bluuebunny/crossref_metadata_2025 huggingface dataset:
Hyperspectral imaging for skin assessment in systemic sclerosis: a pilot study
Authors: Chen Yi-Ming , Lai Kuo-Lung , Chen Hsin-Hua , Huang Wen-Nan , Lin Ching-Tsai , Chao Wen-Cheng , Chen Jun-Peng , Fu Yu-Wen , Chen Hsian-Min , Lui Ping-Wing
Published: January 2020

Objective

Hyperspectral imaging (HSI) is a novel technology for obtaining quantitative measurements from transcutaneous spatial and spectral information. In patients with SSc, the severity of skin tightness is associated with internal organ involvement. However, clinical assessment using the modified Rodnan skin score is highly variable and there are currently no universal standardized protocols. This study aimed to compare the ability to differentiate between SSc patients and healthy controls using skin scores, ultrasound and HSI.

Methods

Short-wave infrared light was utilized to detect the spectral angle mapper (SAM) of HSI. In addition, skin severity was evaluated by skin scores, ultrasound to detect dermal thickness and strain elastography. Spearman’s correlation was used for assessing skin scores, strain ratio, thickness and SAM. Comparisons of various assessment tools were performed by receiver operating characteristic curves.

Results

In total, 31 SSc patients were enrolled. SAM was positively correlated with skin scores and dermal thickness. In SSc patients with normal skin scores, SAM values were still significantly higher than in healthy controls. SAM exhibited the highest area under the curve (AUC: 0.812, P < 0.001) in detecting SSc compared with skin scores (AUC: 0.712, P < 0.001), thickness (AUC: 0.585, P = 0.009) and strain ratio by elastography (AUC: 0.522, P = 0.510). Moreover, the severity of skin tightness was reflected by the incremental changes of waveforms in the spectral diagrams.

Conclusion

SAM was correlated with skin scores and sufficiently sensitive to detect subclinical disease. HSI can be used as a novel, non-invasive method for assessing skin changes in SSc.
An international, multicentre, double-blind, randomized study (DISSCO): effect of diacerein vs celecoxib on symptoms in knee osteoarthritis
Authors: Pelletier Jean-Pierre , Raynauld Jean-Pierre , Dorais Marc , Bessette Louis , Dokoupilova Eva , Morin Frédéric , Pavelka Karel , Paiement Patrice , Martel-Pelletier Johanne ,   for the DISSCO Trial Investigator Group
Published: January 2020

Objective

The objective of this study was to investigate whether diacerein has comparable efficacy with celecoxib in pain reduction for treatment in symptomatic knee OA patients.

Methods

This randomized double-blind multicentre non-inferiority trial evaluated diacerein vs celecoxib treatment in patients with Kellgren–Lawrence grade 2–3 and pain scoring ≥4 (10-cm VAS). Patients were randomized to 6 months of treatment with diacerein 50 mg (n = 187) once daily for 1 month and twice daily thereafter, or celecoxib 200 mg (n = 193) once daily. The primary outcome was the change in WOMAC pain score (0–50 cm) at 6 months, and the secondary outcomes were WOMAC sub-scores, VAS pain score, and the OMERACT–OARSI responder rate.

Results

In the per protocol population, the adjusted mean change from baseline in the WOMAC pain score was –11.1 ( 0.9) with diacerein (n = 140) and –11.8 (0.9) with celecoxib (n = 148). The intergroup difference was 0.7 (95% CI: −1.8, 3.2; P = 0.597), meeting the non-inferiority margin. Supportive analysis of the intention-to-treat population gave similar results. Other outcomes showed no significant difference between treatment groups. The incidence of treatment-related adverse events was low and balanced between groups, but a greater incidence of diarrhoea occurred with diacerein (10.2% vs 3.7%). Diarrhoea was considered mild-to-moderate in all but one case with complete resolution.

Conclusions

Diacerein was non-inferior to celecoxib in reducing knee OA pain and improving physical function. Diacerein also demonstrated a good safety profile.

Trial registration

A multicentre study on the effect of DIacerein on Structure and Symptoms vs Celecoxib in Osteoarthritis is a National Institutes of Health (NCT02688400) and European Clinical Trial Database (2015–002933-23) registered phase III (Canada) or IV (Europe) study.
BACKGROUND RADIATION LEVELS NEAR A MINERAL SAND MINING FACTORY IN SRI LANKA: CORRELATION OF RADIATION MEASUREMENTS WITH MICRONUCLEI FREQUENCY
Authors: Warnakulasuriya Tania , Williams Senani , Weerakkody Thiwanka , Dabarera Mangala , Rodrigo Kusum , Waduge Vajira Ariyaratna , Ediriweera Dileepa , Siriwardena Niroshan , Wickremasinghe Rajitha
Published: January 2020

Lanka Mineral Sands Ltd (LMS) is a company operating in Pulmoddai, Sri Lanka, mining for rare earth minerals along with monazite which contains thorium that emits ionizing gamma and alpha radiation on decay. The objective of the study was to determine the background radiation levels and selected radionuclides and then to correlate these levels with the frequency of micronuclei (MN) among persons residing in the vicinity of LMS. A cross-sectional study was conducted among persons of both sexes between 35 and 45 years of age residing in the vicinity of LMS. Background radiation measurements were obtained by a survey metre, and gamma spectrometry was done on soil samples. Five millilitres of venous blood was drawn for cytokinesis-blocked MN assay. Background radiation levels measured by the survey metre; 232Th, 226Ra and 210Pb mass activities in soil were highest in the samples collected from the LMS. The background radiation measurements positively correlated with MN frequency although the magnitude of the correlation was small (r = 0.176, p = 0.04). This implies that chronic long-term exposure to low-dose radiation may result in genotoxicity. Prospective large-scale studies are recommended to evaluate the long-term effect of exposure to low-dose radiation at Pulmoddai.
Different policy instruments and the threshold effects on collaboration efficiency in China
Authors: Cheng Hua , Zhang Zhiying , Liao Zhongju , Wei Yong , Nkongo Mvondo Joseph Martial
Published: January 2020

University–industry R&D collaboration is an important means to improve innovation efficiency; many governments have issued policies to promote it. The most frequent policy instruments implemented by policy-makers to foster firms’ innovation are subsidies and tax incentives. The article elaborated on how subsidies and tax incentives influence the R&D collaboration efficiency through a panel dataset from 2009 to 2015 in China. The result showed that subsidies and tax incentives have a positive effect on collaboration efficiency, and the effect of subsidies on output is bigger than that of tax incentives. Taking the intensity of subsidy as a threshold variable, there is a significant single threshold effect on collaboration efficiency. However, there is no threshold effect when the intensity of the tax incentive used as the threshold variable.
Accumulation or absorption? Changing disparities of household non-employment in Europe during the Great Recession
Authors: Biegert Thomas , Ebbinghaus Bernhard
Published: January 2020

This comparative study analyzes the impact of the Great Recession on household non-employment across Europe since 2008. We use the EU-SILC (2007–2014) for a shift-share analysis that decomposes annual variations in household non-employment in 30 European countries. Investigating whether job loss is absorbed by or accumulated in households, we break down non-employment variations into changes in individual non-employment, household compositions and polarization. We find that household joblessness increased since 2008, especially in crisis-ridden countries. There is no evidence for the widespread absorption of individual non-employment in families or multi-person households. Instead, household dynamics and unequal distribution of non-employment lead to further risk accumulation within households during the crisis. Surprisingly, this pattern occurs in those crisis-ridden countries known for their traditional household structures and less accommodating welfare systems, which have relied thus far on families to absorb employment risks. The Great Recession has aggravated household disparities in joblessness in Europe.
Dissecting the Student Experience at Australian Medical Schools, 1884–1912
Authors: Pacitti Eugenia
Published: January 2020

Historians of medicine have observed that the student experience of medical school is difficult to capture. While students sometimes left behind notebooks containing lecture notes and diagrams, there is often little evidence that illuminates their lived experiences and responses to their education. This article analyses written submissions to the publication of the Melbourne Medical Students’ Society, Speculum, between 1884 and 1912, to argue that students at the Melbourne Medical School in this era actively participated in discussions about the curriculum on offer, were highly aware of the moral and ethical consequences of their actions in the dissecting room and took great interest in the advancements and debates of the medical profession. It reclaims the student experience of medical school, which has often been hidden in favour of history written from the perspective of those in positions of power, to offer fresh insights into the history of medical education.
Establishing a Baseline: Evidence-Supported State Laws to Advance Stroke Care
Authors: Gilchrist Siobhan , Sloan Arielle A. , Bhuiya Aunima R. , Taylor Lauren N. , Shantharam Sharada S. , Barbero Colleen , Fulmer Erika B.
Published: January 2020

Objective:

Approximately 800 000 strokes occur annually in the United States. Stroke systems of care policies addressing prehospital and in-hospital care have been proposed to improve access to time-sensitive, lifesaving treatments for stroke. Policy surveillance of stroke systems of care laws supported by best available evidence could reveal potential strengths and weaknesses in how stroke care delivery is regulated across the nation.

Design:

This study linked the results of an early evidence assessment of 15 stroke systems of care policy interventions supported by best available evidence to a legal data set of the body of law in effect on January 1, 2018, for the 50 states and Washington, District of Columbia.

Results:

As of January 1, 2018, 39 states addressed 1 or more aspects of prehospital or in-hospital stroke care in law; 36 recognized at least 1 type of stroke center. Thirty states recognizing stroke centers also had evidence-supported prehospital policy interventions authorized in law. Four states authorized 10 or more of 15 evidence-supported policy interventions. Some combinations of prehospital and in-hospital policy interventions were more prevalent than other combinations.

Conclusion:

The analysis revealed that many states had a stroke regulatory infrastructure for in-hospital care that is supported by best available evidence. However, there are gaps in how state law integrates evidence-supported prehospital and in-hospital care that warrant further study. This study provides a baseline for ongoing policy surveillance and serves as a basis for subsequent stroke systems of care policy implementation and policy impact studies.
Risk Factors for Wound Infection After Laparoscopic Surgery for Colon Cancer
Authors: Nakamura Takatoshi , Takayama Yoko , Sato Takeo , Watanabe Masahiko
Published: January 2020

Objective:

To clarify risk factors for wound infection after laparoscopic surgery for colon cancer.

Subjects and Methods:

The study group comprised 1144 patients. Univariate and multivariate analyses were performed to assess the following 14 postoperative risk factors for wound infection.

Results:

Univariate analysis showed that the following 4 risk factors were related to wound infection: tumor location right-sided colon cancer, a preoperative serum albumin level of ≤2.5 g/dL, anastomotic technique [functional end-to-end anastomosis (FEEA)], and sutures used at the time of wound closure non–polydioxanone sutures (PDS)-Plus. Multivariate analysis indicated that 3 factors were independent risk factors for wound infection: a preoperative serum albumin level of ≤2.5 g/dL, FEEA, and the use of non-PDS-Plus sutures wound closure.

Conclusions:

Risk factors for wound infection after laparoscopic surgery for colon cancer were a preoperative serum albumin level of ≤2.5 g/dL, FEEA, and the use of non-PDS-Plus sutures.
Laparoscopic Liver Resection Ameliorates the Postoperative Liver Function Impairment for Hepatocellular Carcinoma Patients
Authors: Hou Hui , Zhou Dachen , Cui Xiao , Wang Lei , Wu Chunli , Xiong Qiru , Geng Xiaoping
Published: January 2020

To study whether laparoscopic liver resection (LLR) is able to alleviate the postoperative liver function impairment for hepatocellular carcinoma patients, the clinical data of 103 patients were retrospectively analyzed, including 42 patients who underwent LLR and 61 patients who underwent open liver resection (OLR), during the period spanning from 2012 to 2017. The postoperative peak aspartate aminotransferase and alanine aminotransferase levels in the LLR group were significantly lower than those of the OLR group (209.76±189.516 vs. 262.55±181.19, P=0.046; 250.56±200.944 vs. 411.01±412.51, P=0.005, for aspartate aminotransferase and alanine aminotransferase, respectively). The recovering of postoperative total protein and albumin in the LLR group was faster than that in the OLR group, and the total protein and albumin levels on the postoperative day-5 were significantly higher in the LLR group than in the OLR group (62.528±9.427 vs. 57.87±6.101, P=0.019; 36.456±4.875 vs. 33.653±4.112, P=0.012, respectively). In conclusion, these data show that LLR alleviates postoperative liver function impairment and increases liver function recovery.
Vagococcus silagei sp. nov., isolated from brewer’s grain used to make silage in Taiwan
Authors: Wu Yen-Chi , Lin Shih-Ting , Guu Jia-Rong , Tamura Tomohiko , Mori Koji , Wang Li-Ting , Huang Lina , Watanabe Koichi
Published: January 2020

A Gram-stain-positive, coccus- or oval-shaped, non-motile, haemolytic, asporogenous, catalase- and oxidase-negative, and facultatively anaerobic strain, 2B-2T, was isolated from a brewer’s grain used to make silage in Taiwan. Comparative analyses of 16S rRNA, hsp60 and pheS gene sequences demonstrated that strain 2B-2T was a member of the genus

Vagococcus

. On the basis of 16S rRNA gene sequence similarity, the type strains of

Vagococcus teuberi

(98.4 % similarity),

Vagococcus carniphilus

(98.4 %),

Vagococcus martis

(98.2 %),

Vagococcus penaei

(98.2 %) and

Vagococcus fluvialis

(98.0 %) were the closest neighbours to this novel strain. The similarity levels of concatenated housekeeping gene sequences (hsp60 and pheS) between strain 2B-2T and these closely related species ranged from 84.5 to 88.0 %. The average nucleotide identity and in silico DNA–DNA hybridization values between strain 2B-2T and its closest relatives were lower than 72.9 and 21.6 %, respectively. The DNA G+C content was 34.7 mol%. Phenotypic and genotypic features demonstrated that strain 2B-2T represents a novel species of the genus

Vagococcus

, for which the name Vagococcus silagei sp. nov. is proposed. The type strain is 2B-2T (=BCRC 81132T=NBRC 113536T).
Population structure of KPC carbapenemase-producing Klebsiella pneumoniae in a long-term acute-care rehabilitation facility: identification of a new lineage of clonal group 101, associated with local hyperendemicity
Authors: Arena Fabio , Di Pilato Vincenzo , Vannetti Federica , Fabbri Laura , Antonelli Alberto , Coppi Marco , Pupillo Roberto , Macchi Claudio , Rossolini Gian Maria
Published: January 2020

In this work, we used a whole-genome sequencing (WGS) approach to study the features of KPC-producing

Klebsiella pneumoniae

(KPC-Kp) spreading in a large Italian long-term acute-care rehabilitation facility (LTACRF), and to track the dynamics of dissemination within this setting. Thirty-eight, non-replicated, KPC-Kp isolates from colonized patients (either already colonized at admission or colonized during admission), collected during 2016, were subjected to antimicrobial-susceptibility testing and WGS. All isolates were resistant to β-lactams, with the exception of ceftazidime/avibactam (97.4 % susceptible). The second most effective agent was fosfomycin, followed by colistin, trimethoprim/sulfamethoxazole, gentamicin and amikacin (92.1, 86.8, 60.5, 44.7 and 50 % of susceptibility, respectively). A large proportion of isolates (n=18/38, 47.4%) belonged to clonal group (CG) 101, and most of them (n=15) to a new sequence type (ST) designated as ST2502. All the CG101 isolates had a capsule locus type KL17. The ST2502 harboured the genes encoding for the yersiniabactin siderophore and the ArmA methylase, conferring high-level resistance to aminoglycosides. The second most represented lineage of isolates (16/38, 42.1%) belonged to ST512 of CG258. Analysing WGS data, we were able to ascertain the common origin of some isolates imported from other hospitals, and to track several clusters of in-LTACRF cross-transmissions. The results revealed that, in peculiar epidemiological settings such as LTACRF, new KPC-Kp clones different from those prevailing in acute-care hospitals and associated with uncommon resistance and virulence determinants can successfully emerge and disseminate.
Peer review and preprint policies are unclear at most major journals
Authors: Klebel Thomas , Reichmann Stefan , Polka Jessica , McDowell Gary , Penfold Naomi , Hindle Samantha , Ross-Hellauer Tony
Published: January 2020

Clear and findable publishing policies are important for authors to choose appropriate journals for publication. We investigated the clarity of policies of 171 major academic journals across disciplines regarding peer review and preprinting. 31.6% of journals surveyed do not provide information on the type of peer review they use. Information on whether preprints can be posted or not is unclear in 39.2% of journals. 58.5% of journals offer no clear information on whether reviewer identities are revealed to authors. Around 75% of journals have no clear policy on co-reviewing, citation of preprints, and publication of reviewer identities. Information regarding practices of Open Peer Review is even more scarce, with <20% of journals providing clear information. Having found a lack of clear information, we conclude by examining the implications this has for researchers (especially early career) and the spread of open research practices.
The Structures of Natively Assembled Clathrin Coated Vesicles
Authors: Paraan Mohammadreza , Mendez Joshua , Sharum Savanna , Kurtin Danielle , He Huan , Stagg Scott M.
Published: January 2020

Vesicle trafficking by clathrin coated vesicles (CCVs) is one of the major mechanisms by which proteins and nutrients are absorbed by the cell and transported between organelles. The individual proteins comprising the coated vesicles include clathrin heavy chain, clathrin light chain, and a variety of adaptor protein complexes. Much is known about the structures of the individual CCV components, but data are lacking about the structures of the fully assembled complexes together with membrane and in complex with cargo. Here we determined the structures of natively assembled CCVs in a variety of geometries. We show that the adaptor β2-appendages crosslink adjacent CHC β-propellers and that the appendage densities reside almost exclusively in CCV hexagonal faces. We resolve how AP2 and other associated factors in hexagonal faces form an assembly hub with an extensive web of interactions between neighboring β-propellers and propose a structural model that explains how adaptor binding can direct the formation of pentagonal and hexagonal faces.
Tailored Design of Protein Nanoparticle Scaffolds for Multivalent Presentation of Viral Glycoprotein Antigens
Authors: Ueda George , Antanasijevic Aleksandar , Fallas Jorge A. , Sheffler William , Copps Jeffrey , Ellis Daniel , Hutchinson Geoffrey , Moyer Adam , Yasmeen Anila , Tsybovsky Yaroslav , Park Young-Jun , Bick Matthew J. , Sankaran Banumathi , Gillespie Rebecca A. , Brouwer Philip J. M. , Zwart Petrus H. , Veesler David , Kanekiyo Masaru , Graham Barney S. , Sanders Rogier , Moore John P. , Klasse Per Johan , Ward Andrew B. , King Neil , Baker David
Published: January 2020

The adaptive immune system is highly sensitive to arrayed antigens, and multivalent display of viral glycoproteins on symmetric scaffolds has been found to substantially increase the elicitation of antigen-specific antibodies. Motivated by the considerable promise of this strategy for next-generation anti-viral vaccines, we set out to design new self-assembling protein nanoparticles with geometries specifically tailored to scaffold ectodomains of different viral glycoproteins. We first designed and characterized homo-trimers from designed repeat proteins with N-terminal helices positioned to match the C termini of several viral glycoprotein trimers. Oligomers found to experimentally adopt the designed configuration were then used to generate nanoparticles with tetrahedral, octahedral, or icosahedral symmetry. Examples of all three target symmetries were experimentally validated by cryo-electron microscopy and several were assessed for their ability to display viral glycoproteins via genetic fusion. Electron microscopy and antibody binding experiments demonstrated that the designed nanoparticles display conformationally intact native-like HIV-1 Env, influenza hemagglutinin, and prefusion RSV F trimers in the predicted geometries. This work demonstrates that novel nanoparticle immunogens can be designed from the bottom up with atomic-level accuracy and provides a general strategy for precisely controlling epitope presentation and accessibility.
An introgressed gene causes meiotic drive inNeurospora sitophila
Authors: Svedberg Jesper , Vogan Aaron A. , Rhoades Nicholas A. , Sarmarajeewa Dilini , Jacobson David J. , Lascoux Martin , Hammond Thomas M. , Johannesson Hanna
Published: January 2020

Meiotic drive elements cause their own preferential transmission following meiosis. In fungi this phenomenon takes the shape of spore killing, and in the filamentous ascomyceteNeurospora sitophila, theSk-1spore killer element is found in many natural populations. In this study, we identify the gene responsible for spore killing inSk-1by generating both long and short-read genomic data and by using these data to perform a genome wide association test. Through molecular dissection, we show that a single 405 nucleotide long open reading frame generates a product that both acts as a poison capable of killing sibling spores and as an antidote that rescues spores that produce it. By phylogenetic analysis, we demonstrate that the gene is likely to have been introgressed from the closely related speciesN. hispaniola, and we identify three subclades ofN. sitophila, one whereSk-1is fixed, another whereSk-1is absent, and a third where both killer and sensitive strain are found. Finally, we show that spore killing can be suppressed through an RNA interference based genome defense pathway known as meiotic silencing by unpaired DNA.Spk-1is not related to other known meiotic drive genes, and similar sequences are only found withinNeurospora. These results shed new light on the diversity of genes capable of causing meiotic drive, their origin and evolution and their interaction with the host genome.

Significance Statement

In order to survive, most organisms have to deal with parasites. Such parasites can be other organisms, or sometimes, selfish genes found within the host genome itself. While much is known about parasitic organisms, the interaction with their hosts and their ability to spread within and between species, much less is known about selfish genes. We here identify a novel selfish “spore killer” gene in the fungusNeurospora sitophila. The gene appears to have evolved within the genus, but has entered the species through hybridization and introgression. We also show that the host can counteract the gene through RNA interference. These results shed new light on the diversity of selfish genes in terms of origin, evolution and host interactions.
Multisensory perception, verbal, visuo-spatial, and motor working memory modulation after a single open- or closed-skill exercise session in children
Authors: O’Brien Jessica , Ottoboni Giovanni , Tessari Alessia , Setti Annalisa
Published: January 2020

Physical activity presents clear benefits for children’s cognition; this study examined the effect of a single exercise session of open- or closed-skill exercise, as opposed to a no-exercise activity on multisensory perception, i.e. the ability to appropriately merge inputs from different sensory modalities, and on working memory (verbal, visuo-spatial, and motor working memory) in 51 preadolescent children (aged 6-8). Using a semi-randomised pre-post design, participants completed a range of cognitive tasks immediately before and after an exercise session or a classroom sedentary activity. Participants were randomised, within each school, to one of the three groups (open-skill, n=16; closed-skill, n=16; classroom activity, n=19). Exercise, but not usual classroom activity, improved children’s multisensory perception, with no difference between exercise types. Results also revealed that a single open-skill session produced verbal working memory (digit span) benefits; a closed-skill exercise session benefitted motor working memory. While the relatively small number of participants should be acknowledged as limitation, these findings contribute to emerging evidence for selective cognitive benefits of exercise, and show, for the first time in children, that multisensory processing sensitivity is improved by exercise.
Long term AAV2/9-mediated silencing of PMP22 prevents CMT1A disease in rats and validates skin biomarkers as treatment outcome measure
Authors: Gautier Benoit , Hajjar Helene , Soares Sylvia , Berthelot Jade , Deck Marie , Abbou Scarlette , Campbell Graham , Fovet Claire-Maelle , Schütza Vlad , Jouvenel Antoine , Rivat Cyril , Zerah Michel , Le Ravazet Virginie François , Le Guiner Caroline , Aubourg Patrick , Fledrich Robert , Tricaud Nicolas
Published: January 2020

Charcot-Marie-Tooth disease 1A (CMT1A) results from a duplication of thePMP22gene leading to an excess of PMP22, a deficit of myelination and an instability of the myelin sheath in peripheral nerves. Patients present with reduced nerve conduction velocity, muscle waste, hand and foot deformations and foot drop walking problems. As gene silencing therapy has been shown to be effective in other monogenic neurological disorders, we evaluated the safety and efficacy of recombinant adeno-associated viral vector serotype 9 (AAV2/9)-based gene therapy for CMT1A. AAV2/9-mediated delivery of eGFP and shRNAs targeting PMP22 mRNA in the sciatic nerve allowed widespread gene expression in myelinating Schwann cells in mouse, rat and nonhuman primate. The treatment restored wild-type PMP22 level, increased myelination and prevented motor and sensory impairment over 12 months in a rat model of CMT1A. Intra-nerve injection limited off-target transduction and immune response to barely detectable levels. A combination of previously characterized human skin biomarkers successfully discriminated treated animals from their untreated littermate controls indicating their potential use as part of outcome measures in future clinical trials. Our results support intra nerve injection of AAV2/9 as an effective strategy for the treatment of CMT1A as well as other demyelinating CMT diseases.
Suspensor-derived somatic embryogenesis in Arabidopsis
Authors: Radoeva Tatyana , Albrecht Catherine , Piepers Marcel , de Vries Sacco , Weijers Dolf
Published: January 2020

In many flowering plants, includingArabidopsis thaliana, asymmetric division of the zygote generates apical and basal cells with different fates. The apical cell continues to produce the embryo while the basal cell undergoes a restricted number of anticlinal divisions leading to a suspensor of 6-9 quiescent cells that remain extra-embryonic and eventually senesce. In some genetic backgrounds, or upon ablation of the embryo, suspensor cells can however undergo periclinal cell divisions and eventually form a second, twin seedling. Likewise, embryogenesis can be induced from somatic cells by various genes, but the relation to suspensor-derived embryos is unclear. Here, we addressed the nature of the suspensor to embryo fate transformation, and its genetic triggers. We expressed most known embryogenesis-inducing transcriptional regulators and receptor-like kinases specifically in suspensor cells. Among these, only RKD1 and WUS could induce a heritable twin seedling phenotype. We next analyzed morphology and fate marker expression in embryos in which suspensor division were activated by different triggers to address the developmental paths towards reprogramming. Our results show that reprogramming of Arabidopsis suspensor cells towards embryonic identity is a specific cellular response that is triggered by defined regulators, follows a conserved developmental trajectory and shares similarity to the process of somatic embryogenesis from post-embryonic tissues.
Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors
Authors: Kult Shiri , Olender Tsviya , Osterwalder Marco , Krief Sharon , Blecher-Gonen Ronnie , Ben-Moshe Shani , Farack Lydia , Keren-Shaul Hadas , Leshkowitz Dena , Salame Tomer Meir , Capellini Terence D. , Itzkovitz Shalev , Amit Ido , Visel Axel , Zelzer Elazar
Published: January 2020

The connection between different tissues is vital for the development and function of any organs and systems. In the musculoskeletal system, the attachment of elastic tendons to stiff bones poses a mechanical challenge that is solved by the formation of a transitional tissue, which allows the transfer of muscle forces to the skeleton without tearing. Here, we show that tendon-to-bone attachment cells are bi-fated, activating a mixture of chondrocyte and tenocyte transcriptomes, which is regulated by sharing regulatory elements with these cells and by Krüppel-like factors transcription factors (KLF).

To uncover the molecular identity of attachment cells, we first applied high-throughput RNA sequencing to murine humeral attachment cells. The results, which were validated byin situhybridization and single-moleculein situhybridization, reveal that attachment cells express hundreds of chondrogenic and tenogenic genes. In search for the underlying mechanism allowing these cells to express these genes, we performed ATAC sequencing and found that attachment cells share a significant fraction of accessible intergenic chromatin areas with either tenocytes or chondrocytes. Epigenomic analysis further revealed transcriptional enhancer signatures for the majority of these regions. We then examined a subset of these regions using transgenic mouse enhancer reporter. Results verified the shared activity of some of these enhancers, supporting the possibility that the transcriptome of attachment cells is regulated by enhancers with shared activities in tenocytes or chondrocytes. Finally, integrative chromatin and motif analyses, as well as the transcriptome data, indicated that KLFs are regulators of attachment cells. Indeed, blocking the expression ofKlf2andKlf4in the developing limb mesenchyme led to abnormal differentiation of attachment cells, establishing these factors as key regulators of the fate of these cells.

In summary, our findings show how the molecular identity of bi-fated attachment cells enables the formation of the unique transitional tissue that connect tendon to bone. More broadly, we show how mixing the transcriptomes of two cell types through shared enhancers and a dedicated set of transcription factors can lead to the formation of a new cell fate that connects them.
Symbiosis between river and dry lands: phycobiont dynamics on river gravel bars
Authors: Vančurová Lucie , Kalníková Veronika , Peksa Ondřej , Škvorová Zuzana , Malíček Jiří , Moya Patricia , Chytrý Kryštof , Černajová Ivana , Škaloud Pavel
Published: January 2020

River gravel bars are dynamic and heterogeneous habitats standing on transition between aquatic and terrestrial environment. Periodical flooding, low nutrient content, frost, missing safe sites, drought, and heat on the ground surface significantly influence life in these habitats. Mutualistic symbiosis may be a successful strategy for organisms to survive and to proliferate under harsh conditions. The lichen genusStereocaulonwas selected as a model symbiotic system among the organisms living on river gravel bars. The aim of our work was to determine effect of this dynamic environment on a phycobiont (i.e., green eukaryotic photobiont) community structure. We analysed 147Stereocaulonspecimens collected in the Swiss Alps using Sanger sequencing (fungal ITS rDNA, algal ITS rDNA, algal actin type I gene) and 8 selected thalli and 12 soil samples using Illumina metabarcoding (ITS2 rDNA). We performed phytosociological sampling on each study plot (n=13). Our analyses of communities of phycobionts, lichens, bryophytes, and vascular plants indicated an ongoing colonisation by phycobionts and gradual change of phycobiont community along to the successional gradient. We recovered great phycobiont diversity associated withStereocaulonmycobionts including algae reported as phycobionts for the first time. Each of twoStereocaulonmycobiont OTUs has distinct pool of predominant phycobionts in the study area. Finally, all thalli selected for Illumina metabarcoding contained a wide range of additional intrathalline algae, i.e., showed algal plurality. In general, succession process on newly emerged or recently disturbed localities also takes place within a community of microscopic symbiotic organisms, such as phycobionts.
The consequences of variant calling decisions in secondary analyses of cancer sequencing data
Authors: Garcia-Prieto Carlos , Martinez Jimenez Francisco , Valencia Alfonso , Porta-Pardo Eduard
Published: January 2020

The analysis of cancer genomes provides fundamental information about its aetiology, the processes driving cell transformation or potential treatments. The first crucial step in the analysis of any tumor genome is the identification of somatic genetic variants that cancer cells have acquired during their evolution. For that purpose, a wide range of somatic variant callers have been developed in recent years. While there have been some efforts to benchmark somatic variant calling tools and strategies, the extent to which variant calling decisions impact the results of downstream analyses of tumor genomes remains unknown. Here we present a study to elucidate whether different variant callers (MuSE, MuTect2, SomaticSniper, VarScan2) and strategies to combine them (Consensus and Union) lead to different results in these three important downstream analyses of cancer genomics data: identification of cancer driver genes, quantification of mutational signatures and detection of clinically actionable variants. To this end, we tested how the results of these three analyses varied depending on the somatic mutation caller in five different projects from The Cancer Genome Atlas (TCGA). Our results show that variant calling decisions have a significant impact on these downstream analyses, creating important differences in driver genes identification and mutational processes attribution among variant call sets, as well as in the detection of clinically actionable targets. More importantly, it seems that Consensus, a very widely used strategy by the research community, is not the optimal strategy, as it can lead to the loss of some cancer driver genes and actionable mutations. On the other hand, the Union seems to be a legit strategy for some downstream analyses with a robust performance overall.
Bistability of prefrontal states gates access to consciousness
Authors: Dwarakanath Abhilash , Kapoor Vishal , Werner Joachim , Safavi Shervin , Fedorov Leonid A. , Logothetis Nikos K. , Panagiotaropoulos Theofanis I.
Published: January 2020

Access of sensory information to consciousness is thought to be mediated through ignition of neural activity in the prefrontal cortex (PFC). Ignition occurs once activity elicited by sensory input crosses a threshold, which has been shown to depend on brain state fluctuations. However, the neural correlates of fluctuations and their interaction with the neural representations of conscious contents within the PFC remain largely unknown. To understand the role of prefrontal state fluctuations in conscious access, we combined multielectrode intracortical recordings with a no-report binocular rivalry (BR) paradigm that induces spontaneously-driven changes in conscious perception. During BR, antagonistic coupling of two prefrontal states, characterised by dominance of low frequency (1-9Hz) or beta (20-40Hz) local field potentials (LFP), reflect competition between two states of visual consciousness; perceptual update and stability, respectively. Low frequency perisynaptic bursts precede spontaneous transitions in conscious perception, signalling upcoming perceptual update of conscious content. We therefore show that it is a global cortical state that seems to drive internal switches, rather than the spiking activity of selective neuronal ensembles, which subsequently, only report the active percept. Beta band bursts were found to be correlated with periods of stable conscious perception, and selectively synchronised the neural ensemble coding for the consciously perceived stimulus. Similar ongoing fluctuations in the LFPs, with dynamics resembling the distribution of perceptual dominance periods during BR, dominated the prefrontal cortex during resting-state, thus pointing to their default, endogenous nature. Our results suggest that the two modes of conscious perception: perceptual update, and stability, can be associated with distinct prefrontal cortical states.
Neurovascular Function in a Novel Model of Experimental Atherosclerosis
Authors: Shabir Osman , Pendry Ben , Heath Paul R , Rebollar Monica A , Howarth Clare , Wharton Stephen B , Berwick Jason , Francis Sheila E
Published: January 2020

Objective

Atherosclerosis is a major risk factor for dementia. The aims of this study were to determine if experimental atherosclerosis leads to altered neurovascular function and causes neurovascular damage.

Approach and Results

We analysed cerebral blood volume in male C57BL6/J mice injected with an adeno-associated virus (AAV) vector for mutated proprotein convertase subtilisin/kexin type 9 (PCSK9D377Y) fed a Western diet for 35 weeks to induce atherosclerosis (ATH) and 9-12m male wild-type (WT) C57BL/6J. We imaged blood volume responses to sensory stimulation and vascular reactivity gas challenges in the cortex of the brain through a thinned cranial window using 2D-optical imaging spectroscopy (2D-OIS). Neural activity was also recorded with multi-channel electrodes. Stimulation-evoked cortical haemodynamics, in terms of cerebral blood volume, were significantly reduced in ATH mice compared to WT and evoked neural activity was also significantly lower. However, vascular reactivity as assessed by 10% hypercapnia, remained intact in ATH mice. Immunohistochemistry in ATH mice revealed a reduced number of cortical neurons and pericytes in the cortex, but increased astrogliosis. qRT-PCR revealed significantly enhanced TNFα & IL1β in ATH mice compared to WT as well as significant upregulation of eNOS.

Conclusion

Systemic atherosclerosis causes significant neurovascular decline by 9m in atherosclerotic mice characterised by reduced neural activity, associated with loss of neurons and subsequent reduced cortical haemodynamics in response to physiological stimulations. The altered neurovascular function in ATH mice is chiefly mediated by TNFα.

Highlights

Systemic atherosclerosis leads to significantly reduced stimulus-evoked hemodynamic responses in the cortex by 9m of age in the rAAV8-mPCSK9-D377Y mouse model of atherosclerosis compared to wild-type controls.

Reduced cerebral haemodynamics are related to reduced neural activity in the cortex that could be due to a loss of cortical neurons potentially caused by significant TNFa-mediated neuroinflammation.
Wide-vergence, multi-spectral adaptive optics scanning laser ophthalmoscope with diffraction-limited illumination and collection
Authors: Mozaffari Sanam , Larocca Francesco , Jaedicke Volker , Tiruveedhula Pavan , Roorda Austin
Published: January 2020

Visualizing and assessing the function of microscopic retinal structures in the human eye is a challenging task that has been greatly facilitated by ophthalmic adaptive optics (AO). Yet, as AO imaging systems advance in functionality by employing multiple spectral channels and larger vergence ranges, achieving optimal resolution and signal-to-noise ratios (SNR) becomes difficult and is often compromised. While current-generation AO retinal imaging systems have demonstrated excellent, near diffraction-limited imaging performance over wide vergence and spectral ranges, a full theoretical and experimental analysis of an AOSLO that includes both the light delivery and collection optics has not been done, and neither has the effects of extending wavefront correction from one wavelength to imaging performance in different spectral channels. Here, we report a methodology and system design for simultaneously achieving diffraction-limited performance in both the illumination and collection paths for a wide-vergence, multi-spectral AO scanning laser ophthalmoscope (SLO) over a 1.2 diopter vergence range while correcting the wavefront in a separate wavelength. To validate the design, an AOSLO was constructed to have three imaging channels spanning different wavelength ranges (543 ± 11 nm, 680 ± 11 nm, and 840 ± 6 nm, respectively) and one near-infrared wavefront sensing channel (940 ± 5 nm). The AOSLO optics and their alignment were determined via simulations in optical and optomechanical design software and then experimentally verified by measuring the AOSLO’s illumination and collection point spread functions (PSF) for each channel using a phase retrieval technique. The collection efficiency was then measured for each channel as a function of confocal pinhole size when imaging a model eye achieving near-theoretical performance. Imaging results from healthy human adult volunteers demonstrate the system’s ability to resolve the foveal cone mosaic in all three imaging channels despite a wide spectral separation between the wavefront sensing and imaging channels.

OCIS codes

(110.1080) Active or adaptive optics; (170.4460) Ophthalmic optics and devices; (170.4470) Ophthalmology
Taking population stratification into account by local permutations in rare-variant association studies on small samples
Authors: Mullaert J. , Bouaziz M. , Seeleuthner Y. , Bigio B. , Casanova J-L. , Alcais A. , Abel L. , Cobat A.
Published: January 2020

Many methods for rare variant association studies require permutations to assess the significance of tests. Standard permutations assume that all individuals are exchangeable and do not take population stratification (PS), a known confounding factor in genetic studies, into account. We propose a novel strategy,LocPerm, in which individuals are permuted only with their closest ancestry-based neighbors. We performed a simulation study, focusing on small samples, to evaluate and compareLocPermwith standard permutations and classical adjustment on first principal components. Under the null hypothesis,LocPermwas the only method providing an acceptable type I error, regardless of sample size and level of stratification. The power ofLocPermwas similar to that of standard permutation in the absence of PS, and remained stable in different PS scenarios. We conclude thatLocPermis a method of choice for taking PS and/or small sample size into account in rare variant association studies.
The role of group I p21-activated kinases in contraction-stimulated skeletal muscle glucose transport
Authors: Møller Lisbeth L. V. , Nielsen Ida L. , Knudsen Jonas R. , Andersen Nicoline R. , Jensen Thomas E. , Sylow Lykke , Richter Erik A.
Published: January 2020

Aim

Muscle contraction stimulates skeletal muscle glucose transport. Since it occurs independently of insulin, it is an important alternative pathway to increase glucose uptake in insulin-resistant states, but the intracellular signalling mechanisms are not fully understood. Muscle contraction activates group I p21-activated kinases (PAKs) in mouse and human skeletal muscle. PAK1 and PAK2 are downstream targets of Rac1, which is a key regulator of contraction-stimulated glucose transport. Thus, PAK1 and PAK2 could be downstream effectors of Rac1 in contraction-stimulated glucose transport. The current study aimed to test the hypothesis that PAK1 and/or PAK2 regulate contraction-induced glucose transport.

Methods

Glucose transport was measured in isolated soleus and extensor digitorum longus (EDL) mouse skeletal muscle incubated either in the presence or absence of a pharmacological inhibitor (IPA-3) of group I PAKs or originating from whole-body PAK1 knockout (KO), muscle-specific PAK2 (m)KO or double whole-body PAK1 and muscle-specific PAK2 knockout mice.

Results

IPA-3 attenuated (−22%) the increase in muscle glucose transport in response to electrically-stimulated contraction. PAK1 was dispensable for contraction-stimulated glucose uptake in both soleus and EDL muscle. Lack of PAK2, either alone (−13%) or in combination with PAK1 (−14%), reduced contraction-stimulated glucose transport compared to control littermates in EDL, but not soleus muscle.

Conclusion

Contraction-stimulated glucose transport in isolated glycolytic mouse EDL muscle is partly dependent on PAK2, but not PAK1.
Unraveling the Mechanism of a LOV Domain Optogenetic Sensor: A Glutamine Lever Induces Unfolding of the Jα Helix
Authors: Iuliano James N. , Collado Jinnette Tolentino , Gil Agnieszka A. , Ravindran Pavithran T. , Lukacs Andras , Shin SeungYoun , Woroniecka Helena A. , Adamczyk Katrin , Aramini James M. , Edupuganti Uthama R. , Hall Christopher R. , Greetham Gregory M. , Sazanovich Igor V. , Clark Ian P. , Daryaee Taraneh , Toettcher Jared E. , French Jarrod B. , Gardner Kevin H. , Simmerling Carlos L. , Meech Stephen R. , Tonge Peter J.
Published: January 2020

Light-activated protein domains provide a convenient, modular, and genetically encodable sensor for optogenetics and optobiology. Although these domains have now been deployed in numerous systems, the precise mechanism of photoactivation and the accompanying structural dynamics that modulate output domain activity remain to be fully elucidated. In the C-terminal light, oxygen, voltage (LOV) domain of plant phototropins (LOV2), blue light activation leads to formation of an adduct between a conserved Cys residue and the embedded FMN chromophore, rotation of a conserved Gln (Q513), and unfolding of a helix (Jα-helix) which is coupled to the output partner. In the present work, we focus on the allosteric pathways leading to Jα helix unfolding inAvena sativaLOV2 (AsLOV2) using an interdisciplinary approach involving molecular dynamics simulations extending to 7 μs, time-resolved infrared spectroscopy, solution NMR spectroscopy, and in-cell optogenetic experiments. In the dark state, the side chain of N414 is hydrogen bonded to the backbone N-H of Q513. The simulations predict a lever-like motion of Q513 after Cys adduct formation resulting in loss of the interaction between the side chain of N414 and the backbone C=O of Q513, and formation of a transient hydrogen bond between the Q513 and N414 side chains. The central role of N414 in signal transduction was evaluated by site-directed mutagenesis supporting a direct link between Jα helix unfolding dynamics and the cellular function of the Zdk2-AsLOV2 optogenetic construct. Through this multifaceted approach, we show that Q513 and N414 are critical mediators of protein structural dynamics, linking the ultrafast (sub-ps) excitation of the FMN chromophore to the microsecond conformational changes that result in photoreceptor activation and biological function.