bluuebunny/crossref_metadata_2025 huggingface dataset:
Determining IDH-Mutational Status in Gliomas Using IDH1-R132H Antibody and Polymerase Chain Reaction
Authors: Gondim Dibson D. , Gener Melissa A. , Curless Kendra L. , Cohen-Gadol Aaron A. , Hattab Eyas M. , Cheng Liang
Published: October 2018

Determination of the isocitrate dehydrogenase (IDH) mutation status, presence or absence of mutation in IDH genes (IDH1 or IDH2), has become one of the most important molecular features taken into account in the management of patients with diffuse gliomas. Tumors that are IDH-mutant have a better prognosis than their counterparts with similar histologic grade and IDH-wildtype phenotype. IDH1-R132H is the most common IDH mutation, present in ~90% of IDH-mutant cases. This mutation yields an altered protein that can be detected by immunohistochemistry. We evaluated the IDH1-R132H antibody (clone H09) to determine IDH mutation status as the first line test and compared with the results of polymerase chain reaction (PCR) testing that can detect more types of mutations in IDH1 or IDH2. A total of 62 gliomas were evaluated: 30 glioblastomas (including 3 gliosarcomas), 11 grade III diffuse gliomas, 17 grade II diffuse gliomas, and 4 circumscribed gliomas. Twelve of 62 cases were IDH-mutant by immunohistochemistry and 15 of 62 by PCR. PCR detected the following mutations: IDH1-R132H (11 cases), IDH1-R132C (1 case), IDH2 R172, NOS (1 case), IDH1 R132, NOS (1 case), and IDH2-R172K (1 case). The R132H antibody had high specificity (100%) and sensitivity (80%) to detect IDH mutation status; the discordant results were 3 false-negatives. IDH-R132H immunostain is suitable as a first line test. Nonimmunoreactive cases could be studied by PCR following recommendations of the 2016 World Health Organization guidelines.
Differentially Expressed Genes in Matched Normal, Cancer, and Lymph Node Metastases Predict Clinical Outcomes in Patients With Breast Cancer
Authors: Kim Ga-Eon , Kim Nah Ihm , Lee Ji Shin , Park Min Ho , Kang Keunsoo
Published: October 2018

Genome-wide screening of transcriptional changes among normal, cancer, and nodal metastases provides insights into the molecular basis of breast cancer (BC) progression and metastasis. To identify transcriptional changes and differentially expressed genes (DEGs) in the metastatic progression of BC and to determine the prognostic role of these DEGs in clinical outcome, we compared transcriptome profiling in matched normal, cancer, and lymph node metastatic tissues of 7 patients with estrogen receptor–positive, HER2-negative BC by using massive parallel RNA sequencing. The global profiles of gene expression in cancer and nodal metastases were highly correlated (r=0.962, P<0.001). In 6 (85.8%) patients, cancer and corresponding nodal metastases from the same patient clustered together. We identified 1522 and 664 DEGs between normal and cancer and between cancer and nodal metastases, respectively. The DEGs in normal versus cancer and cancer versus nodal metastases were significantly clustered in 1 and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, respectively. The chemokine signaling pathway was the most significant pathway in the cancer-to-nodal metastasis transition (false discovery rate=2.15E−13). The expression of 2 dysregulated RAC2 and PTGDS genes was confirmed by quantitative real-time polymerase chain reaction and immunohistochemistry. Interestingly, the lower RAC2 and PTGDS expression were associated with significantly worse disease-free survival in patients with BC. Our results show a high concordance of gene expression in BC and their nodal metastases, and identify DEGs associated with the metastatic progression of BC. The DEGs identified in this study represent novel biomarkers for predicting the prognosis of patients with BC.
Temporal Evaluation of Craniofacial Relationships in Apert Syndrome
Authors: Lu Xiaona , Forte Antonio Jorge , Sawh-Martinez Rajendra , Wu Robin , Cabrejo Raysa , Gabrick Kyle , Steinbacher Derek M. , Alperovich Michael , Alonso Nivaldo , Persing John A.
Published: October 2018

Complicated craniofacial malformations interfacing with multiple intracellular regulatory mechanisms, lead to ambiguous growth patterns in Apert syndrome. This study aims to explore the chronology and pathogenesis of the development of craniofacial anatomic relationships and to verify the positional correlates between skull and facial structures in Apert syndrome. Fifty-four computed tomography scans (Apert, n = 18; control, n = 36) were included and divided into 3 age subgroups. Craniofacial 3-dimensional cephalometries were analyzed by Materialize software. The angle between sella-nasion plane and maxillary plane widens 7.74° (P = 0.003) prior to 6 months of age; thereafter, this widening increases by 10.36° (P < 0.001) in 6 months to 2 years of age, and remains increased by 8.9° (P = 0.046) throughout childhood. The angle between Frankfort horizontal plane and maxillary plane widens 5.17° (P = 0.022) before 6 months. Angles SNA, SNB, and ANB showed decreases, averaging 12.23° (P < 0.001), 5.19° (P = 0.004), and 6.72° (P = 0.001), respectively. The linear measurements showed synchronicity and continuing deformity into adulthood. Between 6 months to 2 years of age, the distance from sella to nasion (S-N), anterior nasal spine (S-ANS), and posterior nasal spine (S-PNS) decreased 8% (P = 0.006), 16% (P < 0.001), and 19% (P = 0.002), respectively, and remained shortened into adulthood. The angulation changes occur earlier in development than linear distance reduction in Apert syndrome patients compared with controls. Angular adjustments were not sufficient to maintain normal cranial base length. Facial deformity of Apert syndrome temporally begins with the midface, and affects orbit and mandible later in life.
The Safety and Feasibility of Gynecologic Cancer Surgery Combined With Surgery for Pelvic Floor Dysfunction
Authors: McConnell Nicole J. , Stewart J. Ryan , Martin Alexandra , Gaskins Jeremy T. , Medlin Erin E.
Published: October 2018

Objectives

Women with gynecologic cancer may also present with pelvic floor dysfunction that can have a significant effect on quality of life. Combined surgical intervention for both malignancy and pelvic floor dysfunction may improve quality of life with minimal additional risk. We sought to determine the safety, feasibility, and frequency of combined gynecologic cancer surgery and surgery for pelvic floor dysfunction.

Methods

This is a retrospective cohort study that utilized the National Surgical Quality Improvement Program database provided through the American College of Surgeons. The National Surgical Quality Improvement Program database was queried for patients with a final diagnosis of gynecologic malignancy from 2011 to 2015. Common Procedural Terminology codes for gynecologic oncology procedures and pelvic floor dysfunction surgery were used to identify the study population. Baseline demographics and postoperative complications were abstracted from the database for these patients and compared for patients with combined surgeries versus gynecologic cancer surgeries alone.

Results

One hundred twenty-nine women underwent combined procedures compared with 25,838 women undergoing gynecologic cancer surgery alone. Patients who underwent combined procedures were older, had lower body mass index, had higher preoperative albumin and hematocrit, and lower morbidity estimates (P < 0.05). Mean operative time was longer (226.4 vs 174.4 minutes, P < 0.01). There were no statistically significant differences in race, ethnicity, or medical comorbidities. There were no statistically significant differences in postoperative complications or readmissions between the 2 groups (P > 0.1).

Conclusions

Combined gynecologic cancer and pelvic floor dysfunction procedures are feasible and can safely be performed without differences in postoperative complications in appropriately selected patients.
The impact of prehospital administration of freeze-dried plasma on casualty outcome
Authors: Shlaifer Amir , Siman-Tov Maya , Radomislensky Irina , Peleg Kobi , Klein Yoram , Glassberg Elon , Yitzhak Avraham
Published: October 2018

BACKGROUND

Hemorrhage is the most common preventable cause of death in both civilian and military trauma. There is no consensus regarding the appropriate fluid resuscitation protocol. Plasma, as a resuscitative fluid, has substantial benefits as a volume expander, owing to its relatively high oncotic pressure and its positive effect on trauma-induced coagulopathy by replenishing the lost coagulation factors, rather than diluting the casualty's remaining factors. The Israel Defense Force Medical Corps decided to use freeze-dried plasma (FDP) as the fluid of choice for casualties in hemorrhagic shock in the prehospital setting. The aim of our study is to compare the differences of coagulation, perfusion measurements, resource utilization, and outcome between casualties receiving FDP to casualties who did not receive FDP in the prehospital setting.

METHODS

This is a retrospective matched cohort study based on two groups of casualties (those treated with FDP vs. those without FDP treatment). The control group was compiled in three steps of precision for age, sex, mechanism of injury and maximum level of severity for each nine injured body regions. Data were collected from the IDF Trauma Registry and The National Israel Trauma Registry.

RESULTS

The study group comprised 48 casualties receiving FDP and 48 controls with no differences in demographic, evacuation time, and injury characteristics. The FDP group demonstrated a lower level of hemoglobin (12.7 gr/dzl) (odds ratio [OR], 3.11; 95% confidence interval [CI], 1.10–8.80), lower level of international normalized ratio (1.1) (OR, 3.09; 95% CI, 1.04–9.14), and lower level of platelets (230 × 109/L) (OR, 3.06; 95% CI, 1.16–8.06). No other differences were found between the two groups.

CONCLUSION

The use of FDP in the prehospital setting has logistic benefits and a positive effect on coagulation profile, with no other significant effects. Future studies need to be performed on larger groups to verify trends or nullify our hypotheses.

LEVEL OF EVIDENCE

Therapeutic, level IV.
Proteomic changes in traumatic brain injury: experimental approaches
Authors: Sowers James L. , Wu Ping , Zhang Kangling , DeWitt Douglas S. , Prough Donald S.
Published: October 2018

Purpose of review

The underlying mechanisms responsible for chronic and progressive neurological damage after traumatic brain injury (TBI) are poorly understood, and therefore, current treatment options are limited. Proteomics is an emerging methodology to study changes to the TBI proteome in both patients and experimental models.

Recent findings

Although experimentally complex, mass spectrometry-based proteomics approaches are converging on a set of common methods. However, these methods are being applied to an increasingly diverse range of experimental models and types of injury.

In this review, our aim is to briefly describe experimental TBI models and the underlying methods common to most proteomic approaches. We will then review a series of articles that have recently appeared in which these approaches have been applied to important TBI questions. We will summarize several recent experimental studies, and suggest how the results of these emerging studies might impact future research as well as patient treatment.
LC3 and STRAP regulate actin filament assembly by JMY during autophagosome formation
Authors: Hu Xiaohua , Mullins R. Dyche
Published: October 2018

During autophagy actin filament networks move and remodel cellular membranes to form autophagosomes that enclose and metabolize cytoplasmic contents. Two actin regulators, WHAMM and JMY, participate in autophagosome formation, but the signals linking autophagy to actin assembly are poorly understood. We show that, in non-starved cells, cytoplasmic JMY co-localizes with STRAP, a regulator of JMY’s nuclear functions, on non-motile vesicles with no associated actin networks. Upon starvation, JMY shifts to motile, LC3-containing membranes that move on actin comet tails. LC3 enhances JMY’s de novo actin nucleation activity via a cryptic actin-binding sequence near JMY’s N-terminus, and STRAP inhibits JMY’s ability to nucleate actin and activate the Arp2/3 complex. Cytoplasmic STRAP negatively regulates autophagy. Finally, we use purified proteins to reconstitute LC3‐ and JMY-dependent actin network formation on membranes, and inhibition of network formation by STRAP. We conclude that LC3 and STRAP regulate JMY’s actin assembly activities in trans during autophagy.

eTOC Blurb

The actin regulator JMY creates filament networks that move membranes during autophagy. We find that, in unstarved cells, JMY is inhibited by interaction with the STRAP protein, but upon starvation JMY is recruited away from STRAP and activated by LC3.
Geometric cues stabilise long-axis polarisation of PAR protein patterns inC. elegans
Authors: Geßele Raphaela , Halatek Jacob , Würthner Laeschkir , Frey Erwin
Published: October 2018

In theCaenorhabditis eleganszygote, PAR protein patterns, driven by mutual anatagonism, determine the anterior-posterior axis and facilitate the redistribution of proteins for the first cell division. Yet, the factors that determine the selection of the polarity axis remain unclear. We present a reaction-diffusion model in realistic cell geometry, based on biomolecular reactions and accounting for the coupling between membrane and cytosolic dynamics. We find that the kinetics of the phosphorylation-dephosphorylation cycle of PARs and the diffusive protein fluxes from the cytosol towards the membrane are crucial for the robust selection of the anterior-posterior axis for polarisation. The local ratio of membrane surface to cytosolic volume is the main geometric cue that initiates pattern formation, while the choice of the long-axis for polarisation is largely determined by the length of the aPAR-pPAR interface, and mediated by processes that minimise the diffusive fluxes of PAR proteins between cytosol and membrane.
SPR-measured dissociation kinetics of PROTAC ternary complexes influence target degradation rate
Authors: Roy Michael J. , Winkler Sandra , Hughes Scott J. , Whitworth Claire , Galant Michael , Farnaby William , Rumpel Klaus , Ciulli Alessio
Published: October 2018

Bifunctional degrader molecules, known as proteolysis-targeting chimeras (PROTACs), function by recruiting a target to an E3 ligase, forming a target:PROTAC:ligase ternary complex. Despite the importance of this key intermediate species, no detailed validation of a method to directly determine binding parameters for ternary complex kinetics has been reported, and it remains to be addressed whether tuning the kinetics of PROTAC ternary complexes may be an effective strategy to improve the efficiency of targeted protein degradation. Here, we develop an SPR-based assay to quantify the stability of PROTAC-induced ternary complexes by measuring for the first time the kinetics of their formation and dissociation in vitro using purified proteins. We benchmark our assay using four PROTACs that target the bromodomains (BDs) of BET proteins Brd2, Brd3 and Brd4 to the E3 ligase VHL. We reveal marked differences in ternary complex off-rates for different PROTACs that exhibit either positive or negative cooperativity for ternary complex formation relative to binary binding. The positively cooperative degrader MZ1 forms comparatively stable and long-lived ternary complexes with either Brd4BD2 or Brd2BD2 and VHL. Equivalent complexes with Brd3BD2 are destabilised due to a single amino acid difference (Glu/Gly swap) present in the bromodomain. We observe that this difference in ternary complex dissociative half-life correlates to a greater initial rate of intracellular degradation of Brd2 and Brd4 relative to Brd3. These findings establish a novel assay to measure the kinetics of PROTAC ternary complexes and elucidate the important kinetic parameters that drive effective target degradation.
Relation between executive functions and polymorphisms in COMT, MAO-A, HTTLPR, SLC1A1 and HT2A in a sample of children with Obsessive Compulsive Disorder
Authors: Avila Campos Jorge Enrique , Pinto Dussan María Cristina , Polanco Barreto Ángela María , Guerrero Esneyder Manuel , Vásquez Rojas Rafael Antonio , Granados Humberto Arboleda
Published: October 2018

Background

Obsessive compulsive disorder (OCD) has a complex etiology related to multiple neuropsychological factors. OCD is associated with several candidate genes but results are discordant. The objective was to explore the association between five polymorphisms related to neurotransmitters, the risk of an OCD diagnosis and the performance in four executive functions tests done with Colombian patients diagnosed with this condition.

Methods

63 patients and 65 controls matched by gender and age were genetically analyzed. For the study of the relation between cognitive function and phenotypes, a subsample of 33 patients and 31 controls was used. The Stroop test, Wisconsin Card Sorting Test (WCST), Tower of London and Trail Making Test (TMT) for executive function assessment were applied and the SNPs analyzed were: COMT (rs4680), MAO-A (rs6323), HTTLPR (rs25531), HT2A (rs6315) and SLC1A1 (rs301434).

Results

Differences in the conceptualization of the WCST test (p = 0.023) and Stroop interference score (p = 0.041) between cases and controls were obtained. After analyzing the relationship between genotypes and sub-scores of the tests, associations between the presence of MAO-A, SLAC1A1, HTTLPR and HT2A alleles and tests sub-scores were found.

Discussion

This characterization of children with OCD is a new field of work in Colombia and one of the first works performed in Latin America. The sample size and the number of polymorphisms analyzed in this population should be increased.
A Haploid Genetic Screening Method for Proteins Influencing Mammalian Nonsense-Mediated mRNA Decay Activity
Authors: Popp Maximilian W. , Maquat Lynne E.
Published: October 2018

Despite a long appreciation for the role of nonsense-mediated mRNA decay (NMD) in the destruction of faulty, disease-causing mRNAs, as well as its role in the maintenance of normal, endogenous transcript abundance, systematic unbiased methods for uncovering modifiers of NMD activity in mammalian cells remain scant. Here we present and validate a haploid genetic screening method for identifying proteins and processes that stimulate NMD activity involving a 3′-untranslated region exon-junction complex. This reporterbased screening method can be adapted for interrogating other pathways whose output can be measured by the intracellular production of fluorescent proteins.
Measuring mobility in chromatin by intensity sorted FCS
Authors: Di Bona M. , Mancini M. A , Mazza D. , Vicidomini G. , Diaspro A. , Lanzanò L.
Published: October 2018

The architectural organization of chromatin can play an important role in genome regulation by affecting the mobility of molecules within its surroundings via binding interactions and molecular crowding. The diffusion of molecules at specific locations in the nucleus can be studied by Fluorescence Correlation Spectroscopy (FCS), a well-established technique based on the analysis of fluorescence intensity fluctuations detected in a confocal observation volume. However, detecting subtle variations of mobility between different chromatin regions remains challenging with currently-available FCS methods.

Here we introduce a method that samples multiple positions by slowly scanning the FCS observation volume across the nucleus. Analyzing the data in short time segments, we preserve the high temporal resolution of single-point FCS while probing different nuclear regions in the same cell. Using the intensity level of the probe (or a DNA marker) as a reference, we efficiently sort the FCS segments into different populations and obtain average correlation functions that are associated to different chromatin regions. This sorting and averaging strategy renders the method statistically robust while preserving the observation of intranuclear variations of mobility.

Using this approach, we quantified diffusion of monomeric GFP in high versus low chromatin density regions. We found that GFP mobility was reduced in heterochromatin, especially within perinucleolar heterochromatin. Moreover, we found that modulation of chromatin compaction by ATP depletion, or treatment with solution of different osmolarity, differentially-affected the ratio of diffusion in both regions. Then, we used the approach to probe the mobility of estrogen receptor-α (ER) in the vicinity of an integrated multicopy prolactin gene array. Finally, we discussed the coupling of this method with stimulated emission depletion (STED)-FCS, for performing FCS at sub-diffraction spatial scales.
The Heterotaxy Gene CCDC11 is Essential for Cytokinesis and Cell-Cell Adhesion via RhoA Regulation
Authors: Kulkarni Saurabh , Stephenson Rachel E. , Amalraj Sarah , Betleja Ewelina , Moresco James J. , Yates John R. , Mahjoub Moe R. , Miller Ann L. , Khokha Mustafa K.
Published: October 2018

Mutations in CCDC11 have been identified in multiple patients with heterotaxy (Htx), a disorder of left-right (LR) patterning of the internal organs. In Xenopus, depletion of Ccdc11 causes defects in LR patterning, recapitulating the patient phenotype. Upon Ccdc11 depletion, normally monociliated cells of the Left-Right Organizer (LRO) exhibit multiple cilia per cell. Unexpectedly, we found that Ccdc11 is necessary for successful cytokinesis, and the multiciliation observed in Ccdc11-depleted cells was due to failed cytokinesis. Furthermore, CCDC11 depletion alters cell-cell adhesion with reduction in junctional localization of adhesion molecules. The small GTPase RhoA is critical for cytokinesis and cell-cell adhesion. Because the CCDC11 depletion phenotypes are reminiscent of RhoA loss of function, we investigated a possible connection to regulation of RhoA signaling. We demonstrate that CCDC11 is localized to the cytokinetic contractile ring overlapping with RhoA during cytokinesis and regulates total RhoA protein levels. Our results suggest that CCDC11 connects cytokinesis and LR patterning via RhoA regulation, providing a potential mechanism for heterotaxy disease pathogenesis.
tbx5 and tbx15 mediate zebrafish posterior lateral line migration and development via a negative feedback loop
Authors: Whitehurst Heather R. , Gallardo Viviana E. , Burgess Shawn
Published: October 2018

The zebrafish posterior lateral line (pLL) is a mechanosensory organ enabling detection of movement in the aqueous environment. Evidence suggests that two T-box transcription factors,tbx5andtbx15, participate in pLL migration and development. Lateral line migration and deposition defects are observed followingtbx5ortbx15morpholino knockdown. Additional studies demonstrate that thetbx5phenotype is partially rescued whentbx15is also knocked down. pLL defects similar to those oftbx5are noted following knockdown ofcamKII-ß2, a known downstream target of Tbx5, suggesting a potential mechanistic pathway. Ectopic expression of humanCamKII-∂Cpartially rescues thetbx5phenotype but exacerbates thetbx15phenotype. These results, combined with in situ hybridization and qRT-PCR profiling, indicate a negative feedback loop controlling multiple primordium patterning markers, includingcxcr4b, cxcr7b, fgf10aandnotch3, which ultimately affects pLL neuromast migration and deposition.
Kinesin-5 forms a stable bipolar spindle in a fast, irreversible snap
Authors: Leary Allen , Nazarova Elena , Sim Shannon , Shulist Kristy , Francois Paul , Vogel Jackie
Published: October 2018

GRAPHICAL ABSTRACT

Separation of duplicated spindle poles is the first step in forming the mitotic spindle. Kinesin-5 crosslinks and slides anti-parallel microtubules, but it is unclear how these two activities contribute to the first steps in spindle formation. In this study we report that in monopolar spindles, the duplicated spindle poles snap apart in a fast and irreversible step that produces a nascent bipolar spindle. Using mutations in Kinesin-5 that inhibit microtubule sliding, we show crosslinking alone drives the fast, irreversible pole separation. Electron tomography revealed microtubule pairs in monopolar spindles have short overlaps that intersect at high angles and are unsuited for ensemble Kinesin-5 sliding. However, maximal extension of a subset of microtubule pairs approaches the length of nascent bipolar spindles and is consistent with a Kinesin-5 crosslinking driven transition. Finally, stochastic microtubule sliding by Kinesin-5 stabilizes the nascent spindle and sets a stereotyped equilibrium length.
A survey of fishes of Hombolo Lake, Dodoma, Tanzania, with evidence for local extinction of a native tilapia as a consequence of stocking
Authors: Turner George F. , Ngatunga Benjamin P. , Genner Martin J
Published: October 2018

The fish community of the Hombolo Lake, an impoundment on the Wami catchment near Dodoma, Tanzania, was surveyed in 2014 and 2017. The lake contains a relatively low diversity community dominated by two Oreochromis species introduced from outside the Wami catchment, O. niloticus and O. esculentus. Evidence from historical collections suggests that the native O. urolepis was formerly present, and its current absence is likely to be the result of competitive exclusion or genetic swamping by non-native species introduced for fishery enhancement. Four other fish species were also recorded.
cTAGE5 acts as a Sar1 GTPase regulator for collagen export
Authors: Sasaki Norito , Shiraiwa Masano , Maeda Miharu , Yorimitsu Tomohiro , Sato Ken , Katada Toshiaki , Saito Kota
Published: October 2018

Secretory proteins synthesized within the endoplasmic reticulum (ER) are exported via coat protein complex II (COPII)-coated vesicles. The formation of the COPII-coated vesicles is initiated by activation of the small GTPase, Sar1. cTAGE5 directly interacts with a guanine-nucleotide exchange factor (GEF), Sec12, and a GTPase-activating protein (GAP) of Sar1, Sec23. We have previously shown that cTAGE5 recruits Sec12 to the ER exit sites for efficient production of activated Sar1 for collagen secretion. However, the functional significance of the interaction between cTAGE5 and Sec23 has not been fully elucidated. In this study, we showed that cTAGE5 enhances the GAP activity of Sec23 toward Sar1. In addition, the interaction of cTAGE5 with Sec23 is necessary for collagen exit from the ER. Our data suggests that cTAGE5 acts as a Sar1 GTPase regulator for collagen secretion.
Interplay between substrate recognition, 5’ end tRNA processing and methylation activity of human mitochondrial RNase P
Authors: Karasik Agnes , Fierke Carol A. , Koutmos Markos
Published: October 2018

Human mitochondrial ribonuclease P (mtRNase P) is an essential three protein complex that catalyzes the 5’ end maturation of mitochondrial precursor tRNAs (pre-tRNAs). MRPP3 (Mitochondrial RNase P Protein 3), a protein-only RNase P (PRORP), is the nuclease component of the mtRNase P complex and requires a two-protein S-adenosyl methionine (SAM)-dependent methyltransferase MRPP1/2 sub-complex to function. Dysfunction of mtRNase P is linked to several human mitochondrial diseases, such as mitochondrial myopathies. Despite its central role in mitochondrial RNA processing, little is known about how the protein subunits of mtRNase P function synergistically. Here we use purified mtRNase P to demonstrate that mtRNase P recognizes, cleaves, and methylates some, but not all, mitochondrial pre-tRNAsin vitro. Additionally, mtRNase P does not process all mitochondrial pre-tRNAs uniformly, suggesting the possibility that some pre-tRNAs require additional factors to be cleavedin vivo. Consistent with this, we found that addition of the MRPP1 co-factor SAM enhances the ability of mtRNase P to bind and cleave some mitochondrial pre-tRNAs. Furthermore, the presence of MRPP3 can enhance the methylation activity of MRPP1/2. Taken together, our data demonstrate that the subunits of mtRNase P work together to efficiently recognize, process and methylate human mitochondrial pre-tRNAs.
Ethnobotanical and nutritional study ofquelitessold in two traditional markets of Oaxaca, Mexico
Authors: Manzanero-Medina G.I. , Pérez-Herrera A. , Lustre-Sánchez H. , Vásquez-Dávila M.A. , Santos-Sánchez N.F. , Sánchez-Medina M.A.
Published: October 2018

Background.

In Mexico, it is calledquelitesto certain edible vegetables (young plants, germ, shoots or flowers). Since pre-Hispanic times,queliteshave been eaten as a source of vitamins, minerals and proteins. Now, its traditional and healthy consumption has decreased. We studied thequelitesof two traditional markets in the Valles Centrales of Oaxaca state, Mexico using an ethnobotanical and nutritional approach.

Methods

From July 2017 to July 2018, weekly ethnobotanical interviews were conducted with 26 collectors-sellers of the Zimatlán market and 36 in the Zaachila market. The vegetal supply was acquired, herborized and identified by through dichotomous keys. There were determined the proximal composition, phenolic compounds, flavonoids, antioxidant capacity and mineral content of the floral structures of twoquelites’types. The statistical analysis was performed through a one-way analysis of variance (ANOVA) of Tukey HSD.

Results

In two sampled markets, 23 species belonging to 11 botanical families were registered, from which leaves, branches, stems, flowers and fruits are eaten. The flowers of the speciesDiphysa americana(Q1) andPhaseolus coccineus(Q2) are the most used for human consumption of the communities involved in the sale of the sampledquelites. Both flowers had important amounts of proteins (2.66-3.29%) and fiber (1.66-2.43%). Q1 had higher content of phenols and flavonoids and therefore higher antioxidant capacity than Q2 (p <0.05). When we talk about Q2 minerals, it presented a greater amount of Zn, Ca and Mg in comparison to Q1 (p> 0.05).

Conclusions

In local markets of the state of Oaxaca, a wide variety ofquelitesare usually found, where their botanical structures, such as flowers, are widely eaten. The flowers of Q1 and Q2 proved to be a rich source of proteins and bioactive compounds, as well as minerals. Showing thus to be a food alternative to enrich the human diet.
Hypothalamic transcriptome analysis reveals the neuroendocrine mechanisms in controlling broodiness of Muscovy duck (Cairina moschata)
Authors: Ye Pengfei , Li Min , Liao Wang , Ge Kai , Jin Sihua , Zhang Cheng , Chen Xingyong , Geng Zhaoyu
Published: October 2018

Broodiness, one of the maternal behaviors and instincts for natural breeding in birds, is an interesting topic in reproductive biology. Broodiness in poultry is characterized by persistent nesting, usually associated with cessation of egg laying. The study of avian broodiness is essential for bird conservation breeding and commercial poultry industry. In this study, we examined the hypothalamus transcriptome of Muscovy duck in three reproductive stages, including egg-laying anaphase (LA), brooding prophase (BP) and brooding metaphase (BM). Differences in gene expression during the transition from egg-laying to broodiness were examined, and 155, 379, 292 differently expressed genes (DEGs) were obtained by pairwise comparisons of LA-vs-BP, LA-vs-BM and BP-vs-BM, respectively (fold change≥ 1.5, P < 0.05). Gene Ontology Term (GO) enrichment analysis suggested a possible role of oxidative stress in the hypothalamus might invoke reproductive costs that potentially change genes expression. KEGG analysis revealed glutamatergic synapse, dopaminergic synapse, serotonergic synapse and GABAergic synapse pathway were significantly enriched, and regulator genes were identified. Eight gene expression patterns were illustrated by trend analysis and further clustered into three clusters. Additional six hub genes were identified through combining trend analysis and protein-protein interaction (PPI) analysis. Our results suggested that the cyclical mechanisms of reproductive function conversion include effects of oxidative stress, biosynthesis of neurotransmitters or their receptors, and interactions between glucocorticoids and thyroid hormones and regulatory genes. These candidate genes and biological pathways may be used as targets for artificial manipulation and marker-assisted breeding in the reproductive behavior.
Limitations of the kinematic approximation in neutron reflectivity measurements for the analysis of bilayers
Authors: Droulias Sotirios A. , Pálsson Gunnar K. , Hjörvarsson Björgvin , Wolff Max
Published: October 2018

The limitations of a phenomenological fitting approach compared to simulations of the optical model including reflection and refraction at all interfaces are demonstrated using the example of hydrogen loading in ultra-thin vanadium layers. Fe/V superlattices are loaded with deuterium and the lattice expansion and deuterium concentration are extracted from neutron reflectivity data. A noticeable difference is found between the extraction of concentrations and bilayer thicknesses directly from the superlattice peaks and fits of the density profile using the Parratt formalism. The results underline the importance of carefully considering the limitations of phenomenological approaches, in order to obtain robust results. The limitations of the kinematic approximation for the analysis are discussed in detail.
Feasibility study of phase-contrast X-ray laminography using X-ray interferometry
Authors: Yoneyama Akio , Hyodo Kazuyuki , Baba Rika , Takeya Satoshi , Takeda Tohoru
Published: October 2018

For fine observation of laminar samples, phase-contrast X-ray laminography using X-ray interferometry was developed. An imaging system fitted with a two-crystal X-ray interferometer was used to perform the observations, and the sectional images were calculated by a three-dimensional iterative reconstruction method. Obtained images of an old flat slab of limestone from the Carnic Alps depicted fusulinids in the Carboniferous period with 3 mg cm−3 density resolution, and those of carbon paper used for a fuel-cell battery displayed the inner fibrous structures clearly.
Towards chemically neutral carbon cleaning processes: plasma cleaning of Ni, Rh and Al reflective optical coatings and thin Al filters for free-electron lasers and synchrotron beamline applications
Authors: Moreno Fernández Harol , Zangrando Marco , Sauthier Guillaume , Goñi Alejandro R. , Carlino Vincent , Pellegrin Eric
Published: October 2018

The choice of a reflective optical coating or filter material has to be adapted to the intended field of application. This is mainly determined by the required photon energy range or by the required reflection angle. Among various materials, nickel and rhodium are common materials used as reflective coatings for (soft) X-ray mirrors. Similarly, aluminium is one of the most commonly used materials for extreme ultraviolet and soft X-ray transmission filters. However, both of these types of optics are subject to carbon contamination, which can be increasingly problematic for the operation of the high-performance free-electron laser and synchrotron beamlines. As an attempt to remove this type of contamination, an inductively coupled plasma source has been used in conjunction with N2/O2/H2 and N2/H2 feedstock gas plasmas. Results from the chemical surface analysis of the above materials before and after plasma treatment using X-ray photoelectron spectroscopy are reported. It is concluded that a favorable combination of an N2/H2 plasma feedstock gas mixture leads to the best chemical surface preservation of Ni, Rh and Al while removing the carbon contamination. However, this feedstock gas mixture does not remove C contamination as rapidly as, for example, an N2/O2/H2 plasma which induces the surface formation of NiO and NiOOH in Ni and RhOOH in Rh foils. As an applied case, the successful carbon removal from ultrathin Al filters previously used at the FERMI FEL1 using an N2/H2 plasma is demonstrated.
Do prestigious Spanish scholarly book publishers have more teaching impact?
Authors: Mas-Bleda Amalia , Thelwall Mike
Published: October 2018

Purpose

The purpose of this paper is to assess the educational value of prestigious and productive Spanish scholarly publishers based on mentions of their books in online scholarly syllabi.

Design/methodology/approach

Syllabus mentions of 15,117 books from 27 publishers were searched for, manually checked and compared with Microsoft Academic (MA) citations.

Findings

Most books published by Ariel, Síntesis, Tecnos and Cátedra have been mentioned in at least one online syllabus, indicating that their books have consistently high educational value. In contrast, few books published by the most productive publishers were mentioned in online syllabi. Prestigious publishers have both the highest educational impact based on syllabus mentions and the highest research impact based on MA citations.

Research limitations/implications

The results might be different for other publishers. The online syllabus mentions found may be a small fraction of the syllabus mentions of the sampled books.

Practical implications

Authors of Spanish-language social sciences and humanities books should consider general prestige when selecting a publisher if they want educational uptake for their work.

Originality/value

This is the first study assessing book publishers based on syllabus mentions.
A tool to benchmark the food safety management systems in Greece
Authors: Souliotis Andreas , Giazitzi Katerina , Boskou George
Published: October 2018

Purpose

The purpose of this paper is to develop and implement methods to benchmark the food safety and hygiene of different companies, regardless the management systems applied.

Design/methodology/approach

The data were collected using a balanced questionnaire which was based on the fishbone model of Ishikawa. The questionnaire includes general questions about the company and 25 questions about personnel, machinery, materials, methods and environment. It was applied to 202 food industries, 42 food retail businesses and 49 food service companies. The data were collected from interviews of industry people related to food safety and from audits of business facilities. The benchmarking methods were descriptive statistics, radar charts, cluster analysis and association rules.

Findings

The radar charts were used to benchmark food companies on safety and hygiene. Food companies can be evaluated with this benchmarking tool with a balanced score of maximum 100 points.

Originality/value

This benchmarking tool could be useful for food control authorities, clusters of companies and certification bodies.
Investigation on firm efficiency: evidence from selected Asia-Pacific countries
Authors: Tan Khar Mang , Kamarudin Fakarudin , Bany-Ariffin Amin Noordin , Rahim Norhuda Abdul
Published: October 2018

Purpose

The purpose of this paper is to examine the firm efficiency or technical efficiency (TE), pure technical efficiency (PTE) and scale efficiency (SE) in the selected developed and developing Asia-Pacific countries.

Design/methodology/approach

The sample consists of a sum of 700 firms in selected developed and developing Asia-Pacific countries over the period from 2009 to 2015. The non-parametric data envelopment analysis under the production approach is used to investigate firm efficiency.

Findings

On average, this paper discovers that the firms in selected Asia-Pacific countries are moderately efficient. Scale inefficiency (SIE) is found to be the dominant source of firms’ technical inefficiency. The analysis of return to scale shows that the large firms tend to operate at decreasing return to scale level, while the small firms tend to operate at increasing return to scale level.

Practical implications

The findings from this paper provide significant insights to the policy makers and firm managers in promoting the efficient firms of Asia-Pacific countries.

Originality/value

The present paper conducts a critical analysis on return to scale in the firms sector of Asia-Pacific context, which is ignored by the past studies on firm efficiency since the analysis of return to scale is mostly emphasized on banking sector. The precise nature of SIE is important for a firm to be efficient in achieving the firm’s primary goals of profit maximization and sustaining market competitiveness.
Supplier relations impact within the UK automotive industry
Authors: Demirbas Dilek , Wilkinson Lauren , Bennett David
Published: October 2018

Purpose

The purpose of this paper is to understand the impact of the recent recession on both the automotive manufacturer as well as their suppliers. The research aims to identify if the impact has been the same at each of the organizations, or if there has been a difference.

Design/methodology/approach

This paper carries out a case study research, into the need for suppliers to increase their responsiveness following recession and the impact this has had on supplier relations. Face-to-face semi-structured interviews were carried out at the vehicle manufacturer with two members of production control staff from VMUK plus seven production control staff at seven tier 1 suppliers to VMUK.

Findings

Supply chains have been enhanced through an increased level of responsiveness, following the economic downturn and supplier relations have had a positive impact post-recession.

Research limitations/implications

Literature argues that competitive advantage can be achieved through responsiveness, and that responsiveness is critical during a period of volatility and market uncertainty. Furthermore, literature also argues that competitive advantage can be achieved through positive supplier relations. This study investigates both of these arguments.

Originality/value

This study concludes that the positive supplier relations offer a competitive advantage when there is no cost advantage to be found elsewhere. Furthermore, this study concludes that as a direct impact of the recession, supplier relations have improved within the case studies investigated.
A quality function deployment strategy for improving mobile-government service quality in the Gulf cooperation council countries
Authors: Alsaadi Meiaad Rashid , Ahmad Syed Zamberi , Hussain Matloub
Published: October 2018

Purpose

The purpose of this paper is to derive mobile-government (m-government) service-quality factors in the Gulf Cooperation Council (GCC) and develop an integrated strategic plan for improving the quality of m-government services from a customer perspective in the GCC.

Design/methodology/approach

A quantitative approach was used in this case study of m-government services in the GCC. Data were collected using focus groups and questionnaires for three similar m-government applications (one from the United Arab Emirates, one from the Saudi Arabia and one from Oman). The house of quality tool, including technical benchmarking, was applied as part of the quality function deployment (QFD) approach to identify customer requirements, translate them to technical requirements and develop a strategic plan for improving the quality of m-government services.

Findings

The results revealed that “real time” had the highest priority for deployment, while “tangible service,” contrary to expectations, had the lowest priority for deployment.

Research limitations/implications

Study findings are limited to the m-government services delivered to citizens. There is scope for further study into m-government services delivered both to businesses and other governments.

Practical implications

The findings imply that the m-government decision makers must involve citizens in all service-development processes to ensure that service delivery meets citizens’ expectations.

Originality/value

Most previous studies regarding m-government service-quality dimensions have used information system service-quality dimensions. This study is one of the pioneering studies to have successfully derived m-government service-quality factors using the QFD matrix.
The psychological secrets behind improving work performance: the individual and cumulative effects of employees pursuing intrinsic and extrinsic goals
Authors: Green Martin Andrew
Published: October 2018

Purpose

This paper aims to review the latest management developments across the globe and pinpoint practical implications from cutting-edge research and case studies.

Design/methodology/approach

This briefing is prepared by an independent writer who adds their own impartial comments and places the articles in context.

Findings

This research paper explores the impact on work performance that an employee’s goal orientation type has. Intrinsically, goal-orientated employees perform well across the board, but having both intrinsic and extrinsic goals simultaneously turbocharges an employee’s work performance.

Practical implications

The paper provides strategic insights and practical thinking that have influenced some of the world’s leading organizations.

Originality/value

The briefing saves busy executives’ and researchers’ hours of reading time by selecting only the very best, most pertinent information and presenting it in a condensed and easy-to-digest format.
Asymmetric Open Government Data (OGD) framework in India
Authors: Saxena Stuti
Published: October 2018

Purpose

With the ongoing drives towards Open Government Data (OGD) initiatives across the globe, governments have been keen on pursuing their OGD policies to ensure transparency, collaboration and efficiency in administration. As a developing country, India has recently adopted the OGD policy (www.data.gov.in); however, the percolation of this policy in the States has remained slow. This paper aims to underpin the “asymmetry” in OGD framework as far as the Indian States are concerned. Besides, the study also assesses the contribution of “Open Citizens” in furthering the OGD initiatives of the country.

Design/methodology/approach

An exploratory qualitative following a case study approach informs the present study using documentary analysis where evidentiary support from five Indian States (Uttar Pradesh, Telangana, West Bengal, Sikkim and Gujarat) is being drawn to assess the nature and scope of the OGD framework. Further, conceptualization for “Open Citizen” framework is provided to emphasize upon the need to have aware, informed and pro-active citizens to spearhead the OGD initiatives in the country.

Findings

While the National OGD portal has a substantial number of data sets across different sectors, the States are lagging behind in the adoption and implementation of OGD policies, and while Telangana and Sikkim have been the frontrunners in adoption of OGD policies in a rudimentary manner, others are yet to catch up with them. Further, there is “asymmetry” in terms of the individual contribution of the government bodies to the open data sets where some government bodies are more reluctant to share their datasets than the others.

Practical implications

It is the conclusion of the study that governments need to institutionalize the OGD framework in the country, and all the States should appreciate the requirement of adopting a robust OGD policy for furthering transparency, collaboration and efficiency in administration.

Social implications

As an “Open Citizen”, it behooves upon the citizens to be pro-active and contribute towards the open data sets which would go a long way in deriving social and economic value out of these data sets.

Originality/value

While there are many studies on OGD in the West, studies focused upon the developing countries are starkly lacking. This study plugs this gap by attempting a comparative analysis of the OGD frameworks across Indian States. Besides, the study has provided a conceptualization of “Open Citizen” (OGD) which may be tapped for further research in developing and developed countries to ascertain the linkage between OGD and OC.