-free survival between two groups. Univariate COX regression and stratified analyses were performed to screen and identify survival predictors for PA-TACE patients. The identified predictive markers were validated in an external cohort.

Results
The propensity analysis matched 116 patients in PA-TACE group to 232 in the control group. Visible protective effect of PA-TACE was shown by survival curves in matched series (log-rank P=0.009 and 0.008), with hazard ratio of being 0.599 (95% confidence interval: 0.420–0.855) and 0.623 (95% confidence interval: 0.449–0.866), respectively, for overall survival and recurrence-free survival. The identified prognostic predictors for PA-TACE included TNM stage, tumor size and number, hepatitis B infection, spleen diameter, preoperative serum α-fetoprotein, alkaline phosphatase, γ-glutamyl transpeptidase and monocyte, and three risk signatures (aspartate aminotransferase-to-alanine aminotransferase ratio, neutrophil-to-lymphocyte ratio, and systemic immune-inflammation index).

Conclusion
The treatment effectiveness of adjuvant transcatheter arterial chemoembolization for patients with hepatocellular carcinoma after surgery was validated in this study, and the best candidates for PA-TACE were identified as well, including patients with late-stage tumor, portal hypertension, and high preoperative serum levels of α-fetoprotein, alkaline phosphatase, γ-glutamyl transpeptidase, and monocytes.
Magma chambers versus mush zones: constraining the architecture of sub-volcanic plumbing systems from microstructural analysis of crystalline enclaves
Authors: Holness Marian B. , Stock Michael J. , Geist Dennis 
Published: January 2019

There are clear microstructural differences between mafic plutonic rocks that formed in a dynamic liquid-rich environment, in which crystals can be moved and re-arranged by magmatic currents, and those in which crystal nucleation and growth are essentiallyin situand static. Crystalline enclaves, derived from deep crustal mushy zones and erupted in many volcanic settings, afford a unique opportunity to use the understanding of microstructural development, established from the study of intrusive plutons, to place constraints on the architecture of sub-volcanic systems. Here, we review the relevant microstructural literature, before applying these techniques to interrogate the crystallization environments of enclaves from the Kameni Islands of Santorini and Rábida Volcano in the Galápagos. Crystals in samples of deep-sourced material from both case studies preserve evidence of at least some time spent in a liquid-rich environment. The Kameni enclaves appear to record an early stage of crystallization during which crystals were free to move, with the bulk of crystallization occurring in a static, mushy environment. By contrast, the Rábida enclaves were sourced from an environment in which hydrodynamic sorting and re-arrangement by magmatic currents were common, consistent with a liquid-rich magma chamber. While presently active volcanoes are thought to be underlain by extensive regions rich in crystal mush, these examples preserve robust evidence for the presence of liquid-rich magma chambers in the geological record.This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics'.
Melt movement through the Icelandic crust
Authors: White Robert S. , Edmonds Marie , Maclennan John , Greenfield Tim , Agustsdottir Thorbjorg 
Published: January 2019

We use both seismology and geobarometry to investigate the movement of melt through the volcanic crust of Iceland. We have captured melt in the act of moving within or through a series of sills ranging from the upper mantle to the shallow crust by the clusters of small earthquakes it produces as it forces its way upward. The melt is injected not just beneath the central volcanoes, but also at discrete locations along the rift zones and above the centre of the underlying mantle plume. We suggest that the high strain rates required to produce seismicity at depths of 10–25 km in a normally ductile part of the Icelandic crust are linked to the exsolution of carbon dioxide from the basaltic melts. The seismicity and geobarometry provide complementary information on the way that the melt moves through the crust, stalling and fractionating, and often freezing in one or more melt lenses on its way upwards: the seismicity shows what is happening instantaneously today, while the geobarometry gives constraints averaged over longer time scales on the depths of residence in the crust of melts prior to their eruption.This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics'.
How do volatiles escape their shallow magmatic hearth?
Authors: Degruyter Wim , Parmigiani Andrea , Huber Christian , Bachmann Olivier 
Published: January 2019

Only a small fraction (approx. 1–20%) of magmas generated in the mantle erupt at the surface. While volcanic eruptions are typically considered as the main exhaust pipes for volatile elements to escape into the atmosphere, the contribution of magma reservoirs crystallizing in the crust is likely to dominate the volatile transfer from depth to the surface. Here, we use multiscale physical modelling to identify and quantify the main mechanisms of gas escape from crystallizing magma bodies. We show that most of the outgassing occurs at intermediate to high crystal fraction, when the system has reached a mature mush state. It is particularly true for shallow volatile-rich systems that tend to exsolve volatiles through second boiling, leading to efficient construction of gas channels as soon as the crystallinity reaches approximately 40–50 vol.%. We, therefore, argue that estimates of volatile budgets based on volcanic activity may be misleading because they tend to significantly underestimate the magmatic volatile flux and can provide biased volatile compositions. Recognition of the compositional signature and volumetric dominance of intrusive outgassing is, therefore, necessary to build robust models of volatile recycling between the mantle and the surface.
This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Identifying the ingredients of hydrous arc magmas: insights from Mt Lamington, Papua New Guinea
Authors: Humphreys M. C. S. , Zhang J. , Cooper G. F. , Macpherson C. G. , Ottley C. J. 
Published: January 2019

Volcanism is the surface expression of magma intrusion, crystallization, assimilation and hybridization processes operating throughout the crust over a range of time periods. Many magmas, including those erupted at subduction zones, have complex textures that reflect these processes. Here, we use textural and geochemical characteristics of calcic amphiboles to help identify multiple ingredients of subduction zone magmatism at Mt Lamington volcano, Papua New Guinea. Our approach uses existing trace element partitioning schemes to calculate the compositions of amphibole equilibrium melts (AEMs). The AEM compositions show that Mt Lamington andesites and plutonic enclaves are dominated by fractionation of amphibole + plagioclase + biotite, with assimilation of plagioclase and zircon. Magnesiohastingsite crystals in the andesite and diktytaxitic mafic enclaves reflect multiple episodes of recharge by more primitive, geochemically variable melts. The andesite also contains clots with rounded grains and melt on grain boundaries. These features indicate slow crystallization, and the retention of melt films could significantly enhance the potential for remobilization of crystals by infiltrating melts or during magma mixing. Variations in crystallization conditions could thus significantly affect the mush microstructure. We suggest that this could result in a significant bias of the volcanic record towards the preferential incorporation of more slowly cooled plutonic material from the lower crust or from more thermally mature plumbing systems.
This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
Architecture and dynamics of magma reservoirs
Authors: Edmonds Marie , Cashman Katharine V. , Holness Marian , Jackson Matthew 
Published: January 2019

This introductory article provides a synopsis of our current understanding of the form and dynamics of magma reservoirs in the crust. This knowledge is based on a range of experimental, observational and theoretical approaches, some of which are multidisclipinary and pioneering. We introduce and provide a contextual background for the papers in this issue, which cover a wide range of topics, encompassing magma storage, transport, behaviour and rheology, as well as the timescales on which magma reservoirs operate. We summarize the key findings that emerged from the meeting and the challenges that remain. The study of magma reservoirs has wide implications not only for understanding geothermal and magmatic systems, but also for natural oil and gas reservoirs and for ore deposit formation.This article is part of the Theo Murphy meeting issue ‘Magma reservoir architecture and dynamics’.
DO-MS: Data-Driven Optimization of Mass Spectrometry Methods
Authors: Huffman Gray , Specht Harrison , Chen Albert , Slavov Nikolai 
Published: January 2019

AbstractThe performance of ultrasensitive LC-MS/MS methods, such as Single-Cell Proteomics by Mass Spectrometry (SCoPE-MS), depends on multiple interdependent parameters. This interdependence makes it challenging to specifically pinpoint bottlenecks in the LC-MS/MS methods and approaches for resolving them. For example, low signal at MS2 level can be due to poor LC separation, ionization, apex targeting, ion transfer, or ion detection. We sought to specifically diagnose such bottlenecks by interactively visualizing data from all levels of bottom-up LC-MS/MS analysis. Many search engines, such as MaxQuant, already provide such data, and we developed an open source platform for their interactive visualization and analysis: Data-driven Optimization of MS (DO-MS). We found that in many cases DO-MS not only specifically diagnosed bottlenecks but also enabled us to rationally optimize them. For example, we used DO-MS to diagnose poor sampling of the elution peak apex and to optimize it, which increased the efficiency of delivering ions for MS2 analysis by 370%. DO-MS is easy to install and use, and its GUI allows for interactive data subsetting and high-quality figure generation. The modular design of DO-MS facilitates customization and expansion. DO-MS is available for download from GitHub: github.com/SlavovLab/DO-MS
scSVA: an interactive tool for big data visualization and exploration in single-cell omics
Authors: Tabaka Marcin , Gould Joshua , Regev Aviv 
Published: January 2019

AbstractWe present scSVA (single-cell Scalable Visualization and Analytics), a lightweight R package for interactive two- and three-dimensional visualization and exploration of massive single-cell omics data. Building in part of methods originally developed for astronomy datasets, scSVA is memory efficient for more than hundreds of millions of cells, can be run locally or in a cloud, and generates high-quality figures. In particular, we introduce a numerically efficient method for single-cell data embedding in 3D which combines an optimized implementation of diffusion maps with a 3D force-directed layout, enabling generation of 3D data visualizations at the scale of a million cells. To facilitate reproducible research, scSVA supports interactive analytics in a cloud with containerized tools. scSVA is available online at https://github.com/klarman-cell-observatory/scSVA.
Microtubule plus-end dynamics link wound repair to the innate immune response
Authors: Taffoni Clara , Omi Shizue , Huber Caroline , Mailfert Sebastien , Fallet Matthieu , Ewbank Jonathan J. , Pujol Nathalie 
Published: January 2019

AbstractAs a first line of defence against the environment, the epidermis protect animals from infection and physical damage. In C. elegans, wounding the epidermal epithelium triggers both an immune reaction and a repair response. Exactly how these are controlled, and the degree to which they are inter-connected remains unclear. To address these questions, we established a simple system for simultaneously inflicting precise laser wounds and imaging at high spatial and temporal resolution. We show that in C. elegans, wounding provokes a rapid sealing of the plasma membrane, involving reorganisation of phosphatidylinositol 4,5- bisphosphate domains. This is followed by a radial recruitment at the wound site of EBP-2/EB1, a protein that binds the plus ends of microtubules. EB1 recruitment is accompanied by a reorganisation of microtubules, required for the subsequent recruitment of actin and wound closure. It is also required for the directed trafficking towards the site of injury of the key signalling protein SNF-12. In the absence of SNF-12 recruitment, there is an abrogation of the immune response. Our results suggest that microtubule dynamics coordinate the cytoskeletal changes required for wound repair and the concomitant activation of the innate immune response.
Colonial ascidians strongly preyed upon, yet dominate the substrate in a subtropical fouling community
Authors: Hiebert Laurel Sky , Vieira Edson A. , Dias Gustavo M. , Tiozzo Stefano , Brown Federico D. 
Published: January 2019

AbstractHigher diversity and dominance at lower latitudes has been suggested for colonial species. We verified the latitudinal pattern in species richness of ascidians, finding that higher colonial-to-solitary species ratios occur in the tropics and subtropics. At the latitudinal region with the highest ratio, in south-eastern Brazil, we confirmed that colonial species dominate the space on artificial plates in two independent studies of five fouling communities. We manipulated settlement plates to measure effects of predation and competition on growth and survivorship of colonial vs. solitary ascidians. Eight ascidian species were subjected to a predation treatment, i.e. caged vs. exposed to predators, and a competition treatment, i.e. leaving vs. removing competitors, to assess main and interactive effects. Predation had a greater effect on growth and survivorship of colonial compared to solitary species, whereas competition did not show consistent patterns between the two life histories. We hypothesize that colonial ascidians dominate at this subtropical site despite being highly preyed upon because they regrow when partially consumed and can adjust in shape and space to grow into refuges. We contend that these means of avoiding mortality from predation can have large influences on the diversification patterns of colonial species at low latitudes, where predation intensity is greater.
A Preliminary Occurrence of Extended-Spectrum and AmpC Beta-Lactamases in Clinical Isolates of EnteropathogenicEscherichia coliin Najaf, Iraq
Authors: Alsherees Hashim Ali Abdulameer , Ali Sumaya Najim Abed 
Published: January 2019

AbstractExtended-spectrum β-lactamase (ESBL) and AmpC β-lactamase producing enteropathogenicEscherichia coli(EPEC) have become an important clinical problem due to their resistance to multiple antibiotics. The purpose of this study was to evaluate the multi-drug resistant (MDR) and β-lactamases producing EPEC isolated from children with diarrhea. Twenty two EPEC strains were gathered from another study performed from September to November 2009. Antibiotic susceptibilities against 20 antibiotics determined by the agar disk diffusion according to the protocol recommended by Clinical and Laboratory Standards Institute guidelines (CLSI). Phenotypic confirmatory tests carried out for screening of ESBLs and AmpC β-lactamase. The isolates subjected to PCR assays with specific primers forbla-genes (blaSHV,blaTEM,blaCTX-MandblaOXA,blaPER,blaVEBandblaGES). Only 22 (3.4%) EPEC isolates recovered from clinical infections. MDR rate in EPEC was 90.9%. Phenotypic confirmatory tests showed that 13.6% and 20.0% of isolates were ESBL and AmpC β-lactamase producers, respectively. Among the EPEC isolates, percent recovery ofblaSHV,blaTEM,blaCTX-MandblaOXAgenes was 100%, 81.8%, 77.3% and 9.1%, respectively. Only 2 (9.1%) isolates hadblaAmpCgene and none of the isolates carriedblaPER,blaVEBandblaGESgenes. The results of our study showed that the ESBLs were common among EPEC isolates. Such high dissemination of ESBLs is a serious problem for public health and therefore, it is necessary to seek a program for monitoring ESBLs in Najaf hospitals. This study is the first report on the presence of thebla-genes in EPEC isolates in Najaf.
Cdc42 promotes epithelial morphogenesis by coupling Par-complex and Crumbs recruitment via Par6-aPKC
Authors: Nunes de Almeida Francisca , Walther Rhian F. , Pressé Mary , Vlassaks Evi , Pichaud Franck 
Published: January 2019

ABSTRACTEpithelial morphogenesis depends on Cdc42, which acts in part through the Par-complex (Baz/Par3-Par6-aPKC), and Crumbs (Crb/CRB3). However, how these proteins come together and interact during morphogenesis is not well understood. Here we show that inDrosophilacells, Cdc42 is active at the apical membrane and cell-cell contacts, and couples apical recruitment of Par6-aPKC and Crb to promote apical identify. This coupling depends on Cdc42 and aPKC binding to Par6, and is mediated by Par6 binding to Crb. Conversely, Crb promotes the apical retention of Par6-aPKC, and thus Cdc42-Par6-aPKC and Crb promote each other’s apical accumulation to specify the apical membrane andZonula Adherens (ZA). Altogether, our work shows that epithelial morphogenesis relies on a two tiered-mechanism whereby Cdc42 coordinates Par-complex assembly and apical recruitment of Crb through Par6-aPKC.
Hypoxia induces rapid changes to histone methylation reprogramming chromatin for the cellular response
Authors: Batie Michael , Frost Julianty , Frost Mark , Wilson James W. , Schofield Pieta , Rocha Sonia 
Published: January 2019

AbstractMolecular dioxygenases include JmjC-containing histone demethylases and PHD enzymes, but only PHDs are considered to be molecular oxygen sensors in cells. Although, it is known that hypoxia can alter chromatin, whether this is a direct effect on histone demethylases or due to hypoxia induced HIF-dependent transcriptional changes is not known. Here, we report that hypoxia induces a rapid and HIF-independent alteration to a variety of histone methylation marks. Genomic locations of H3K4me3 and H3K36me3 following short hypoxia predict the hypoxia gene signature observed several hours later in cells. We show that KDM5A inactivation mimics hypoxic changes to H3K4me3 in its targets and is required for the cellular response to hypoxia. Our results demonstrate a direct link between oxygen sensing and chromatin changes via KDM inhibition.One Sentence SummaryRapid oxygen sensing by chromatin