bluuebunny/crossref_metadata_2025_split huggingface dataset:
Poor Survival After Retransplantation in NASH Cirrhosis
Authors: Thuluvath Avesh J. , Chen Po-Hung , Thuluvath Paul J. , Kantsevoy Sergey , Savva Yulia 
Published: February 2018

Background
Nonalcoholic steatohepatitis (NASH) cirrhosis is a common indication for liver transplantation (LT) in the United States. There is a paucity of data on retransplantation (re-LT) in those who were initially transplanted for NASH.

Methods
We queried the United Network for Organ Sharing data sets from 2002 to 2016 to analyze the outcomes of adults with NASH (n = 128) and compared them with groups that received re-LT for cryptogenic cirrhosis (n = 189), alcoholic cirrhosis (n = 300) or autoimmune hepatitis cirrhosis (n = 118) after excluding multiple-organ re-LT and individuals with hepatocellular carcinoma. We estimated survival probabilities using a Kaplan-Meier estimator, and a relative risk of patient and graft mortality using proportional hazards regression.

Results
The NASH group was older and had a higher prevalence of obesity, type II diabetes mellitus, renal insufficiency, portal vein thrombosis, and poor performance status. The median interval between the first and the second LT was shorter in the NASH group (27 days). The graft and patient 5-year survival rates were lower for the NASH group after re-LT compared with the other 3 groups. After adjusting for demographic and disease complication factors, the factors that increased a risk of patient or graft failure were a poor performance status (hazard ratio [HR], 1.64; 1.19-2.26), Donor Risk Index (HR, 1.51; 1.08-2.12), and a high Model for End-stage Liver Disease score (HR, 1.02; 1.00-1.04).

Conclusions
Despite the comparable outcomes reported for initial LT among the various etiologies, the outcome of re-LT is significantly worse for NASH cirrhosis.
Enhanced instructed fear learning in delusion-proneness
Authors: Louzolo Anaïs , Almeida Rita , Guitart-Masip Marc , Björnsdotter Malin , Ingvar Martin , Olsson Andreas , Petrovic Predrag 
Published: February 2018

AbstractPsychosis is characterized by distorted perceptions and deficient low-level learning, including reward learning and fear conditioning. This has been interpreted as reflecting imprecise priors in a predictive coding system. However, this idea is not compatible with formation of overly strong beliefs and delusions in psychosis-associated states. A reconciliation of these paradoxical observations is that these individuals actively develop and use higher-order beliefs in order to interpret a chaotic environment. In the present behavioural and fMRI study, we compared delusion-prone individuals (n=20), a trait related to psychotic disorders, with controls (n=23; n=20 in fMRI-part) to study the effect of beliefs on fear learning. We show that instructed fear learning, involving explicit change of beliefs and an associated activation of lateral orbitofrontal cortex, is expressed to a higher degree in delusion-prone subjects. Our results suggest that strong high-level top-down learning co-exists with previously reported weak low-level bottom-up learning in psychosis-associated states.
Dual-layer transposon repression in heads of Drosophila melanogaster
Authors: van den Beek Marius , da Silva Bruno , Pouch Juliette , Ali Chaouche Mohammed el amine , Carré Clément , Antoniewski Christophe 
Published: February 2018

AbstractpiRNA-mediated repression of transposable elements (TE) in the germline limits the accumulation of heritable mutations caused by their transposition in the genome. It is not clear whether the piRNA pathway plays a functional role in adult, non-gonadal tissues in Drosophila melanogaster. To address this question, we first analyzed the small RNA content of adult Drosophila melanogaster heads. We found that varying amount of piRNA-sized, ping-pong positive molecules in heads correlates with contamination by gonadal tissue during RNA extraction, suggesting that most of piRNAs detected in head sequencing libraries originate from gonads. We next sequenced the heads of wild type and piwi mutants to address whether piwi loss of function would affect the low amount of piRNA-sized, ping-pong negative molecules that are still detected in heads hand-checked to avoid gonadal contamination. We find that loss of piwi does not affect significantly these 24-28 RNA molecules. Instead, we observe increased siRNA levels against the majority of Drosophila transposable element families. To determine the effect of this siRNA level change on transposon expression, we sequenced the transcriptome of wild type, piwi, dicer-2 and piwi, dicer-2 double-mutant fly heads. We find that RNA expression levels of the majority of TE families in piwi or dicer-2 mutants remain unchanged and that TE transcript abundance increases significantly only in piwi, dicer-2 double-mutants. These results lead us to suggest a dual-layer model for TE repression in adult somatic tissues. Piwi-mediated transcriptional gene silencing (TGS) established during embryogenesis constitutes the first layer of TE repression whereas Dicer-2-dependent siRNA-mediated post-transcriptional gene silencing (PTGS) provide a backup mechanism to repress TEs that escape silencing by piwi-mediated TGS.
Borderline personality disorder with cocaine dependence: impulsivity, emotional dysregulation and amygdala functional connectivity
Authors: Balducci Thania , Gonzalez-Olvera Jorge J , Angeles-Valdez Diego , Espinoza-Luna Isabel , Garza-Villarreal Eduardo A 
Published: February 2018

AbstractObjective: Borderline personality disorder (BPD) is present in 19% of cocaine dependence (CD) cases; however, this dual pathology (DP) is poorly understood. We assessed impulsivity, emotional dysregulation (ED) and amygdala functional connectivity in this DP.Methods. We recruited 69 participants divided into 4 groups: DP (n = 20), CD without BPD (n = 19), BPD without CD (n = 10) and healthy controls (HC, n = 20). We used self-reported instruments to measure impulsivity and ED. We acquired resting state fMRI and performed seed-based analyses of functional connectivity (FC) of bilateral amygdalas.Results. BPD and CD factors had opposing effects in impulsivity and ED, as well as on FC between left amygdala and medial prefrontal cortex. For the FC between right amygdala and left insula, the effect of having both disorders was additive, reducing FC strength. Significant FC clusters were correlated with impulsivity and ED.Conclusions. In this preliminary study, we found that clinical scores of DP patients were closer to those of BPD without CD than to those of CD without BPD, while amygdala to medial prefrontal cortex FC patterns in DP patients were closer to HC than expected.
Microbial Treatment of Soil Contaminated with Spent engine Oil / Biotreatment of Soil Contaminated with Spent Engine by Microorganisms
Authors: Ayandele A. A. 
Published: February 2018

AbstractThe potential of six microorganisms (Pseudomonas aeruginosa, Micrococcus sp, Flavobacterium sp, Rhizopus sp, Penicillium sp and Fusarium sp) isolated from hydrocarbon contaminated site were evaluated for their biodegradation ability. The soil samples were contaminated with 5% (w/v) of spent engine oil and the rate of biodegradation of the oil was studied for a period of 10weeks under greenhouse experiment. The total heterotrophic bacteria count (THBC), total hydrocarbon degrading bacteria count (THDBC), physicochemical and heavy metals properties of the soil samples and Total Petroleum Hydrocarbon (TPH) were determined after treatment with test organisms. THBC and THDBC ranged from 0.175 to 0.280 CFUg-1 and 0.47 CFUg-1 respectively for the control plot, while THBC is ranging from 0.197 to 0.275 CFUg-1 and THDBC was 0.180 to 0. 473 CFUg-1 for the contaminated plot. There was a slight increase in the pH value of the contaminated soil sample and the treated soil samples as the experimental weeks increased. The results obtained showed a significant decrease (at p ≤ 0.05) in the nutrients content of the soil samples. There was an increase from 1.09 in the control to 15.5% in the content of organic matter after contamination and from 1.88% to 26.8% in the % of organic matter too. There was a significant reduction (at p ≤ 0.05) in the concentration of Fe, Zn, Pb, Cd, Cu, Cr and Ni after 10 weeks of incubation with the tested organisms. Plant growth in the treated contaminated soil samples ranged from 32.6cm to 38.6cm, while that of the control 1 (Uncontaminated soil) was 51.2cm and 19.7cm high was observed in the Control 2 (contaminated untreated soil) after 22 days of the experiment. The TPH degradation (% loss) ranged from 79.7 to 89. 2% after 10 weeks of treatment. P. aeruginosa had the highest level of degradation (89.2%), while Micrococcus sp and Rhizopus sp had the least degradation at 79.9%.All the microorganisms used in this study had the abilities to remediating soil contaminated with spent engine oil and the remediated soil samples were able to support the growth of Zea mays at 5% (w/v) level of contamination.
Early lethality of embryos derived from transgenic Xenopus females is associated with reduced ovarian grem1 expression
Authors: Beck Caroline W. , Ward Joanna , Troise Lisa , Brochard Catherine 
Published: February 2018

AbstractThe grem1 gene codes a protein that inhibits the action of multiple members of a growth factor family known as bone morphogenetic proteins (BMPs). Certain members of this BMP family can regulate both fecundity and fertility in mammals via their action on oocyte (egg) development, and grem1 has been identified as a marker of oocyte quality in humans. The model amphibian Xenopus laevis is far more fecund than mammals, producing thousands of eggs in a clutch. However, female transgenic frogs carrying grem1 under the control of a stress inducible hsp70 promoter (“G” frogs) produce very few viable offspring. Here, we show that this is not due to reduced fecundity or fertilization rate, but results from a significant reduction in subsequent survival over the first day of development. Embryos that successfully survive for the first day were found to go on to develop normally when compared to their peers. Both the morphology and stage distribution of oocytes from G females appears normal, and oocytes develop at expected rates, although stage VI oocytes were found to have a lower response to in vitro progesterone treatment. Unexpectedly, levels of grem1 mRNA were found to be consistently lower in the female ovaries from four independent G transgenic lines than in wild type ovaries. Both transgenic and wild type offspring were equally affected, confirming a maternal effect. Our study shows that transgenic females with the lowest levels of grem1 transcripts in the ovary have the lowest rates of survival past the first day of amphibian embryogenesis, equivalent to pre-implantation staged mammalian embryos. The reduced expression of grem1 in the oocytes of transgenic females suggests transgene supression of an endogenous locus may occur in the Xenopus female germline, an unexpected finding.
Understanding 6th-Century Barbarian Social Organization and Migration through Paleogenomics
Authors: Amorim Carlos Eduardo G. , Vai Stefania , Posth Cosimo , Modi Alessandra , Koncz István , Hakenbeck Susanne , La Rocca Maria Cristina , Mende Balazs , Bobo Dean , Pohl Walter , Baricco Luisella Pejrani , Bedini Elena , Francalacci Paolo , Giostra Caterina , Vida Tivadar , Winger Daniel , von Freeden Uta , Ghirotto Silvia , Lari Martina , Barbujani Guido , Krause Johannes , Caramelli David , Geary Patrick J. , Veeramah Krishna R. 
Published: February 2018

ABSTARCTDespite centuries of research, much about the barbarian migrations that took place between the fourth and sixth centuries in Europe remains hotly debated. To better understand this key era that marks the dawn of modern European societies, we obtained ancient genomic DNA from 63 samples from two cemeteries (from Hungary and Northern Italy) that have been previously associated with the Longobards, a barbarian people that ruled large parts of Italy for over 200 years after invading from Pannonia in 568 CE. Our dense cemetery-based sampling revealed that each cemetery was primarily organized around one large pedigree, suggesting that biological relationships played an important role in these early Medieval societies. Moreover, we identified genetic structure in each cemetery involving at least two groups with different ancestry that were very distinct in terms of their funerary customs. Finally, our data was consistent with the proposed long-distance migration from Pannonia to Northern Italy.
Making honey bees lie: experimental dissociation of flight experience and dance communication
Authors: Chatterjee Arumoy , Prabhudev M.V. , George Ebi A. , Basu Pallab , Brockmann Axel 
Published: February 2018

AbstractHoney bees use their dance to communicate flight distance and direction of a food source to their nest mates in the hive. How bees transpose flight information to generate a corresponding walking (dance) behavior is still unknown. We now present a detailed study of the changes in dance duration of individual bees after shifting feeder distance. Our experiments indicated that most bees needed two or more foraging trips to the new position before showing an updated dance duration. In addition, only a few bees significantly changed dance duration immediately, whereas most bees first produced intermediary durations. Double shift experiments showed that under certain conditions bees do not update dance duration but continued to perform dance duration for the previously visited feeder position. We propose that generation of dance information involves two memory contents one for newly acquired and one for previously stored distance information.One Sentence SummaryGeneration of dance information is temporally separated from immediate flight experience and involves two different memory contents.
Dynamic Network Analysis of the 4D Nucleome
Authors: Liu Sijia , Chen Pin-Yu , Hero Alfred , Rajapakse Indika 
Published: February 2018

AbstractMotivationFor many biological systems, it is essential to capture simultaneously the function, structure, and dynamics in order to form a comprehensive understanding of underlying phenomena. The dynamical interaction between 3D genome spatial structure and transcriptional activity creates a genomic signature that we refer to as the four-dimensional organization of the nucleus, or 4D Nucleome (4DN). The study of 4DN requires assessment of genome-wide structure and gene expression as well as development of new approaches for data analysis.ResultsWe propose a dynamic multilayer network approach to study the co-evolution of form and function in the 4D Nucleome. We model the dynamic biological system as a temporal network with node dynamics, where the network topology is captured by chromosome conformation (Hi-C), and the function of a node is measured by RNA sequencing (RNA-seq). Network-based approaches such as von Neumann graph entropy, network centrality, and multilayer network theory are applied to reveal universal patterns of the dynamic genome. Our model integrates knowledge of genome structure and gene expression along with temporal evolution and leads to a description of genome behavior on a system wide level. We illustrate the benefits of our model via a real biological dataset on MYOD1-mediated reprogramming of human fibroblasts into the myogenic lineage. We show that our methods enable better predictions on form-function relationships and refine our understanding on how cell dynamics change during cellular reprogramming.Availability: The software is available upon request.Contactindikar@umich.eduSupplementary informationSee Supplementary Material.
Delineating feedback activity in the MAPK and AKT pathways using feedback-enabled Inference of Signaling Activity
Authors: Thijssen Bram , Jastrzebski Katarzyna , Beijersbergen Roderick L. , Wessels Lodewyk F.A. 
Published: February 2018

AbstractAn important aspect of cellular signaling networks is the existence of feedback mechanisms. However, due to the complexity of signaling networks, as well as the presence of multiple interrelated feedback events, it can be difficult to identify which signaling routes are active in any particular context. We have previously shown that Inference of Signaling Activity (ISA) can be a useful method to study steady-state oncogenic signaling across different cell lines and inhibitor treatments. However, ISA did not explicitly include feedback signaling events. Incorporating feedback will increase the complexity and computational cost of the model, and more data is likely to be needed to infer feedback activities. Here, we developed feedback-ISA (f-ISA), an extension of the ISA modeling approach which incorporates feedback signaling events. It also includes integrated batch correction in order to fit the models to multiple, independent datasets simultaneously. We find that the identifiability of feedback activities can be counter-intuitive, which shows the importance of analyzing the full, joint uncertainty in model parameters. By iteratively adapting the model and including multiple datasets, including both steady state and intervention data, we constructed a model that can explain a large part of the phosphorylation levels of several signaling molecules in the MAPK and AKT pathways, across many breast cancer cell lines and across various conditions. The resulting model delineates which routes in the signaling network are likely to be active in each cell line and condition, given all of the data. Additionally, such models can indicate whether datasets agree with each other, and identify which parts of the data cannot be explained, thereby highlighting gaps in the current knowledge. We conclude that this modeling approach can be useful to quantitatively understand how complex cellular signaling networks behave across different cell lines and conditions.
Precise Slow Oscillation-Spindle Coupling Promotes Memory Consolidation in Younger and Older Adults
Authors: Muehlroth Beate E. , Sander Myriam C. , Fandakova Yana , Grandy Thomas H. , Rasch Björn , Shing Yee Lee , Werkle-Bergner Markus 
Published: February 2018

AbstractMemory consolidation during sleep relies on the precisely timed interaction of rhythmic neural events. Here, we investigate differences in slow oscillations (SO) and sleep spindles (SP) and their coupling across the adult human lifespan and ask whether observed alterations relate to the ability to retain associative memories across sleep. We demonstrate that the fine-tuned SO–SP coupling that is present in younger adults diffuses with advanced age and shifts both in time and frequency. Crucially, we show that the tight precision of SO–SP coupling promotes memory consolidation in younger and older adults, and that brain integrity in source regions for the generation of SOs and SPs reinforces this beneficial SO–SP coupling in old age. Our results reveal age-related differences in SO–SP coupling in healthy elderly individuals. Furthermore, they broaden our understanding of the conditions and the functional significance of SO–SP coupling across the entire adult lifespan.
Identification and Structure-Activity Relationship of HDAC6 Zinc-finger Ubiquitin Binding Domain Inhibitors
Authors: de Freitas Renato Ferreira , Harding Rachel J. , Franzoni Ivan , Ravichandran Mani , Mann Mandeep K. , Ouyang Hui , Lautens Mark , Santhakumar Vjayaratnam , Arrowsmith Cheryl H. , Schapira Matthieu 
Published: February 2018

AbstractHDAC6 plays a central role in the recruitment of protein aggregates for lysosomal degradation, and is a promising target for combination therapy with proteasome inhibitors in multiple myeloma. Pharmacologically displacing ubiquitin from the zinc-finger ubiquitin-binding domain (ZnF-UBD) of HDAC6 is an underexplored alternative to catalytic inhibition. Here, we present the discovery of a HDAC6 ZnF-UBD-focused chemical series and its progression from virtual screening hits to low micromolar inhibitors. A carboxylate mimicking the C-terminal extremity of ubiquitin, and an extended aromatic system stacking with W1182 and R1155 are necessary for activity. One of the compounds induced a conformational remodeling of the binding site where the primary binding pocket opens-up onto a ligand-able secondary pocket that may be exploited to increase potency. The preliminary structure-activity relationship accompanied by nine crystal structures should enable further optimization into a chemical probe to investigate the merit of targeting the ZnF-UBD of HDAC6 in multiple myeloma and other diseases.
Validation of Davson’s equation in patients suffering from idiopathic Normal Pressure Hydrocephalus
Authors: Lalou Afroditi-Despina , Levrini Virginia , Garnett Matthew , Nabbanja Eva , Kim Dong-Joo , Gergele Laurent , Bjornson Anna , Czosnyka Zofia , Czosnyka Marek 
Published: February 2018

AbstractIntroductionThe so called Davson’s equation relates baseline intracranial pressure (ICP) to resistance to cerebrospinal fluid outflow (Rout), formation of cerebrospinal fluid (If) and sagittal sinus pressure (PSS) There is a controversy over whether this fundamental equation is applicable in patients with normal pressure hydrocephalus (NPH). We investigated the relationship between Rout and ICP and also other compensatory, clinical and demographic parameters in NPH patients.MethodWe carried out a retrospective study of 229 patients with primary NPH who had undergone constant-rate infusion studies in our hospital. Data was recorded and processed using ICM+ software. Relationships between variables were sought by calculating Pearson product correlation coefficients and p values.ResultsWe found a significant, albeit weak, relationship between ICP and Rout (R=0.17, p=0.0049), Rout and peak-to-peak amplitude of ICP (AMP) (R=0.27, p=3.577e−05) and Rout and age (R=0.16, p=0.01306).ConclusionsThe relationship found between ICP and Rout provides indirect evidence to support disturbed Cerebrospinal fluid circulation as a key factor in disturbed CSF dynamics in NPH. Weak correlation may indicate that other factors: variable Pss and formation of CSF outflow contribute heavily to linear model expressed by Davson’s equation.
Relative Patlak Plot for Dynamic PET Parametric Imaging Without the Need for Early-time Input Function
Authors: Zuo Yang , Qi Jinyi , Wang Guobao 
Published: February 2018

AbstractThe Patlak graphical method is widely used in parametric imaging for modeling irreversible radiotracer kinetics in dynamic PET. The net influx rate of radiotracer can be determined from the slope of the Patlak plot. The implementation of the standard Patlak method requires the knowledge of full-time input function from the injection time until the scan end time, which presents a challenge for use in the clinic. This paper proposes a new relative Patlak plot method that does not require early-time input function and therefore can be more efficient for parametric imaging. Theoretical analysis proves that the effect of early-time input function is a constant scaling factor on the Patlak slope estimation. Thus, the parametric image of the slope of the relative Patlak plot is related to the parametric image of standard Patlak slope by a global scaling factor. This theoretical finding has been further demonstrated by computer simulation and real patient data. The study indicates that parametric imaging of the relative Patlak slope can be used as a substitute of parametric imaging of standard Patlak slope for certain clinical tasks such as lesion detection and tumor volume segmentation.