bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plasticity of archaeal C/D box sRNA biogenesis
Authors: Tripp Vanessa , Martin Roman , Orell Alvaro , Alkhnbashi Omer S. , Backofen Rolf , Randau Lennart 
Published: October 2016

SummaryArchaeal and eukaryotic organisms contain sets of C/D box s(no)RNAs with guide sequences that determine ribose 2′‐O‐methylation sites of target RNAs. The composition of these C/D box sRNA sets is highly variable between organisms and results in varying RNA modification patterns which are important for ribosomal RNA folding and stability. Little is known about the genomic organization of C/D box sRNA genes in archaea. Here, we aimed to obtain first insights into the biogenesis of these archaeal C/D box sRNAs and analyzed the genetic context of more than 300 archaeal sRNA genes. We found that the majority of these genes do not possess independent promoters but are rather located at positions that allow for co‐transcription with neighboring genes and their start or stop codons were frequently incorporated into the conserved boxC and D motifs. The biogenesis of plasmid‐encoded C/D box sRNA variants was analyzed in vivo in Sulfolobus acidocaldarius. It was found that C/D box sRNA maturation occurs independent of their genetic context and relies solely on the presence of intact RNA kink‐turn structures. The observed plasticity of C/D box sRNA biogenesis is suggested to enable their accelerated evolution and, consequently, allow for adjustments of the RNA modification landscape.
Physical activity and obesity: what we know and what we need to know*
Authors: Chin S.‐H. , Kahathuduwa C. N. , Binks M. 
Published: October 2016

SummaryCreating a negative energy balance by decreasing caloric consumption and increasing physical activity is a common strategy used to treat obesity. A large number of review and original research papers have considered the role of physical activity in weight loss and maintenance. However, their conclusions are at times conflicting. In this review, we have critically evaluated the findings of systematic reviews and meta‐analyses and supplemented their conclusions with recently published, high‐quality clinical trials. We have eliminated studies that were methodologically flawed in an attempt to reduce the ambiguity in the literature. We further sought, through selective review of these publications, to isolate the effects of various types of exercise, independent of dietary interventions, to further clarify their independent contributions. Thus, our review describes (i) combined calorie restriction with physical activity interventions, (ii) physical activity interventions without calorie restriction and (iii) the role of physical activity on maintenance of weight loss. Through this critical examination of the literature, we have provided conclusions to address certain ambiguities regarding the role of physical activity in obesity treatment that will inform clinical practice. We have also identified several long‐standing gaps in knowledge that will inform future research.
Adaptive emotion regulation mediates the relationship between self‐compassion and depression in individuals with unipolar depression
Authors: Diedrich Alice , Burger Julian , Kirchner Mareike , Berking Matthias 
Published: October 2016

ObjectivesTo identify the mechanisms involved in the association between self‐compassion and depression, we examined whether adaptive emotion regulation would mediate the relationship between self‐compassion and depression in individuals with unipolar depression. Furthermore, we explored which specific emotion regulation skills would be most important in this relationship.Design and methodSixty‐nine individuals with unipolar depression were assessed with the Self‐Compassion Scale and the Emotion Regulation Skills Questionnaire at baseline and with the Beck Depression Inventory‐II 1 week later.ResultsThe results showed that successful application of emotion regulation skills mediates the association between self‐compassion and depression. Among eight specific emotion regulation skills, only the ability to tolerate negative emotions was identified as a significant mediator in the self‐compassion–depression relationship.ConclusionsThese findings provide preliminary evidence that systematically fostering self‐compassion might help depressed individuals cope with their symptoms by enhancing their abilities to tolerate undesired emotions.Practitioner points

Systematically fostering self‐compassion through specific compassion‐focused interventions might facilitate a reduction in depressive symptoms by improving the person's emotion regulation abilities, especially by improving his or her ability to tolerate negative emotions.

Hence, compassion‐focused interventions might be particularly promising in depressed patients with a tendency to avoid negative emotions and deficits in tolerating them.
Therapeutic conversations: Therapists’ use of observational language contributes to optimal therapeutic outcomes
Authors: Banham James A. , Schweitzer Robert D. 
Published: October 2016

ObjectiveReflexivity is the process of critically examining one's own experience. Emerging literature suggests that reflexivity is a positive predictor of outcomes in psychotherapy. However, limited research has been conducted regarding therapists’ use of reflexivity as a therapeutic technique. In particular, we have a limited understanding of how therapists use language to initiate reflexive conversations. This study investigates the characteristics of therapist language that elicit reflexivity focused on internal and external processes.Design and MethodsTherapeutic outcomes of 42 trainee‐therapists who provided psychotherapy to 173 clients were tracked with the OQ‐45.2 with the view of identifying client–trainee‐therapist dyads (CTTDs) with the best and poorest outcomes. Six best outcome and six poorest outcome CTTDs were identified. Thirty‐six therapy transcripts were initially coded with the Narrative Process Coding System to identify each Narrative Process Mode (NPM). Sixty external, internal, and reflexive NPMs (N = 180 NPMs) were randomly selected across all therapy transcripts for the best outcome group and the same number for the poorest outcome group. The Narrative Initiating Language Element Coding Manual, developed for this study, was used to code therapists’ use of language to initiate each NPM.ResultsTherapists belonging to the best outcome group utilized more observational language to initiate internal and reflexive NPMs. Therapists belonging to the poorest outcome group evidenced high proportions of questioning language to elicit each NPM.ConclusionsExamining how therapists use language to elicit NPMs provides further insight as to how therapeutic language may contribute to successful therapeutic outcomes.Practitioner points

Reflexive therapeutic conversations characterized by a greater use of observational language were associated with positive therapeutic outcomes.

Therapeutic conversations characterized by a high proportion of questioning language were associated with poorer therapeutic outcomes.

Supervisors of trainee‐therapists have a key role in coaching supervisees to use language that contributes to client treatment outcomes.
Targeted use of prednisolone with the second IVIG dose for refractory Kawasaki disease
Authors: Kimura Mitsuaki , Harazaki Masashi , Fukuoka Tetsuya , Asakura Isao , Sakai Hidemasa , Kamimaki Tsutomu , Ohkawara Ichiro , Akiyama Naoe , Tsurui Satoshi , Iwashima Satoru , Shimomura Masaki , Morishita Hideaki , Meguro Takaaki , Seto Shiro 
Published: October 2016

AbstractBackgroundPrednisolone (PSL) has been suggested to be useful for the treatment of Kawasaki disease (KD) resistant to i.v. immunoglobulin (IVIG), but much remains to be elucidated regarding its use.MethodsA total of 1087 subjects were involved in a two‐study multicenter prospective investigation of the effects of acute phase therapy on IVIG‐resistant KD. Subjects resistant to the first dose of IVIG were classified into high (≥10 mg/dL) and low (<10 mg/dL) serum C‐reactive protein (CRP) groups after the first dose of IVIG.ResultsIn the first study, the efficacy of the second dose of IVIG in the high CRP group was significantly lower than in the low CRP group (47.8% vs 76.8%, P < 0.005). In the second study, PSL was co‐administered with the second dose of IVIG to the high CRP patients (intensified regimen). The efficacy of the intensified regimen was similar to that of the second dose of IVIG in the low CRP group (79.4% vs 83.3%). Although the difference in the incidence of persistent coronary artery lesions (CAL) between the high and low CRP groups was significant in the first study (19.6% vs 3.0%, P < 0.005), it was not significant in the second study (8.8% vs 2.4%).ConclusionsThe targeted use of PSL with the second dose of IVIG in KD patients resistant to the first dose of IVIG and who are predicted to be resistant to the second dose of IVIG, appears to be effective.
Prevalence and outcomes of diaphragmatic dysfunction assessed by ultrasound technology during acute exacerbation of COPD: A pilot study
Authors: Antenora Federico , Fantini Riccardo , Iattoni Andrea , Castaniere Ivana , Sdanganelli Antonia , Livrieri Francesco , Tonelli Roberto , Zona Stefano , Monelli Marco , Clini Enrico M. , Marchioni Alessandro 
Published: October 2016

ABSTRACTBackground and objectiveThe prevalence and clinical consequences of diaphragmatic dysfunction (DD) during acute exacerbations of COPD (AECOPD) remain unknown. The aim of this study was (i) to evaluate the prevalence of DD as assessed by ultrasonography (US) and (ii) to report the impact of DD on non‐invasive mechanical ventilation (NIV) failure, length of hospital stay and mortality in severe AECOPD admitted to respiratory intensive care unit (RICU).MethodsForty‐one consecutive AECOPD patients with respiratory acidosis admitted over a 12‐month period to the RICU of the University Hospital of Modena were studied. Diaphragmatic ultrasound (DU) was performed on admission before starting NIV. A change in diaphragmatic thickness (ΔTdi) less than 20% during spontaneous breathing was considered to confirm the presence of dysfunction (DD+). NIV failure and other clinical outcomes (duration of mechanical ventilation MV, tracheostomy, length of hospital stay and mortality) were recorded.ResultsA total of 10 out of 41 patients (24.3%) presented DD+, which was significantly associated with steroid use (P = 0.002, R‐squared = 0.19). DD+ correlated with NIV failure (P < 0.001, R‐squared = 0.27), longer intensive care unit (ICU) stay (P = 0.02, R‐squared = 0.13), prolonged MV (P = 0.023, R‐squared = 0.15) and need for tracheostomy (P = 0.006, R‐squared = 0.20). Moreover, the Kaplan–Meyer survival estimates showed that NIV failure (log‐rank test P value = 0.001, HR = 8.09 (95% CI: 2.7–24.2)) and mortality in RICU (log‐rank test P value = 0.039, HR = 4.08 (95% CI: 1.0–16.4)) were significantly associated with DD+.ConclusionIn hospitalized AECOPD patients submitted to NIV, severe DD was seen in almost one‐quarter of patients. DD may cause NIV failure, and impacts on the use of clinical resources and on the patient's short‐term mortality.
Choline transporter‐like1 (CHER1) is crucial for plasmodesmata maturation in Arabidopsis thaliana
Authors: Kraner Max E. , Link Katrin , Melzer Michael , Ekici Arif B. , Uebe Steffen , Tarazona Pablo , Feussner Ivo , Hofmann Jörg , Sonnewald Uwe 
Published: October 2016

SummaryPlasmodesmata (PD) are microscopic pores connecting plant cells and enable cell‐to‐cell transport. Currently, little information is known about the molecular mechanisms regulating PD formation and development. To uncover components of PD development we made use of the 17 kDa movement protein (MP17) encoded by the Potato leafroll virus (PLRV). The protein is required for cell‐to‐cell movement of the virus and localises to complex PD. Forward genetic screening for Arabidopsis mutants with altered PD binding of MP17 revealed several mutant lines, while molecular genetics, biochemical and microscopic studies allowed further characterisation. Map‐based cloning of one mutant revealed a point mutation in the choline transporter‐like 1 (CHER1) protein, changing glycine247 into glutamate. Mutation in CHER1 resulted in a starch excess phenotype and stunted growth. Ultrastructure analysis of shoot apical meristems, developing and fully developed leaves showed reduced PD numbers and the absence of complex PD in fully developed leaves. This indicates that cher1 mutants are impaired in PD formation and development. Global lipid profiling revealed only slight modifications in the overall lipid composition, however, altered composition of PD‐associated lipids cannot be ruled out. Thus, cher1 is devoid of complex PD in developed leaves and provides insights into the formation of complex PD at the molecular level.
The evolution of plant microRNAs: insights from a basal eudicot sacred lotus
Authors: Shi Tao , Wang Kun , Yang Pingfang 
Published: October 2016

SummarymicroRNAs (miRNAs) are important noncoding small RNAs that regulate mRNAs in eukaryotes. However, under which circumstances different miRNAs/miRNA families exhibit different evolutionary trajectories in plants remains unclear. In this study, we sequenced the small RNAs and degradome from a basal eudicot, sacred lotus (Nelumbo nucifera or lotus), to identify miRNAs and their targets. Combining with public miRNAs, we predicted 57 pre‐eudicot miRNA families from different evolutionary stages. We found that miRNA families featuring older age, higher copy and target number tend to show lower propensity for miRNA family loss (PGL) and stronger signature of purifying selection during divergence of temperate and tropical lotus. Further analyses of lotus genome revealed that there is an association between loss of miRNA families in descendent plants and in duplicated genomes. Gene dosage balance is crucial in maintaining those preferentially retained MIRNA duplicates by imposing stronger purifying selection. However, these factors and selection influencing miRNA family evolution are not applicable to the putative MIRNA‐likes. Additionally, the MIRNAs participating in lotus pollen–pistil interaction, a conserved process in angiosperms, also have a strong signature of purifying selection. Functionally, sequence divergence in MIRNAs escalates expression divergence of their target genes between temperate and tropical lotus during rhizome and leaf growth. Overall, our study unravels several important factors and selection that determine the miRNA family distribution in plants and duplicated genomes, and provides evidence for functional impact of MIRNA sequence evolution.
The RNA recognition motif protein CP33A is a global ligand of chloroplast mRNAs and is essential for plastid biogenesis and plant development
Authors: Teubner Marlene , Fuß Janina , Kühn Kristina , Krause Kirsten , Schmitz‐Linneweber Christian 
Published: October 2016

SummaryChloroplast RNA metabolism depends on a multitude of nuclear‐encoded RNA‐binding proteins (RBPs). Most known chloroplast RBPs address specific RNA targets and RNA‐processing functions. However, members of the small chloroplast ribonucleoprotein family (cpRNPs) play a global role in processing and stabilizing chloroplast RNAs. Here, we show that the cpRNP CP33A localizes to a distinct sub‐chloroplastic domain and is essential for chloroplast development. The loss of CP33A yields albino seedlings that exhibit aberrant leaf development and can only survive in the presence of an external carbon source. Genome‐wide RNA association studies demonstrate that CP33A associates with all chloroplast mRNAs. For a given transcript, quantification of CP33A‐bound versus free RNAs demonstrates that CP33A associates with the majority of most mRNAs analyzed. Our results further show that CP33A is required for the accumulation of a number of tested mRNAs, and is particularly relevant for unspliced and unprocessed precursor mRNAs. Finally, CP33A fails to associate with polysomes or to strongly co‐precipitate with ribosomal RNA, suggesting that it defines a ribodomain that is separate from the chloroplast translation machinery. Collectively, these findings suggest that CP33A contributes to globally essential RNA processes in the chloroplasts of higher plants.
Microbial N Transformations and N
2
O Emission after Simulated Grassland Cultivation: Effects of the Nitrification Inhibitor 3,4-Dimethylpyrazole Phosphate (DMPP)
Authors: Duan Yun-Feng , Kong Xian-Wang , Schramm Andreas , Labouriau Rodrigo , Eriksen Jørgen , Petersen Søren O. 
Published: October 2016

ABSTRACT

Grassland cultivation can mobilize large pools of N in the soil, with the potential for N leaching and N
2
O emissions. Spraying with the nitrification inhibitor 3,4-dimethylpyrazole phosphate (DMPP) before cultivation was simulated by use of soil columns in which the residue distribution corresponded to plowing or rotovation to study the effects of soil-residue contact on N transformations. DMPP was sprayed on aboveground parts of ryegrass and white clover plants before incorporation. During a 42-day incubation, soil mineral N dynamics, potential ammonia oxidation (PAO), denitrifying enzyme activity (DEA), nitrifier and denitrifier populations, and N
2
O emissions were investigated. The soil NO
3
−
pool was enriched with
15
N to trace sources of N
2
O. Ammonium was rapidly released from decomposing residues, and PAO was stimulated in soil near residues. DMPP effectively reduced NH
4
+
transformation irrespective of residue distribution. Ammonia-oxidizing archaea (AOA) and bacteria (AOB) were both present, but only the AOB
amoA
transcript abundance correlated with PAO. DMPP inhibited the transcription of AOB
amoA
genes. Denitrifier genes and transcripts (
nirK
,
nirS
, and clades I and II of
nosZ
) were recovered, and a correlation was found between
nirS
mRNA and DEA. DMPP showed no adverse effects on the abundance or activity of denitrifiers. The
15
N enrichment of N
2
O showed that denitrification was responsible for 80 to 90% of emissions. With support from a control experiment without NO
3
−
amendment, it was concluded that DMPP will generally reduce the potential for leaching of residue-derived N, whereas the effect of DMPP on N
2
O emissions will be significant only when soil NO
3
−
availability is limiting.

IMPORTANCE
Residue incorporation following grassland cultivation can lead to mobilization of large pools of N and potentially to significant N losses via leaching and N
2
O emissions. This study proposed a mitigation strategy of applying 3,4-dimethylpyrazole phosphate (DMPP) prior to grassland cultivation and investigated its efficacy in a laboratory incubation study. DMPP inhibited the growth and activity of ammonia-oxidizing bacteria but had no adverse effects on ammonia-oxidizing archaea and denitrifiers. DMPP can effectively reduce the potential for leaching of NO
3
−
derived from residue decomposition, while the effect on reducing N
2
O emissions will be significant only when soil NO
3
−
availability is limiting. Our findings provide insight into how DMPP affects soil nitrifier and denitrifier populations and have direct implications for improving N use efficiency and reducing environmental impacts during grassland cultivation.
Identification and Characterization of a Large Protein Essential for Degradation of the Crystalline Region of Cellulose by Cytophaga hutchinsonii
Authors: Wang Sen , Zhao Dong , Bai Xinfeng , Zhang Weican , Lu Xuemei 
Published: October 2016

ABSTRACT

Cytophaga hutchinsonii
is a Gram-negative bacterium that can efficiently degrade crystalline cellulose by a unique mechanism different from the free cellulase or cellulosome strategy. In this study,
chu_3220
, encoding the hypothetical protein CHU_3220 (205 kDa), was identified by insertional mutation and gene deletion as the first gene essential for degradation of the crystalline region but not the amorphous region of cellulose by
C. hutchinsonii
. A
chu_3220
deletion mutant was defective in the degradation of crystalline cellulose and increased the degree of crystallinity of Avicel PH101 but could still degrade amorphous cellulose completely. CHU_3220 was found to be located on the outer surface of the outer membrane and could bind to cellulose. It contains 15 PbH1 domains and a C-terminal domain (CHU_C) that was proved to be critical for the localization of CHU_3220 on the cell surface and the function of CHU_3220 in crystalline cellulose degradation. Moreover, the degradation of crystalline cellulose was intact-cell dependent and inhibited by NaN
3
. Further study showed that
chu_3220
was induced by cellulose and that the endoglucanase activity on the cell surface was significantly reduced without
chu_3220
. Real-time PCR revealed that the transcription of most genes encoding endoglucanases located on the cell surface was decreased in the
chu_3220
deletion mutant, indicating that
chu_3220
might also play a role in the regulation of the expression of some endoglucanases.

IMPORTANCE
Cytophaga hutchinsonii
could efficiently degrade crystalline cellulose with a unique mechanism without cellulosomes and free cellulases. It lacks proteins that are thought to play important roles in disruption of the crystalline region of cellulose, including exoglucanases, lytic polysaccharide monooxygenases, expansins, expansin-like proteins, or swollenins, and most of its endoglucanases lack carbohydrate binding modules. The mechanism of the degradation of crystalline cellulose is still unknown. In this study,
chu_3220
was identified as the first gene essential for the degradation of the crystalline region but not the amorphous region of cellulose. CHU_3220 is a high-molecular-weight protein located on the outer surface of the outer membrane and could bind to cellulose. We proposed that CHU_3220 might be an essential component of a protein complex on the cell surface in charge of the decrystallization of crystalline cellulose. The degradation of crystalline cellulose by
C. hutchinsonii
was not only dependent on intact cells but also required the energy supplied by the cells. This was obviously different from other known cellulose depolymerization system. Our study has shed more light on the novel strategy of crystalline cellulose degradation by
C. hutchinsonii
.