bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functions of cyclins and CDKs in mammalian gametogenesis†
Authors: Chotiner Jessica Y , Wolgemuth Debra J , Wang P Jeremy 
Published: April 2019

AbstractCyclins and cyclin-dependent kinases (CDKs) are key regulators of the cell cycle. Most of our understanding of their functions has been obtained from studies in single-cell organisms and mitotically proliferating cultured cells. In mammals, there are more than 20 cyclins and 20 CDKs. Although genetic ablation studies in mice have shown that most of these factors are dispensable for viability and fertility, uncovering their functional redundancy, CCNA2, CCNB1, and CDK1 are essential for embryonic development. Cyclin/CDK complexes are known to regulate both mitotic and meiotic cell cycles. While some mechanisms are common to both types of cell divisions, meiosis has unique characteristics and requirements. During meiosis, DNA replication is followed by two successive rounds of cell division. In addition, mammalian germ cells experience a prolonged prophase I in males or a long period of arrest in prophase I in females. Therefore, cyclins and CDKs may have functions in meiosis distinct from their mitotic functions and indeed, meiosis-specific cyclins, CCNA1 and CCNB3, have been identified. Here, we describe recent advances in the field of cyclins and CDKs with a focus on meiosis and early embryogenesis.
Systematic Review of Literature: Social Capital and Adolescents who are Deaf or Hard of Hearing
Authors: Byatt Timothy J , Dally Kerry , Duncan Jill 
Published: April 2019

AbstractOutcomes have improved for adolescents who are deaf or hard of hearing (DHH) in recent years in areas such as language and speech; however, outcomes such as pragmatic and psychosocial development are still not equal to adolescents with typical hearing. This systematic review of literature explored recent research as it pertains to social capital and adolescents who are DHH. The inclusion criteria were extended to include other populations who are DHH and adolescents with other disabilities to identify future research directions. Themes identified in the reviewed literature viewed through social capital theory included psychosocial outcomes; the importance of language; the benefit of online social networking sites; the role of the family; the role of the school; inclusion and identity; role models; and post-school transition. Results demonstrated that social capital is an area with much promise as it relates to buffering outcomes for adolescents who are DHH. More empirical evidence is required in the form of quantitative research using validated social capital instruments and qualitative research that gives a voice to adolescents who are DHH. The role of social capital in facilitating inclusion, identity, and friendships, were identified as possible future research directions.
The BFK20 phage replication origin confers a phage-encoded resistance phenotype to the industrial strain Brevibacterium flavum
Authors: Bukovska Gabriela , Ugorcakova Jana , Halgasova Nora , Bocanova Lucia , Tkacova Adela 
Published: April 2019

ABSTRACT
The phage BFK20 replication origin was identified using bioinformatics tools and a fragment with the origin nucleotide sequence was cloned into the tetracycline resistance gene of Escherichia coli vector pBR328, to make the plasmid pBOS. After transformation into the host strain Brevibacterium flavum CCM 251, pBOS was able to replicate, showing that the cloned region may function as a replication origin. The presence of the BFK20 origin sequence in a pBOS plasmid isolated from B. flavum CCM 251 was confirmed by Southern hybridisation. Monitoring pBOS stability in corynebacterial hosts showed that pBOS was stable in Corynebacterium glutamicum RM3 for 20 generations and in B. flavum CCM 251 for 10 generations. The effect of the cloned BFK20 replication origin on host resistance to BFK20 infection was tested. Growth of a B. flavum CCM 251 strain harbouring pBOS stopped after phage infection, but without complete lysis. Five hours after infection, the viability of the modified strain was about five times higher than the viability of wild-type B. flavum CCM 251. Thus, the ability of the BFK20 replication origin to confer the origin-derived phage-encoded resistance phenotype to B. flavum CCM 251 was confirmed.
Biophysical Effects on the Scaling of Plant Growth, Form, and Ecology
Authors: Niklas K J , Hammond S T 
Published: April 2019

Abstract
Physical laws and processes influence the ability of plants to exchange mass and energy with their external environments, thereby directly influencing global ecosystem functions such as water and CO2 cycles. Six fundamental physical laws and processes (e.g., Fick’s law of diffusion and the Euler–Greenhill equation for elastic self-similarity) are reviewed in the context of how they affect growth, body size, shape, and ecology. This review shows that biophysical effects on energy–mass exchange rates significantly influence the scaling of plant growth and form, while simultaneously providing opportunities for adaptation and the exploration of unoccupied regions in the plant morphospace.
Non-lytic antibiotic treatment in community-acquired pneumococcal pneumonia does not attenuate inflammation: the PRISTINE trial
Authors: Groeneveld Geert H , van der Reyden Tanny J , Joosten Simone A , Bootsma Hester J , Cobbaert Christa M , de Vries Jutte J C , Kuijper Ed J , van Dissel Jaap T 
Published: April 2019

AbstractBackgroundThe inflammatory response in pneumococcal infection is primarily driven by immunoreactive bacterial cell wall components [lipoteichoic acid (LTA)]. An acute release of these components occurs when pneumococcal infection is treated with β-lactam antibiotics.ObjectivesWe hypothesized that non-lytic rifampicin compared with lytic β-lactam antibiotic treatment would attenuate the inflammatory response in patients with pneumococcal pneumonia.MethodsIn the PRISTINE (Pneumonia treated with RIfampicin aTtenuates INflammation) trial, a randomized, therapeutic controlled, exploratory study in patients with community-acquired pneumococcal pneumonia, we looked at LTA release and inflammatory and clinical response during treatment with both rifampicin and β-lactam compared with treatment with β-lactam antibiotics only. The trial is registered in the Dutch trial registry, number NTR3751 (European Clinical Trials Database number 2012-003067-22).ResultsForty-one patients with community-acquired pneumonia were included; 17 of them had pneumococcal pneumonia. LTA release, LTA-mediated inflammatory responses, clinical outcomes, inflammatory biomarkers and transcription profiles were not different between treatment groups.ConclusionsThe PRISTINE study demonstrated the feasibility of adding rifampicin to β-lactam antibiotics in the treatment of community-acquired pneumococcal pneumonia, but, despite solid in vitro and experimental animal research evidence, failed to demonstrate a difference in plasma LTA concentrations and subsequent inflammatory and clinical responses. Most likely, an inhibitory effect of human plasma contributes to the low immune response in these patients. In addition, LTA plasma concentration could be too low to mount a response via Toll-like receptor 2 in vitro, but may nonetheless have an effect in vivo.
Temperature-sensitive mutants of MscL mechanosensitive channel
Authors: Owada Naoto , Yoshida Megumi , Morita Kohei , Yoshimura Kenjiro 
Published: April 2019

Abstract
MscL is a mechanosensitive channel that undergoes a global conformational change upon application of membrane stretching. To elucidate how the structural stability and flexibility occur, we isolated temperature-sensitive (Ts) mutants of Escherichia coli MscL that allowed cell growth at 32°C but not at 42°C. Two Ts mutants, L86P and D127V, were identified. The L86P mutation occurred in the second transmembrane helix, TM2. Substitution of residues neighbouring L86 with proline also led to a Ts mutation, but the substitution of L86 with other amino acids did not result in a Ts phenotype, indicating that the Ts phenotype was due to a structural change of TM2 helix by the introduction of a proline residue. The D127V mutation was localized in the electrostatic belt of the bundle of cytoplasmic helices, indicating that stability of the pentameric bundle of the cytoplasmic helix affects MscL structure. Together, this study described a novel class of MscL mutations that were correlated with the thermodynamic stability of the MscL structure.
Gene–Environment Correlation in Humans: Lessons from Psychology for Quantitative Genetics
Authors: Saltz Julia B 
Published: April 2019

Abstract
Evolutionary biologists have long been aware that the effects of genes can reach beyond the boundary of the individual, that is, the phenotypic effects of genes can alter the environment. Yet, we rarely apply a quantitative genetics approach to understand the causes and consequences of genetic variation in the ways that individuals choose and manipulate their environments, particularly in wild populations. Here, I aim to stimulate research in this area by reviewing empirical examples of such processes from the psychology literature. Indeed, psychology researchers have been actively investigating genetic variation in the environments that individuals experience—a phenomenon termed “gene–environment correlation” (rGE)—since the 1970s. rGE emerges from genetic variation in individuals’ behavior and personality traits, which in turn affects the environments that they experience. I highlight concepts and examples from this literature, emphasizing the relevance to quantitative geneticists working on wild, nonhuman organisms. I point out fruitful areas of crossover between these disciplines, including how quantitative geneticists can test ideas about rGE in wild populations.
Neoadjuvant FOLFIRINOX in Patients With Borderline Resectable Pancreatic Cancer: A Systematic Review and Patient-Level Meta-Analysis
Authors: Janssen Quisette P , Buettner Stefan , Suker Mustafa , Beumer Berend R , Addeo Pietro , Bachellier Philippe , Bahary Nathan , Bekaii-Saab Tanios , Bali Maria A , Besselink Marc G , Boone Brian A , Chau Ian , Clarke Stephen , Dillhoff Mary , El-Rayes Bassel F , Frakes Jessica M , Grose Derek , Hosein Peter J , Jamieson Nigel B , Javed Ammar A , Khan Khurum , Kim Kyu-Pyo , Kim Song Cheol , Kim Sunhee S , Ko Andrew H , Lacy Jill , Margonis Georgios A , McCarter Martin D , McKay Colin J , Mellon Eric A , Moorcraft Sing Yu , Okada Ken-Ichi , Paniccia Alessandro , Parikh Parag J , Peters Niek A , Rabl Hans , Samra Jaswinder , Tinchon Christoph , van Tienhoven Geertjan , van Veldhuisen Eran , Wang-Gillam Andrea , Weiss Matthew J , Wilmink Johanna W , Yamaue Hiroki , Homs Marjolein Y V , van Eijck Casper H J , Katz Matthew H G , Groot Koerkamp Bas 
Published: April 2019

Abstract

Background
FOLFIRINOX is a standard treatment for metastatic pancreatic cancer patients. The effectiveness of neoadjuvant FOLFIRINOX in patients with borderline resectable pancreatic cancer (BRPC) remains debated.

Methods
We performed a systematic review and patient-level meta-analysis on neoadjuvant FOLFIRINOX in patients with BRPC. Studies with BRPC patients who received FOLFIRINOX as first-line neoadjuvant treatment were included. The primary endpoint was overall survival (OS), and secondary endpoints were progression-free survival, resection rate, R0 resection rate, and grade III–IV adverse events. Patient-level survival outcomes were obtained from authors of the included studies and analyzed using the Kaplan-Meier method.

Results
We included 24 studies (8 prospective, 16 retrospective), comprising 313 (38.1%) BRPC patients treated with FOLFIRINOX. Most studies (n = 20) presented intention-to-treat results. The median number of administered neoadjuvant FOLFIRINOX cycles ranged from 4 to 9. The resection rate was 67.8% (95% confidence interval [CI] = 60.1% to 74.6%), and the R0-resection rate was 83.9% (95% CI = 76.8% to 89.1%). The median OS varied from 11.0 to 34.2 months across studies. Patient-level survival data were obtained for 20 studies representing 283 BRPC patients. The patient-level median OS was 22.2 months (95% CI = 18.8 to 25.6 months), and patient-level median progression-free survival was 18.0 months (95% CI = 14.5 to 21.5 months). Pooled event rates for grade III–IV adverse events were highest for neutropenia (17.5 per 100 patients, 95% CI = 10.3% to 28.3%), diarrhea (11.1 per 100 patients, 95% CI = 8.6 to 14.3), and fatigue (10.8 per 100 patients, 95% CI = 8.1 to 14.2). No deaths were attributed to FOLFIRINOX.

Conclusions
This patient-level meta-analysis of BRPC patients treated with neoadjuvant FOLFIRINOX showed a favorable median OS, resection rate, and R0-resection rate. These results need to be assessed in a randomized trial.
Functional divergence between soybean FLOWERING LOCUS T orthologues FT2a and FT5a in post-flowering stem growth
Authors: Takeshima Ryoma , Nan Haiyang , Harigai Kohei , Dong Lidong , Zhu Jianghui , Lu Sijia , Xu Meilan , Yamagishi Noriko , Yoshikawa Nobuyuki , Liu Baohui , Yamada Tetsuya , Kong Fanjiang , Abe Jun 
Published: April 2019

Abstract
Genes in the FLOWERING LOCUS T (FT) family integrate external and internal signals to control various aspects of plant development. In soybean (Glycine max), FT2a and FT5a play a major role in floral induction, but their roles in post-flowering reproductive development remain undetermined. Ectopic overexpression analyses revealed that FT2a and FT5a similarly induced flowering, but FT5a was markedly more effective than FT2a for the post-flowering termination of stem growth. The down-regulation of Dt1, a soybean orthologue of Arabidopsis TERMINAL FLOWER1, in shoot apices in early growing stages of FT5a-overexpressing plants was concomitant with highly up-regulated expression of APETALA1 orthologues. The Dt2 gene, a repressor of Dt1, was up-regulated similarly by the overexpression of FT2a and FT5a, suggesting that it was not involved in the control of stem termination by FT5a. In addition to the previously reported interaction with FDL19, a homologue of the Arabidopsis bZIP protein FD, both FT2a and FT5a interacted with FDL12, but only FT5a interacted with FDL06. Our results suggest that FT2a and FT5a have different functions in the control of post-flowering stem growth. A specific interaction of FT5a with FDL06 may play a key role in determining post-flowering stem growth in soybean.
Cellular and molecular characterization of a thick-walled variant reveal a pivotal role of shoot apical meristem in transverse development of bamboo culm
Authors: Wang Yujun , Sun Xuepeng , Ding Yulong , Fei Zhangjun , Jiao Chen , Fan Mingyuan , Yao Bingfan , Xin Peiyong , Chu Jinfang , Wei Qiang 
Published: April 2019

AbstractLittle is known about the mechanisms underlying the development of bamboo culm. Using anatomical, mathematical modeling, and genomics methods, we investigated the role of shoot apical meristem (SAM) in the development of the transverse morphology of bamboo culm and explored the underlying cellular and molecular processes. We discovered that maintenance of SAM morphology that can produce circular culm and increase in SAM cell numbers, especially corpus cells, is the means by which bamboo makes a larger culm with a regular pith cavity and culm wall during development. A less cellular form of SAM with a lower proportion of corpus cells causes an abnormal higher ratio of wall component cells to pith cells, which breaks the balance of their interaction and triggers the random invasion of wall component cells into pith tissues during development, and finally results in the various thick culm walls of Phyllostachys nidularia f. farcta. The smaller SAM also results in a lower level of hormones such as cytokinin and auxin, and down-regulates hormone signaling and the downstream functional genes such as those related to metabolism, which finally results in a dwarf and smaller diameter culm with lower biomass. These results provide an important perspective on the culm development of bamboo, and support a plausible mechanism causing the size-reduced culm and various thick culm walls of P. nidularia f. farcta.
OrthoVenn2: a web server for whole-genome comparison and annotation of orthologous clusters across multiple species
Authors: Xu Ling , Dong Zhaobin , Fang Lu , Luo Yongjiang , Wei Zhaoyuan , Guo Hailong , Zhang Guoqing , Gu Yong Q , Coleman-Derr Devin , Xia Qingyou , Wang Yi 
Published: April 2019

AbstractOrthoVenn is a powerful web platform for the comparison and analysis of whole-genome orthologous clusters. Here we present an updated version, OrthoVenn2, which provides new features that facilitate the comparative analysis of orthologous clusters among up to 12 species. Additionally, this update offers improvements to data visualization and interpretation, including an occurrence pattern table for interrogating the overlap of each orthologous group for the queried species. Within the occurrence table, the functional annotations and summaries of the disjunctions and intersections of clusters between the chosen species can be displayed through an interactive Venn diagram. To facilitate a broader range of comparisons, a larger number of species, including vertebrates, metazoa, protists, fungi, plants and bacteria, have been added in OrthoVenn2. Finally, a stand-alone version is available to perform large dataset comparisons and to visualize results locally without limitation of species number. In summary, OrthoVenn2 is an efficient and user-friendly web server freely accessible at https://orthovenn2.bioinfotoolkits.net.
AlloDriver: a method for the identification and analysis of cancer driver targets
Authors: Song Kun , Li Qian , Gao Wei , Lu Shaoyong , Shen Qiancheng , Liu Xinyi , Wu Yongyan , Wang Binquan , Lin Houwen , Chen Guoqiang , Zhang Jian 
Published: April 2019

Abstract
Identifying the variants that alter protein function is a promising strategy for deciphering the biological consequences of somatic mutations during tumorigenesis, which could provide novel targets for the development of cancer therapies. Here, based on our previously developed method, we present a strategy called AlloDriver that identifies cancer driver genes/proteins as possible targets from mutations. AlloDriver utilizes structural and dynamic features to prioritize potentially functional genes/proteins in individual cancers via mapping mutations generated from clinical cancer samples to allosteric/orthosteric sites derived from three-dimensional protein structures. This strategy exhibits desirable performance in the reemergence of known cancer driver mutations and genes/proteins from clinical samples. Significantly, the practicability of AlloDriver to discover novel cancer driver proteins in head and neck squamous cell carcinoma (HNSC) was tested in a real case of human protein tyrosine phosphatase, receptor type K (PTPRK) through a L1143F driver mutation located at the allosteric site of PTPRK, which was experimentally validated by cell proliferation assay. AlloDriver is expected to help to uncover innovative molecular mechanisms of tumorigenesis by perturbing proteins and to discover novel targets based on cancer driver mutations. The AlloDriver is freely available to all users at http://mdl.shsmu.edu.cn/ALD.
Light-Induced Artemisinin Biosynthesis Is Regulated by the bZIP Transcription Factor AaHY5 in Artemisia annua
Authors: Hao Xiaolong , Zhong Yijun , N�tzmann Hans-Wilhelm , Fu Xueqing , Yan Tingxiang , Shen Qian , Chen Minghui , Ma Yanan , Zhao Jingya , Osbourn Anne , Li Ling , Tang Kexuan 
Published: April 2019

Abstract
Artemisinin, the frontline drug against malaria, is a sesquiterpenoid extracted from Artemisia annua. Light has been proposed to play an important role in the activation of artemisinin biosynthesis. Here, we report the basic leucine zipper transcription factor (TF) AaHY5 as a key regulator of light-induced biosynthesis of artemisinin. We show that AaHY5 transcription overlaps with that of artemisinin biosynthesis genes in response to light and in A. annua tissues. Analysis of AaHY5 overexpression and RNAi-suppression lines suggests that AaHY5 is a positive regulator of the expression of artemisinin biosynthesis genes and accumulation of artemisinin. We show that AaHY5 complements the hy5 mutant in Arabidopsis thaliana. Our data further suggest that AaHY5 interacts with AaCOP1, the ubiquitin E3 ligase CONSTITUTIVE PHOTOMORPHOGENIC1 in A. annua. In yeast one-hybrid and transient expression assays, we demonstrate that AaHY5 acts via the TF GLANDULAR TRICHOME-SPECIFIC WRKY 1 (AaGSW1) in artemisinin regulation. In summary, we present a novel regulator of artemisinin gene expression and propose a model in which AaHY5 indirectly controls artemisinin production in response to changing light conditions.
Vortioxetine in the Treatment of Mood Disorders Associated with Burning Mouth Syndrome: Results of an Open-Label, Flexible-Dose Pilot Study
Authors: Adamo Daniela , Pecoraro Giuseppe , Aria Massimo , Favia Gianfranco , Mignogna Michele Davide 
Published: April 2019

Abstract

Objective
To evaluate the efficacy of a new multimodal antidepressant, vortioxetine (VO), in the management of burning mouth syndrome (BMS).

Design
Longitudinal single-assessment open-label pilot study.

Setting
University hospital. Subjects. Thirty BMS patients were enrolled.

Methods
BMS patients were treated with topical clonazepam and a flexible dose of VO (10 mg, 15 mg, or 20 mg). The visual analog scale (VAS), the Total Pain Rating Index (T-PRI), the Hamilton Rating Scales for Depression (HAM-D) and Anxiety (HAM-A), and the Pittsburgh Sleep Quality Index (PSQI) were performed at baseline (time 0) and after two (time 1), four (time 2), six (time 3), and 12 months (time 4) of treatment. Descriptive statistics and the Wilcoxon nonparametric test for two paired samples were used.

Results
The BMS patients showed a statistically significant improvement in VAS and T-PRI scores from baseline (median [interquartile range {IQR}] = 10.0 [10–10] and 22.0 [20–24], respectively) to time 4 (median [IQR] = 0.0 [0–0] and 8.0 [7–9], P < 0.001, respectively). Similarly, the HAM-A and HAM-D and PSQI scores showed an improvement from time 0 (median [IQR] = 20 [15.8–22], 19 [16–20.3], and 4.0 [4–7.3], respectively) to time 4 (median [IQR] = 6.0 [6–7], 6.0 [6–7], and 3.0 [3–4], respectively, P < 0.001).

Conclusions
VO is efficacious and well tolerated in the treatment of BMS in firstline therapy on account of its better receptor pharmacological profile and in second-line treatment for patients who have only partially responded or have reported adverse effects to previous treatments.
Managing a Pregnancy With Maternal Amelia
Authors: Siwatch Sujata , Gainder Shalini , Prasad Gurgunjakunta Ramabhadraraju Venkateshwara , Jain Vanita , Rohilla Meenakshi , Kuberan Aswini 
Published: April 2019

INTRODUCTION:
Amelia, the complete absence of a limb, presents various management issues in pregnancy and delivery.

CASE:
A woman with amelia of both lower limbs and flipper-like upper limb buds (phocomelia) presented in her first pregnancy at 19 weeks of gestation. Challenging issues encountered in the care of the patient included venous access, reliable blood pressure measurement, recommendations regarding mode of delivery, and preparation for caring for the child. The patient had abnormalities of the pelvis but an adequate midpelvis, so she was able to deliver vaginally without complication.

CONCLUSION:
Careful planning to allow necessary modification of intrapartum management can allow for normal vaginal birth for a patient with severe limb reduction abnormalities such as amelia and phocomelia.