julilili42/papers huggingface dataset:
The anterior insula channels prefrontal expectancy signals during affective processing
2019-02-04

Abstract Expectancy shapes our perception of impending events. Although such an interplay between cognitive and affective processes is often impaired in mental disorders, it is not well understood how top-down expectancy signals modulate future affect. We therefore track the information flow in the brain during cognitive and affective processing segregated in time using task-specific cross-correlations. Participants in two independent fMRI studies (N 1 = 37 &amp; N 2 = 55) were instructed to imagine a situation with affective content as indicated by a cue, which was then followed by an emotional picture congruent with expectancy. To correct for intrinsic covariance of brain function, we calculate resting-state cross-correlations analogous to the task. First, using factorial modeling of delta cross-correlations (task-rest) of the first study, we find that the magnitude of expectancy signals in the anterior insula cortex (AIC) modulates the BOLD response to emotional pictures in the anterior cingulate and dorsomedial prefrontal cortex in opposite directions. Second, using hierarchical linear modeling of lagged connectivity, we demonstrate that expectancy signals in the AIC indeed foreshadow this opposing pattern in the prefrontal cortex. Third, we replicate the results in the second study using a higher temporal resolution, showing that our task-specific cross-correlation approach robustly uncovers the dynamics of information flow. We conclude that the AIC arbitrates the recruitment of distinct prefrontal networks during cued picture processing according to triggered expectations. Taken together, our study provides new insights into neuronal pathways channeling cognition and affect within well-defined brain networks. Better understanding of such dynamics could lead to new applications tracking aberrant information processing in mental disorders.
Supplementary material to "Detection and Explanation of Spatiotemporal Patterns in Late Cenozoic Palaeoclimate Change Relevant to Earth Surface Processes"
2019-02-04

Large scale patterns and modes of climate changeThe geographical subdivisions of South Alaska in the LGM and PLIO (Fig. S10 b,c) results are more stable than clusters calculated for the MH.LGM-C1 and LGM-C2 experience a strong decrease in 2m air temperature, air temperature amplitude and freeze-thaw days, as well as increases in consecutive freezing days and meridional wind speeds (Fig. S10 e).LGM-C4 is the only cluster not covered with ice during the LGM, and characterised by increases in consecutive dry days and 2m air temperature amplitude, and decreases in consecutive wet days, maximum precipitation and zonal wind speeds (Fig. S10 e).The geographically dominant modes of changes in the PLIO are PLIO-C3 and PLIO-C4.The former is has a more continental setting and is characterised by increases in consecutive wet days, maximum precipitation, 2m air temperature, while the latter is a mode of change observed in greater coastal proximity and characterised by moderate increases in 2m air temperature and zonal wind speeds only (Fig. S10 f). DiscriminabilityClusters in the LGM and PLIO are associated with higher discrimination scores than the MH.LGM-C2 andLGM-C3 have the highest discriminability cause primarily by changes in meridional winds (30%-40%) and maximum precipitation (40%-50%) and consecutive freezing days (10%-20%) respectively (Fig. S10 e).PLIO-C1 and PLIO-C2 show highest discriminability in the PLIO, which is contributed to most by 2m air temperature amplitude (Fig. S10 f).
Brain-Machine Interface in Chronic Stroke: Randomized Trial Long-Term Follow-up
2019-02-05

Background. Brain-machine interfaces (BMIs) have been recently proposed as a new tool to induce functional recovery in stroke patients. Objective. Here we evaluated long-term effects of BMI training and physiotherapy in motor function of severely paralyzed chronic stroke patients 6 months after intervention. Methods. A total of 30 chronic stroke patients with severe hand paresis from our previous study were invited, and 28 underwent follow-up assessments. BMI training included voluntary desynchronization of ipsilesional EEG-sensorimotor rhythms triggering paretic upper-limb movements via robotic orthoses (experimental group, n = 16) or random orthoses movements (sham group, n = 12). Both groups received identical physiotherapy following BMI sessions and a home-based training program after intervention. Upper-limb motor assessment scores, electromyography (EMG), and functional magnetic resonance imaging (fMRI) were assessed before (Pre), immediately after (Post1), and 6 months after intervention (Post2). Results. The experimental group presented with upper-limb Fugl-Meyer assessment (cFMA) scores significantly higher in Post2 (13.44 ± 1.96) as compared with the Pre session (11.16 ± 1.73; P = .015) and no significant changes between Post1 and Post2 sessions. The Sham group showed no significant changes on cFMA scores. Ashworth scores and EMG activity in both groups increased from Post1 to Post2. Moreover, fMRI-BOLD laterality index showed no significant difference from Pre or Post1 to Post2 sessions. Conclusions. BMI-based rehabilitation promotes long-lasting improvements in motor function of chronic stroke patients with severe paresis and represents a promising strategy in severe stroke neurorehabilitation.
HIF-1α-Deficiency in Myeloid Cells Leads to a Disturbed Accumulation of Myeloid Derived Suppressor Cells (MDSC) During Pregnancy and to an Increased Abortion Rate in Mice
2019-02-05

Abortions are the most important reason for unintentional childlessness. During pregnancy, maternal immune cells are in close contact to cells of the semi-allogeneic fetus. Dysregulation of the maternal immune system leading to defective adaptation to pregnancy often plays a role in pathogenesis of abortions. Myeloid-derived suppressor cells (MDSC) are myeloid cells that suppress functions of other immune cells, especially T-cells, thereby negatively affecting diseases such as cancer, sepsis or trauma. They seem, however, also necessary for maintenance of maternal-fetal tolerance. Mechanisms regulating MDSC expansion and function during pregnancy are only incompletely understood. In tumor environment, hypoxia is crucial for MDSC accumulation and activation. Hypoxia is also important for early placenta and embryo development. Effects of hypoxia are mediated through hypoxia-inducible factor 1α (HIF-1α). In the present study we aimed to examine the role of HIF-1α in myeloid cells for MDSC accumulation and MDSC function during pregnancy and for pregnancy outcome. We therefore used a mouse model with targeted deletion of HIF-1α in myeloid cells (myeloid HIF-KO) and analyzed blood, spleens and uteri of pregnant mice at gestational day E 10.5 in comparison to non-pregnant animals and wildtype (WT) animals. Further we analyzed pregnancy success by determining rates of failed implantation and abortion in WT and myeloid HIF-KO animals. We found that myeloid HIF-KO in mice led to an abrogated MDSC accumulation in the pregnant uterus and to impaired suppressive activity of MDSC. While expression of chemokine receptors and integrins on MDSC was not affected by HIF-1α, myeloid HIF-KO led to increased apoptosis rates of MDSC in the uterus. Myeloid-HIF-KO resulted in increased proportions of non-pregnant animals after positive vaginal plug and increased abortion rates, suggesting that activation of HIF-1α dependent pathways in MDSC are important for maintenance of pregnancy.
Development of a Bioelectrochemical System as a Tool to Enrich H2-Producing Syntrophic Bacteria
2019-02-05

Syntrophic microbial partnerships are found in many environments and play critical roles in wastewater treatment, global nutrient cycles, and gut systems. An important type of syntrophy for the anaerobic conversion of carboxylic acids is H<sub>2</sub> syntrophy. In this type of microbial partnership, dissolved H<sub>2</sub> is produced by a bacterium and rapidly consumed by an archeon (methanogen), resulting in methane gas. This is referred to as interspecies H<sub>2</sub> transfer, and some conversions rely on this mechanism to become thermodynamically feasible. For this reason, syntrophic partners are often not possible to separate in the lab, which hampers the full understanding of their physiology. Bioelectrochemical systems (BESs) may show promise to ultimately separate and study the behavior of the syntrophic bacterium by employing an abiotic H<sub>2</sub> oxidation reaction at the anode, actively removing dissolved H<sub>2</sub>. Here, we performed a proof-of-concept study to ascertain whether an H<sub>2</sub>-removing anode can: (1) provide a growth advantage for the syntrophic bacterium; and (2) compete with the methanogenic partner. A mathematical model was developed to design a BES to perform competition experiments. Indeed, the operated BES demonstrated the ability to provide a growth advantage to the syntrophic bacterium <i>Syntrophus aciditrophicus</i> compared to its methanogenic partner <i>Methanospirillum hungatei</i> when grown in co-culture. Further, the BES provided the never-before isolated <i>Syntrophomonas zehnderi</i> with a growth advantage compared to <i>Methanobacterium formicicum</i>. Our results demonstrate a potential to use this BES to enrich H<sub>2</sub>-sensitive syntrophic bacteria, and gives prospects for the development of an effective method for the separation of obligate syntrophs.
XOC: Explainable Observer-Classifier for Explainable Binary Decisions.
2019-02-05

Explanations help develop a better understanding of the rationale behind the predictions of a deep neural network and improve trust. We propose an explainable observer-classifier framework that exposes the steps taken through the decision-making process in a transparent manner. Instead of assigning a label to an image in a single step, our model makes iterative binary sub-decisions, and as a byproduct reveals a decision tree in the form of an introspective explanation. In addition, our model creates rationalizations as it assigns each binary decision a semantic meaning in the form of attributes imitating human-annotations. On six benchmark datasets with increasing size and granularity, our model outperforms classical decision-trees and generates easy-to-understand binary decision sequences explaining the network's predictions.
Tissue‐specific study across the stem reveals the chemistry and transcriptome dynamics of birch bark
2019-02-06

Summary Tree bark is a highly specialized array of tissues that plays important roles in plant protection and development. Bark tissues develop from two lateral meristems; the phellogen (cork cambium) produces the outermost stem–environment barrier called the periderm, while the vascular cambium contributes with phloem tissues. Although bark is diverse in terms of tissues, functions and species, it remains understudied at higher resolution. We dissected the stem of silver birch ( Betula pendula ) into eight major tissue types, and characterized these by a combined transcriptomics and metabolomics approach. We further analyzed the varying bark types within the Betulaceae family. The two meristems had a distinct contribution to the stem transcriptomic landscape. Furthermore, inter‐ and intraspecies analyses illustrated the unique molecular profile of the phellem. We identified multiple tissue‐specific metabolic pathways, such as the mevalonate/betulin biosynthesis pathway, that displayed differential evolution within the Betulaceae. A detailed analysis of suberin and betulin biosynthesis pathways identified a set of underlying regulators and highlighted the important role of local, small‐scale gene duplication events in the evolution of metabolic pathways. This work reveals the transcriptome and metabolic diversity among bark tissues and provides insights to its development and evolution, as well as its biotechnological applications.
New short-term heat inactivation method of cytomegalovirus (CMV) in breast milk: impact on CMV inactivation, CMV antibodies and enzyme activities
2019-02-06

Objectives Breast milk (BM) is the primary source of cytomegalovirus (CMV) transmission to premature infants with potentially harmful consequences. We therefore wanted to evaluate temperature and duration of short-term BM pasteurisation with respect to CMV inactivation, effect on CMV-IgG antibodies and BM enzyme activities. Methods 116 artificially CMV-spiked BM and 15 wild-type virus-infected samples were subjected for 5 s to different temperatures (55°C–72°C). CMV-IE-1 expression in fibroblast nuclei was assessed using the milk whey fraction in short-term microculture. BM lipase and alkaline phosphatase (AP) activities and CMV binding using CMV-recomLine immunoblotting and neutralising antibodies using epithelial target cells were analysed before and after heating. Results A minimum of 5 s above 60°C was necessary for CMV inactivation in both CMV-AD-169 spiked and wild-type infected BM. Lipase was very heat sensitive (activities of 54% at 55°C, 5% at 60°C and 2% at 65°C). AP showed activities of 77%, 88% and 10%, respectively. CMV-p150 IgG antibodies were mostly preserved at 62°C for 5 s. Conclusion Our results show that short-term pasteurisation of BM at 62°C for 5 s might be efficient for CMV inactivation and reduces loss of enzyme activities, as well as CMV binding, and functional CMV antibodies.
Randomized phase-II trial evaluating induction therapy with idarubicin and etoposide plus sequential or concurrent azacitidine and maintenance therapy with azacitidine
2019-02-06

The aim of this randomized phase-II study was to evaluate the effect of substituting cytarabine by azacitidine in intensive induction therapy of patients with acute myeloid leukemia (AML). Patients were randomized to four induction schedules for two cycles: STANDARD (idarubicin, cytarabine, etoposide); and azacitidine given prior (PRIOR), concurrently (CONCURRENT), or after (AFTER) therapy with idarubicin and etoposide. Consolidation therapy consisted of allogeneic hematopoietic-cell transplantation or three courses of high-dose cytarabine followed by 2-year maintenance therapy with azacitidine in the azacitidine-arms. AML with CBFB-MYH11, RUNX1-RUNX1T1, mutated NPM1, and FLT3-ITD were excluded and accrued to genotype-specific trials. The primary end point was response to induction therapy. The statistical design was based on an optimal two-stage design applied for each arm separately. During the first stage, 104 patients (median age 62.6, range 18-82 years) were randomized; the study arms PRIOR and CONCURRENT were terminated early due to inefficacy. After randomization of 268 patients, all azacitidine-containing arms showed inferior response rates compared to STANDARD. Event-free and overall survival were significantly inferior in the azacitidine-containing arms compared to the standard arm (p < 0.001 and p = 0.03, respectively). The data from this trial do not support the substitution of cytarabine by azacitidine in intensive induction therapy.
Off-Pump Coronary Artery Bypass Grafting in Acute Coronary Syndrome: Focus on Safety and Completeness of Revascularization
2019-02-06

Abstract Background Emergency coronary artery bypass grafting (CABG) in the setting of acute coronary syndrome (ACS) has been associated with increased morbidity and mortality. Avoiding cardiopulmonary bypass might be advantageous, but the role of off-pump CABG (OPCAB) remains controversial, as it has been associated with incomplete revascularization in several studies. The objective of this study was to evaluate the feasibility, efficacy, and outcome of OPCAB surgery in ACS patients. Methods We performed a retrospective review of ACS patients who underwent on-pump CABG (ONCAB) or OPCAB, either emergently or delayed, at our institution. Results Between January 2015 and December 2016, a total of 205 consecutive ACS patients underwent either ONCAB (109 patients, 53.2%) or OPCAB surgery (96 patients, 46.8%). EuroSCORE II levels (5.6 ± 7.2 vs 4.9 ± 6.5, p = 0.226) and demography were comparable between groups. A trend towards lower postoperative mortality was observed in OPCAB patients (2.1 vs 5.5%). The incidence of postoperative stroke and low cardiac output syndrome, as well as the duration of inotropic support and the need for re-sternotomy, was significantly lower in the OPCAB group (p &lt; 0.05). CABG performed instantly in an emergency situation was not associated with increased mortality or morbidity when compared with delayed procedures, and OPCAB surgery in emergency patients was associated with lower postoperative morbidity and shorter stays in the intensive care unit (p &lt; 0.05). There were no differences in completeness of revascularization between groups (median 1 [1–1.33;0.33–1.67] OPCAB versus median 1 (1–1.33;0.67–2) ONCAB, p = 0.617), even in the emergency setting. Conclusion OPCAB surgery is safe and effective in ACS and may be considered in hemodynamically stable patients in the emergency setting.
Development of Modular, Dual-Perfused Osteochondral Constructs for Cartilage Repair
2019-02-06

This study describes methods for fabricating, culturing, and characterizing modular microbeads containing progenitor cells that can be used to create osteochondral tissue constructs. Such biphasic engineered tissues were cultured in a low flow rate perfusion bioreactor chamber to maintain tissue-specific differentiation while allowing development of the osteochondral interface.
The FtsK-like motor TraB is a DNA-dependent ATPase that forms higher-order assemblies
2019-02-06

TraB is an FtsK-like DNA translocase responsible for conjugative plasmid transfer in mycelial <i>Streptomyces</i> Unlike other conjugative systems, which depend on a type IV secretion system, <i>Streptomyces</i> requires only TraB protein to transfer the plasmid as dsDNA. The γ-domain of this protein specifically binds to repeated 8-bp motifs on the plasmid sequence, following a mechanism that is reminiscent of the FtsK/SpoIIIE chromosome segregation system. In this work, we purified and characterized the enzymatic activity of TraB, revealing that it is a DNA-dependent ATPase that is highly stimulated by dsDNA substrates. Interestingly, we found that unlike the SpoIIIE protein, the γ-domain of TraB does not confer sequence-specific ATPase stimulation. We also found that TraB binds G-quadruplex DNA structures with higher affinity than TraB-recognition sequences (TRSs). An EM-based structural analysis revealed that TraB tends to assemble as large complexes comprising four TraB hexamers, which might be a prerequisite for DNA translocation across cell membranes. In summary, our findings shed light on the molecular mechanism used by the DNA-translocating motor TraB, which may be shared by other membrane-associated machineries involved in DNA binding and translocation.
Long-term outcome after allogeneic hematopoietic cell transplantation for myelofibrosis
2019-02-07

Allogeneic hematopoietic stem cell transplant remains the only curative treatment for myelofibrosis. Most post-transplantation events occur during the first two years and hence we aimed to analyze the outcome of 2-year disease-free survivors. A total of 1055 patients with myelofibrosis transplanted between 1995 and 2014 and registered in the registry of the European Society for Blood and Marrow Transplantation were included. Survival was compared to the matched general population to determine excess mortality and the risk factors that are associated. In the 2-year survivors, disease-free survival was 64% (60-68%) and overall survival was 74% (71-78%) at ten years; results were better in younger individuals and in women. Excess mortality was 14% (8-21%) in patients aged <45 years and 33% (13-53%) in patients aged ≥65 years. The main cause of death was relapse of the primary disease. Graft-<i>versus</i>-host disease (GvHD) before two years decreased the risk of relapse. Multivariable analysis of excess mortality showed that age, male sex recipient, secondary myelofibrosis and no GvHD disease prior to the 2-year landmark increased the risk of excess mortality. This is the largest study to date analyzing long-term outcome in patients with myelofibrosis undergoing transplant. Overall it shows a good survival in patients alive and in remission at two years. However, the occurrence of late complications, including late relapses, infectious complications and secondary malignancies, highlights the importance of screening and monitoring of long-term survivors.
Effect of laparoscopic endometrioma cystectomy on anti-Müllerian hormone (AMH) levels
2019-02-07

Objective: To investigate temporary or long-term changes of AMH after laparoscopic endometrioma cystectomy and its dependency on characteristics of endometriomas.Methods: One hundred and seventy-one women, open-labeled prospective study; five groups divided according age ≤/> 35, uni-/bilateral, cyst ≤/> 7 cm, coagulation/suture surgery, stage III/IV; between- and within-group analyses after 1, 3, 6, and 12 months.Results: After 12 months, compared to pretreament, AMH decreased significantly for patients with bilateral cysts, cyst size >7 cm and endometriosis stage IV. In the between-group analysis all comparisons were significant, with exception of the surgery type. However, this was different performing the multiple linear regression analysis suggesting lower postoperative decrease using suturing technique. This analysis also showed higher age at pretreatment and bilateral cysts as risk factor for AMH decline.Conclusions: Effects of endometrioma cystectomy on AMH are dependent on characteristics of the endometrioma, showing long-term a decrease in patients with larger, bilateral cysts and in stage IV endometriosis, but only short-time decrease in smaller, unilateral cysts and stage III which sometimes also can fully recover in AMH production within one year. In our study suture compared to coagulation surgery was protective, i.e. may lead to lower postoperative AMH decline.
Evolution of the eyes of vipers with and without infrared-sensing pit organs
2019-02-07

We examined lens and brille transmittance, photoreceptors, visual pigments, and visual opsin gene sequences of viperid snakes with and without infrared-sensing pit organs. Ocular media transmittance was high in both groups. Contrary to previous reports, both small and large single cones occur in pit vipers. Non-pit vipers differ from pit vipers in having a two-tiered retina, but few taxa have been examined for this poorly understood feature. All vipers sampled express rh1, sws1 and lws visual opsin genes. Opsin spectral tuning varies but not in accordance with the presence/absence of pit organs, and not always as predicted from gene sequences. The visual opsin genes were generally under purifying selection, with positive selection at spectral tuning amino acids in RH1 and SWS1 opsins, and at retinal pocket stabilization sites in RH1 or LWS (and without substantial differences between pit and non-pit vipers). A lack of evidence for a sensory trade-off between viperid eyes (in the aspects examined) and pit organs might be explained by the high degree of neural integration of vision and infrared detection; the latter represents an elaboration of an existing sense with addition of a novel sense organ, rather than involving the evolution of a wholly novel sensory system.