bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using technology to understand how therapist variables are associated with clinical outcomes in IAPT
Authors: Bateup S.E. , Palmer C.R. , Catarino A. 
Published: July 2020

Abstract
The UK’s Improving Access to Psychological Therapy Programme (IAPT) has improved transparency of primary mental health care in relation to the mandatory reporting of clinical outcomes. However, the data reveal a significant variance in outcomes. These findings have led to a growing body of research investigating to what extent therapist variables account for the difference in clinical outcomes. Previous studies have not had access to sufficient recordings or transcripts of therapy sessions in order to fully address this question. The purpose of this study was to use therapy transcripts derived from internet enabled cognitive behavioural therapy (CBT) treatment sessions in order to investigate whether and how therapist variables are associated with clinical outcome. A hierarchical log-linear analysis examined the relationship between therapist/patient variables and clinical outcome. Therapist fidelity to the CBT model and associated adherence to an evidence-based protocol were significantly related to clinical outcome. A graphical representation of the statistical model suggests that patient recovery is directly linked with fidelity and indirectly with adherence, after adjusting for patient attributes of age, gender and clinical presentation. Corroborating previous research, therapist competence and adherence to an evidence-based treatment protocol appear to be important in improving outcomes. These findings have implications for the continuing professional development of qualified therapists, potentially reinforcing the importance of reducing therapist drift.

Key learning aims

(1)
To develop an understanding in relation to which therapist variables are associated with clinical outcome in IAPT.

(2)
To reflect on how fidelity to the CBT model and adherence to evidence-based treatment protocols may affect clinical outcomes.

(3)
To exemplify use of a statistical method for enhanced visual understanding of complex multi-factorial data.
Global history of science as a knowledge resource for the Anthropocene
Authors: Schemmel Matthias 
Published: July 2020

Non-technical summaryThe article addresses the role of science in the present global ecological crisis, both as a factor in bringing it about and as a means to confront it. It is argued that the history of science, pursued in a global and long-term perspective, is an important knowledge resource for understanding the development of science in society. Pivotal episodes from that history, ranging from the origin of science in antiquity via the early modern scientific revolution to recent developments in industrial societies, are discussed with a particular emphasis on the case of China and with a view to the present crisis.
El Niño–Southern Oscillation Evolution Modulated by Atlantic Forcing
Authors: Chikamoto Y. , Johnson Z. F. , Wang S.‐Y. Simon , McPhaden M. J. , Mochizuki T. 
Published: July 2020

AbstractThe El Niño–Southern Oscillation (ENSO) exerts a strong influence on tropical Atlantic variability, but it is also affected by Atlantic forcing. Previous research has proposed three Atlantic precursors for ENSO: the North tropical Atlantic, the equatorial Atlantic, and the entire tropical Atlantic. However, the relative importance of these Atlantic precursors for ENSO remains unclear. Here, we present evidence from a set of multimodel partial ocean assimilation experiments that equatorial Atlantic cooling is the main contributor for weakening equatorial zonal winds in the Indo‐Pacific sector and subsequent ocean warming in the tropical Pacific. Opposite tendencies occur for a warmer equatorial Atlantic. The equatorial Atlantic affects the interbasin climate seesaw between the Atlantic and Pacific through an atmospheric zonal Wavenumber 1 pattern. However, model mean state biases and systematic errors prevent a precise assessment of the response times for the equatorial Pacific trade winds to Atlantic forcing.
Dynamics of Spontaneous (Multi) Centennial‐Scale Variations of the Atlantic Meridional Overturning Circulation Strength During the Last Interglacial
Authors: Kessler A. , Bouttes N. , Roche D. M. , Ninnemann U. S. , Tjiputra J. 
Published: July 2020

AbstractRecent reconstructions of bottom water δ13C during the last interglacial (LIG) suggest short‐lived variability in the Atlantic meridional overturning circulation (AMOC). Spontaneous (multi) centennial‐scale variability of the AMOC simulated in the Earth system model of intermediate complexity iLOVECLIM are investigated for that period. The model simulates abrupt AMOC transitions occurring at 300 years frequency and correspond to a switch of the AMOC vigor between a strong (∼17 Sv) and a weak (∼11 Sv) state. The onset of these abrupt transitions is associated with changes in orbital forcings resulting in the decline of summer insolation in the high latitudes of the North Atlantic and affecting the sea ice cover in two key deep convection regions: (1) the northern Nordic Seas (NNS) and (2) the northwest North Atlantic (NWNA). Northward inflow of Atlantic surface water increases the convection depth in (1) and strengthens the Greenland Iceland Norway (GIN) Seas overturning circulation. Subsequent ocean‐atmosphere interactions involving sea ice, ocean heat release, anomalies of evaporation‐precipitation, and wind stress over the Nordic Seas lead also to an increase in deep convection in (2), followed by increase in the AMOC strength.
Cognitive and emotional empathy after stimulation of brain mineralocorticoid and NMDA receptors in patients with major depression and healthy controls
Authors: Nowacki Jan , Wingenfeld Katja , Kaczmarczyk Michael , Chae Woo Ri , Abu-Tir Ikram , Deuter Christian Eric , Piber Dominique , Hellmann-Regen Julian , Otte Christian 
Published: July 2020

AbstractMineralocorticoid receptors (MR) are predominantly expressed in the hippocampus and prefrontal cortex. Both brain areas are associated with social cognition, which includes cognitive empathy (ability to understand others’ emotions) and emotional empathy (ability to empathize with another person). MR stimulation improves memory and executive functioning in patients with major depressive disorder (MDD) and healthy controls, and leads to glutamate-mediated N-methyl-D-aspartate receptor (NMDA-R) signaling. We examined whether the beneficial effects of MR stimulation can be extended to social cognition (empathy), and whether DCS would have additional beneficial effects. In this double-blind placebo-controlled single-dose study, we randomized 116 unmedicated MDD patients (mean age 34 years, 78% women) and 116 age-, sex-, and education years-matched healthy controls to four conditions: MR stimulation (fludrocortisone (0.4 mg) + placebo), NMDA-R stimulation (placebo + D-cycloserine (250 mg)), MR and NMDA-R stimulation (both drugs), or placebo. Cognitive and emotional empathy were assessed by the Multifaceted Empathy Test. The study was registered on clinicaltrials.gov (NCT03062150). MR stimulation increased cognitive empathy across groups, whereas NMDA-R stimulation decreased cognitive empathy in MDD patients only. Independent of receptor stimulation, cognitive empathy did not differ between groups. Emotional empathy was not affected by MR or NMDA-R stimulation. However, MDD patients showed decreased emotional empathy compared with controls but, according to exploratory analyses, only for positive emotions. We conclude that MR stimulation has beneficial effects on cognitive empathy in MDD patients and healthy controls, whereas NMDA-R stimulation decreased cognitive empathy in MDD patients. It appears that MR rather than NMDA-R are potential treatment targets to modulate cognitive empathy in MDD.
In vitro and ex vivo gene expression profiling reveals differential kinetic response of HSPs and UPR genes is associated with PI resistance in multiple myeloma
Authors: Mitra Amit Kumar , Kumar Harish , Ramakrishnan Vijay , Chen Li , Baughn Linda , Kumar Shaji , Rajkumar S. Vincent , Van Ness Brian G. 
Published: July 2020

AbstractExtensive inter-individual variation in response to chemotherapy (sensitive vs resistant tumors) is a serious cause of concern in the treatment of multiple myeloma (MM). In this study, we used human myeloma cell lines (HMCLs), and patient-derived CD138+ cells to compare kinetic changes in gene expression patterns between innate proteasome inhibitor (PI)-sensitive and PI-resistant HMCLs following test dosing with the second-generation PI Ixazomib. We found 1553 genes that changed significantly post treatment in PI-sensitive HMCLs compared with only seven in PI-resistant HMCLs (p < 0.05). Genes that were uniquely regulated in PI-resistant lines were RICTOR (activated), HNF4A, miR-16-5p (activated), MYCN (inhibited), and MYC (inhibited). Ingenuity pathway analysis (IPA) using top kinetic response genes identified the proteasome ubiquitination pathway (PUP), and nuclear factor erythroid 2-related factor 2 (NRF2)-mediated oxidative stress response as top canonical pathways in Ix-sensitive cell lines and patient-derived cells, whereas EIF2 signaling and mTOR signaling pathways were unique to PI resistance. Further, 10 genes were common between our in vitro and ex vivo post-treatment kinetic PI response profiles and Shaughnessy’s GEP80-postBz gene expression signature, including the high-risk PUP gene PSMD4. Notably, we found that heat shock proteins and PUP pathway genes showed significant higher upregulation in Ix-sensitive lines compared with the fold-change in Ix-resistant myelomas.
Protein-coated corrole nanoparticles for the treatment of prostate cancer cells
Authors: Soll Matan , Chen Qiu-Cheng , Zhitomirsky Benny , Lim Punnajit P. , Termini John , Gray Harry B. , Assaraf Yehuda G. , Gross Zeev 
Published: July 2020

AbstractDevelopment of novel therapeutic strategies to eradicate malignant tumors is of paramount importance in cancer research. In a recent study, we have introduced a facile protocol for the preparation of corrole-protein nanoparticles (NPs). These NPs consist of a corrole-core coated with protein. We now report that a novel lipophilic corrole, (2)Ga, delivered as human serum albumin (HSA)-coated NPs, displayed antineoplastic activity towards human prostate cancer DU-145 cells. Cryo-TEM analysis of these NPs revealed an average diameter of 50.2 ± 8.1 nm with a spherical architecture exhibiting low polydispersity. In vitro cellular uptake of (2)Ga/albumin NPs was attributable to rapid internalization of the corrole through ligand binding-dependent extracellular release and intercalation of the corrole cargo into the lipid bilayer of the plasma membrane. This finding is in contrast with a previously reported study on corrole-protein NPs that displayed cellular uptake via endocytosis. Investigation of the non-light-induced mechanism of action of (2)Ga suggested the induction of necrosis through plasma membrane destabilization, impairment of calcium homeostasis, lysosomal stress and rupture, as well as formation of reactive oxygen species (ROS). (2)Ga also exhibited potent light-induced cytotoxicity through ROS generation. These findings demonstrate a rapid cellular uptake of (2)Ga/protein NPs along with targeted induction of tumor cell necrosis.
Defect-mediated Rashba engineering for optimizing electrical transport in thermoelectric BiTeI
Authors: Li Xin , Sheng Ye , Wu Lihua , Hu Shunbo , Yang Jiong , Singh David J. , Yang Jihui , Zhang Wenqing 
Published: July 2020

AbstractThe Rashba effect plays a vital role in electronic structures and related functional properties. The strength of the Rashba effect can be measured by the Rashba parameter αR; it is desirable to manipulate αR to control the functional properties. The current work illustrates how αR can be systematically tuned by doping, taking BiTeI as an example. A five-point-spin-texture method is proposed to efficiently screen doped BiTeI systems with the Rashba effect. Our results show that αR in doped BiTeI can be manipulated within the range of 0–4.05 eV Å by doping different elements. The dopants change αR by affecting both the spin–orbit coupling strength and band gap. Some dopants with low atomic masses give rise to unexpected and sizable αR, mainly due to the local strains. The calculated electrical transport properties reveal an optimal αR range of 2.75–3.55 eV Å for maximizing the thermoelectric power factors. αR thus serves as an effective indicator for high-throughput screening of proper dopants and subsequently reveals a few promising Rashba thermoelectrics. This work demonstrates the feasibility of defect-mediated Rashba engineering for optimizing the thermoelectric properties, as well as for manipulating other spin-related functional properties.
Thread-based multiplexed sensor patch for real-time sweat monitoring
Authors: Terse-Thakoor Trupti , Punjiya Meera , Matharu Zimple , Lyu Boyang , Ahmad Meraj , Giles Grace E. , Owyeung Rachel , Alaimo Francesco , Shojaei Baghini Maryam , Brunyé Tad T. , Sonkusale Sameer 
Published: July 2020

AbstractSensor platforms that exploit the fibrous textile threads as substrates offer great promise since they can be directly sewn, woven or stitched on to any clothing. They can also be placed directly in intimate contact with the skin. In this work, we present a thread-based sensing platform in the form of a multiplexed sensing patch for continuous simultaneous on-skin monitoring of sweat. The patch performs real-time, on-body measurements of important biomarkers present in sweat such as electrolytes (sodium and ammonium ions), metabolites (lactate) and acidity (pH). Flexible threads coated with conductive inks were used as sensing electrodes. Selective potentiometric detection of electrolytes and pH was made possible through ion-selective membrane deposition and pH-sensitive polyaniline coating on threads, respectively. An amperometric enzymatic sensing scheme with lactate oxidase was used for the detection of lactate. An array of the thread sensors is integrated onto a patch with connectivity to a miniaturized circuit module containing a potentiostat, microprocessor and wireless circuitry for wireless smartphone readout. Extensive in vitro validation and an in vivo human pilot study involving a maximal exertion test show the promise of this platform for real-time physiological monitoring of human performance/fitness under stress, as well as diagnostic monitoring through sweat analysis.
SimpylCellCounter: an automated solution for quantifying cells in brain tissue
Authors: Bal Aneesh , Maureira Fidel , Arguello Amy A. 
Published: July 2020

AbstractManual quantification of activated cells can provide valuable information about stimuli-induced changes within brain regions; however, this analysis remains time intensive. Therefore, we created SimpylCellCounter (SCC), an automated method to quantify cells that express cFos protein, an index of neuronal activity, in brain tissue and benchmarked it against two widely-used methods: OpenColonyFormingUnit (OCFU) and ImageJ Edge Detection Macro (IMJM). In Experiment 1, manually-obtained cell counts were compared to those detected via OCFU, IMJM and SCC. The absolute error in counts (manual versus automated method) was calculated and error types were categorized as false positives or negatives. In Experiment 2, performance analytics of OCFU, IMJM and SCC were compared. In Experiment 3, SCC analysis was conducted on images it was not trained on, to assess its general utility. We found SCC to be highly accurate and efficient in quantifying cells with circular morphologies that expressed cFos. Additionally, SCC utilized a new approach to count overlapping cells with a pretrained convolutional neural network classifier. The current study demonstrates that SCC is a novel, automated tool to quantify cells in brain tissue and complements current, open-sourced methods designed to detect cells in vitro.
Quantum entanglement maintained by virtual excitations in an ultrastrongly-coupled-oscillator system
Authors: Zhou Jian-Yong , Zhou Yue-Hui , Yin Xian-Li , Huang Jin-Feng , Liao Jie-Qiao 
Published: July 2020

AbstractWe study the effect of quantum entanglement maintained by virtual excitations in an ultrastrongly-coupled harmonic-oscillator system. Here, the quantum entanglement is caused by the counterrotating interaction terms and hence it is maintained by the virtual excitations. We obtain the analytical expression for the ground state of the system and analyze the relationship between the average excitation numbers and the ground-state entanglement. We also study the entanglement dynamics between the two oscillators in both the closed- and open-system cases. In the latter case, the quantum master equation is microscopically derived in the normal-mode representation of the coupled-oscillator system. This work will open a route to the study of quantum information processing and quantum physics based on virtual excitations.
Investigating the biological potential of galactic cosmic ray-induced radiation-driven chemical disequilibrium in the Martian subsurface environment
Authors: Atri Dimitra 
Published: July 2020

AbstractThere is growing evidence suggesting the presence of aqueous environment on ancient Mars, raising the question of the possibility of life in such an environment. Subsequently, with the erosion of the Martian atmosphere resulting in drastic changes in its climate, surface water disappeared, shrinking habitable spaces on the planet, with only a limited amount of water remaining near the surface in form of brines and water–ice deposits. Life, if it ever existed, would have had to adapt to harsh modern conditions, which includes low temperatures and surface pressure, and high radiation dose. Presently, there is no evidence of any biological activity on the planet’s surface, however, the subsurface environment, which is yet to be explored, is less harsh, has traces of water in form of water–ice and brines, and undergoes radiation-driven redox chemistry. I hypothesize that Galactic Cosmic Ray (GCR)-induced radiation-driven chemical disequilibrium can be used for metabolic energy by extant life, and host organisms using mechanisms seen in similar chemical and radiation environments on Earth. I propose a GCR-induced radiolytic zone, and discuss the prospects of finding such life with Rosalind Franklin rover of the ExoMars mission.
Transcriptional portrait of M. bovis BCG during biofilm production shows genes differentially expressed during intercellular aggregation and substrate attachment
Authors: Flores-Valdez Mario Alberto , Aceves-Sánchez Michel de Jesús , Peterson Eliza J. R. , Baliga Nitin , Bravo-Madrigal Jorge , De la Cruz-Villegas Miguel Ángel , Ares Miguel A. , Born Sarah , Voskuil Martin , Pérez-Padilla Nayeli Areli , Burciaga-Flores Mirna , Camacho-Villegas Tanya Amanda , Espinoza-Jorge María Guadalupe 
Published: July 2020

AbstractMycobacterium tuberculosis and M. smegmatis form drug-tolerant biofilms through dedicated genetic programs. In support of a stepwise process regulating biofilm production in mycobacteria, it was shown elsewhere that lsr2 participates in intercellular aggregation, while groEL1 was required for biofilm maturation in M. smegmatis. Here, by means of RNA-Seq, we monitored the early steps of biofilm production in M. bovis BCG, to distinguish intercellular aggregation from attachment to a surface. Genes encoding for the transcriptional regulators dosR and BCG0114 (Rv0081) were significantly regulated and responded differently to intercellular aggregation and surface attachment. Moreover, a M. tuberculosis H37Rv deletion mutant in the Rv3134c-dosS-dosR regulon, formed less biofilm than wild type M. tuberculosis, a phenotype reverted upon reintroduction of this operon into the mutant. Combining RT-qPCR with microbiological assays (colony and surface pellicle morphologies, biofilm quantification, Ziehl–Neelsen staining, growth curve and replication of planktonic cells), we found that BCG0642c affected biofilm production and replication of planktonic BCG, whereas ethR affected only phenotypes linked to planktonic cells despite its downregulation at the intercellular aggregation step. Our results provide evidence for a stage-dependent expression of genes that contribute to biofilm production in slow-growing mycobacteria.
Adverse perinatal outcomes of chronic intervillositis of unknown etiology: an observational retrospective study of 122 cases
Authors: Mattuizzi Aurélien , Sauvestre Fanny , André Gwenaëlle , Poingt Marion , Camberlein Camille , Carles Dominique , Pelluard Fanny , Blanco Patrick , Sentilhes Loïc , Lazaro Estibaliz 
Published: July 2020

AbstractOur study aimed to assess perinatal outcomes and recurrence rate of Chronic Intervillositis of Unknown Etiology (CIUE). We conducted an observational retrospective study in a tertiary care university hospital in France from January 1, 1997 to July 31, 2018. 122 pregnancies (102 women) with CIUE were included. Cases of the Department of Histopathology placenta database were re-analysed independently by three pathologists specializing in fetal pathology. Diagnosis of CIUE was confirmed according to: (1) the presence of cellular infiltrate in the intervillous space, (2) ~ 80% of the mononuclear cells in the intervillous space positive for CD68, (3) infiltration occupying at least 5% of the intervillous space, and (4) no clinical or histopathological sign of infection. Outcomes of pregnancies with CIUE (miscarriages, stillbirths, terminations of pregnancy, live birth with or without prematurity or fetal growth restriction) and proportion of CIUE recurrence were analysed. The lost pregnancies comprised 17 (13.9%) miscarriages, 17 (13.9%) stillbirths, and 18 (14.8%) terminations of pregnancy. Of the 70 (57.4%) pregnancies that led to a live birth, 38 (54.3%) new-borns were premature and 50 (72.5%) exhibited fetal growth restriction. Among the 102 women, 23 subsequently became pregnant, half of whom (n = 11) developed recurrent CIUE. CIUE was associated with high rates of adverse perinatal outcomes, including pregnancy loss, fetal growth restriction, and preterm birth with a risk of recurrence nearly 50%.
Convolutional neural networks improve fungal classification
Authors: Vu Duong , Groenewald Marizeth , Verkley Gerard 
Published: July 2020

AbstractSequence classification plays an important role in metagenomics studies. We assess the deep neural network approach for fungal sequence classification as it has emerged as a successful paradigm for big data classification and clustering. Two deep learning-based classifiers, a convolutional neural network (CNN) and a deep belief network (DBN) were trained using our recently released barcode datasets. Experimental results show that CNN outperformed the traditional BLAST classification and the most accurate machine learning based Ribosomal Database Project (RDP) classifier on datasets that had many of the labels present in the training datasets. When classifying an independent dataset namely the “Top 50 Most Wanted Fungi”, CNN and DBN assigned less sequences than BLAST. However, they could assign much more sequences than the RDP classifier. In terms of efficiency, it took the machine learning classifiers up to two seconds to classify a test dataset while it was 53 s for BLAST. The result of the current study will enable us to speed up the taxonomic assignments for the fungal barcode sequences generated at our institute as ~ 70% of them still need to be validated for public release. In addition, it will help to quickly provide a taxonomic profile for metagenomics samples.