bluuebunny/crossref_metadata_2025 huggingface dataset:
The fishery of sea-cucumber Holothuridae in Kilbat Village, Central Maluku Regency, Indonesia
Authors: Lewerissa Y A , Ongkers O T S , Pattikawa J A , Tetelepta J M S , Divinubun A
Published: June 2021

Sea cumber is one of the valuable high economic resources. Worldwide, most sea cucumber fisheries are ineffectively managed, leading to declining stocks and potentially eroding the resilience of fisheries. The local fishermen of Kilbat Village have been exploiting sea cucumber for a long time with un-proper management pan. This study was aimed to investigate the utilization of sea cumber and assess its sustainability, and propose a sustainable management strategy. Field observation was used to analyze sea cucumber utilization, the Rapid appraisal to Fisheries (Rapfish) approach was used to assess its sustainability, whilst DPSIR was applied to perform a sustainable management strategy. The result shows that the local sea cucumber fishermen utilize sea cucumber as a source of income and self-consumption. The average sustainability was 61.17% of 100% sustainable scale and considered as fair sustain with institutional dimension being unsustain. There are 8 strategies proposed for sea cumber sustainable management with responses at D, P, S, and I level, A traditional indigenous knowledge (sasi) has been proposed for sea cucumber community-based fishery management.
Antibacterial activity of Rhizophora apiculata extract originated from Inner Ambon Bay against selected pathogen bacteria
Authors: Sormin R B D , Nendissa D M , Mailoa M N , Rieuwpassa F , Wenno M R
Published: June 2021

Inner Ambon bay, Ambon Island, Maluku Province, is a good place for mangrove to growth. Some mangroves have been known as a source of germplasm that has antimicrobial properties. This research goals to study the antibacterial activity of various extract of Rhizophora apiculata from the coast of the Inner Ambon Bay, against several pathogenic bacteria. The experimental design was complete random design with two factors, firstly, the type of extract solvent was extract namely methanol, ethyl acetate and n-hexane, and the second four strains of bacteria consist of Gram positive strains: Bacillus cereus and Gram negative strains: Escherichia coli, Salmonella typhi Staphylococcus aureus.The highest antibacterial activity was resulted by ethyl acetate extracts with an average value of inhibition zone was 18.64±3.88b mm, then followed by methanol extract 15.02±5.17b mm and n-hexane extract 8.48±1.25a mm. The strongest extract against the bacterial pathogen was ethyl acetate extract. The most susceptible bacteria to the three extracts tested with an inhibition zone was (18.02±7.49b) mm, followed by B. cereus, E. coli and S. aureus with the inhibition zones were (13.48±4.50a) mm, (12.94±4.69a) mm and (11.74±3.90a) mm, respectively.
Utilization of garlic as traditional fish handling in Molluccas Islands: case study on layang fish (Decapterus macrosoma, BLECKER)
Authors: Wenno M R , Kaya A O W , Lewerissa S , Wattimena M L , Sormin R B D , Nanlohy E E E M
Published: June 2021

Fish form part of a highly nutritional diet and provide a source of essential proteins. However, they can rapidly degrade, particularly when in a fresh state and not handled properly. Degradation can occur either biochemically or microbiologically. Various methods can be implemented to maintain the quality of fresh fish; for example, the utilization of natural preservatives such as garlic. Garlic is a herb which has been proven to inhibit the growth of microorganisms. Tubers of garlic contain antimicrobial compounds such as allicin (diallyl thiosulfinate) and ajoene. This study aimed to determine the effect of immersion duration in a garlic solution on the freshness level of shortfin scad fish. The Total Volatile Base Nitrogen (TVBN) values ranged from 25.33 mg%N to 78.66 mg%N, the bacterial TPC (Total Plate Count) was 7.5×101 to 1.6×105 CFU/g, and the pH 5.9 to 8.0. Visibility ranged from 4.64 to 8.33, odor 3.47 to 8.75, and texture 3.62 to 8.20. This study found that immersion treatment using garlic can maintain fish quality for eight hours, with a 20-minute immersion treatment obtaining optimal parameter values.
Nutrition content and amino acid profile of paper squid (Loligo edulis)
Authors: Loppies C R M , Apituley D A N , Tentua E
Published: June 2021

One of the ways to diversify squid products into ready to eat food that has the potential to be developed is paper squid. The main stages in paper squid processing are drying under the sun, pressing, and drying in oven. This research aims to determine the proximate and the amino acid profile contained in paper squid (Loligo edulis, Hoyle). The proximate analysis results showed that paper squid contains 8.25% of moisture content, 3.65% of ash content, 72.28% of protein content, and 11.96% of carbohydrates content. Amino acids detected in paper squid are 15 types of amino acids consisting of 9 essential amino acids and 6 non-essential amino acids. The highest essential amino acid in paper squid is arginine containing 6.24% and the lowest is histidine which is 1.43%. The highest non-essential amino acid in paper squid is glutamic acid which is 12.13% and the lowest is tyrosine which is 2.49%.
Chemical properties of dried anchovy (Stolephorus sp) from Buru Island
Authors: Savitri I K E , Tohata V D , Sormin R B D , Lalopua V M N , Mailoa M N , Rieuwpassa F
Published: June 2021

The objective of this study was determined proximate, amino acid and some minerals of dried anchovy from Kayeli bay Buru Island. Dried anchovy from Buru island has a good quality indexes and a good feasibility business while the nutritional composition unexplored, so determine the proximate, amino acid and ash content are appropriate to complete its nutritional data. Protein in dried anchovy is relatively high, almost 60% and the amino acids profile were Phenylalanine, Valine, Threonine, Isoleucine, Methionine, Histidin, Lysine, Leucine, Arginine, Aspartic, Tyrosine, Serine, Glutamate and Glysine. There are 8 essential amino acids, 1 semy essential amino acid and 6 non essential amino acids and the highest non essential amino acid is Glutamate and followed by Aspartic. Dried anchovy has a good amino acid profile especially essential group with a good taste and also highly Phosphorous, Calcium, Iron and Iodine.
Externally definable quotients and NIP expansions of the real ordered additive group
Authors: Walsberg Erik
Published: June 2021

Let

R

\mathscr {R}

be an

N
I
P

\mathrm {NIP}

expansion of

(

R

,
>
,
+
)

(\mathbb {R},>,+)

by closed subsets of

R

n

\mathbb {R}^n

and continuous functions

f
:

R

m

→

R

n

f : \mathbb {R}^m \to \mathbb {R}^n

. Then

R

\mathscr {R}

is generically locally o-minimal. This follows from a more general theorem on

N
I
P

\mathrm {NIP}

expansions of locally compact groups, which itself follows from a result on quotients of definable sets in

ℵ
1

\aleph _1

-saturated

N
I
P

\mathrm {NIP}

structures by equivalence relations which are both externally definable and

⋀
\bigwedge

-definable. We also show that

R

\mathscr {R}

is strongly dependent if and only if

R

\mathscr {R}

is either o-minimal or

(

R

,
>
,
+
,
α

Z

)

(\mathbb {R},>,+,\alpha \mathbb {Z})

-minimal for some

α
>
0

\alpha > 0

.
Boundedness for finite subgroups of linear algebraic groups
Authors: Shramov Constantin , Vologodsky Vadim
Published: June 2021

We show the boundedness of finite subgroups in any anisotropic reductive group over a perfect field that contains all roots of 

1
1

. Also, we provide explicit bounds for orders of finite subgroups of automorphism groups of Severi–Brauer varieties and quadrics over such fields.
Urban renewal in Ibadan, Nigeria: World class but essentially Yoruba
Authors: Roelofs Portia
Published: June 2021

Urban renewal is central to ‘world-class’ city aspirations on the African continent: demolitions and evictions exemplify the power of the state to restructure urban space, prioritizing elite forms of accumulation and enforcing aesthetic norms of cleanliness, order and modernity. The ubiquity of world-class city-making has been taken by urban studies scholars as evidence of African leaders’ converging on a unitary aspirational urban imaginary. This article contends that the concept of world class should instead be understood as a key terrain on which African governments’ distinctive and diverse ideational ambitions are expressed. In Oyo State, southwest Nigeria, vernacular political traditions—in this case Yoruba cultural nationalism centred on the ideas of Obafemi Awolowo—were deployed by the state governor to legitimize urban renewal. Drawing on the Yoruba notion that elitism can be ‘generalized’, the cultivation of globalized urban forms was not only a project of becoming ever more homogenously ‘international’ but a historically grounded aspiration to become ever more essentially Yoruba. Thus, beyond commonalities across the discourses used to legitimize neoliberal urban development—world class, international and global—these universal sounding imaginaries may at the same time express much more particularistic political projects.
Translingual Discrimination: Skilled Transnational Migrants in the Labour Market of Australia
Authors: Dovchin Sender , Dryden Stephanie
Published: June 2021

Drawing on linguistic ethnographic data, this study examines the language-based discriminatory experiences of skilled transnational migrants in the labour market of Australia. Moving beyond two main concepts of ‘interlingual’ and ‘intra-lingual’ discrimination in applied linguistics, this article points out the concept of ‘translingual discrimination’, which refers to inequality based on transnational identities’ specific linguistic repertoires and backgrounds that are substantiated by the national order of things. Translingual discrimination adds intensity to transnational processes, with the skilled migrants showing particular potential for exclusion regarding two factors: translingual ‘name discrimination’ and ‘English discrimination’. ‘Translingual name discrimination’ is a homogenous form of ‘name’ policing, evident in multiple examples where the skilled transnational migrants’ job applications are often largely rejected on the grounds of their ‘birth name’ written on their curriculum vitae. ‘Translingual English discrimination’ is another common form of discrimination, where the skilled transnational migrants become subject to discrimination based on their English proficiency and their overall language skills, leading to ‘the paradoxes of migration’—discrepancies between the imagination and the reality—where they fall from ‘hero to zero’ in the host society.
A 3-Level Impaction Technique for Dorsal Reshaping and Reduction Without Dorsal Soft Tissue Envelope Dissection
Authors: Finocchi Valerio , Vellone Valentino , Mattioli Rubens Giorgio , Daniel Rollin K
Published: June 2021

Background

Preservation rhinoplasty (PR) techniques are continuously evolving and many variations of established techniques have been proposed since Daniel coined this term in 2018.

Objectives

The aim of this study was to describe indications for a new “3-level impaction” technique, allowing, in selected cases, a complete profile correction and dorsal reduction without dissection of the dorsal soft tissue envelope (STE).

Methods

Three hundred and fifty primary closed rhinoplasty cases were retrospectively studied from January 2018 and October 2019. Age, sex, race, technical details, surgical time, and complications were registered. Ninety-five dorsa were reduced and shaped without dissecting the dorsal STE by combining: (1) a swinging-door septoplasty with low septal strip resection, (2) endonasal bony cap mosaic osteotomies, and (3) let-down or push-down operation.

Results

All patients showed a dramatic change in profile height and shape without either dorsal STE dissection or bony cartilage dorsal tissue resection. Mosaic osteotomies converted the dorsal keystone area from S- to V-shaped dorsum, let-down-operation and low septal strip resection enabled impaction, and profile setting was achieved by quadrangular cartilage flap rotation. The average follow-up time was 14 months (range, 12-16 months).

Conclusions

In selected patients, dorsum can be preserved without STE dissection. By combining multiple endonasal maneuvers it is possible to obtain a dramatic change without dissecting the STE, while simultaneously avoiding any dorsal tissue resection. This method offers a versatile technique in selected patients, which leads to fast recovery and natural results.

Level of Evidence: 4
Eight genes are necessary and sufficient for biogenesis of quinohemoprotein amine dehydrogenase
Authors: Nakai Tadashi , Tanizawa Katsuyuki , Okajima Toshihide
Published: June 2021

Quinohemoprotein amine dehydrogenase (QHNDH) containing a peptidyl quinone cofactor, cysteine tryptophylquinone, is produced in the periplasm of Gram-negative bacteria through an intricate process of post-translational modification that requires at least 8 genes including those encoding 3 nonidentical subunits and 3 modifying enzymes. Our heterologous expression study has revealed that the 8 genes are necessary and sufficient for the QHNDH biogenesis.
Involvement of an FNR-like oxygen sensor in Komagataeibacter medellinensis for survival under oxygen depletion
Authors: Watanabe Seiji , Shirai Mutsunori , Kishi Mikiya , Ohnishi Yasuo
Published: June 2021

During acetic acid fermentation, acetic acid bacteria face oxygen depletion stress caused by the vigorous oxidation of ethanol to acetic acid. However, the molecular mechanisms underlying the response to oxygen depletion stress remain largely unknown. Here, we focused on an oxygen-sensing FNR homolog, FnrG, in Komagataeibacter medellinensis. Comparative transcriptomic analysis between the wild-type and fnrG-disrupted strains revealed that FnrG upregulated 8 genes (fold change >3). Recombinant FnrG bound to a specific DNA sequence only when FnrG was reconstituted anaerobically. An operon consisting of acetate kinase and xylulose-5-phosphate/fructose-6-phosphate phosphoketolase genes was found to be an FnrG regulon involved in cell survival under oxygen-limiting conditions. Moreover, a strain that overexpressed these 2 genes accumulated more acetic acid than the wild-type strain harboring an empty vector. Thus, these 2 genes could be new targets for the molecular breeding of acetic acid bacteria with high acetic acid productivity.
MultiDTI: drug–target interaction prediction based on multi-modal representation learning to bridge the gap between new chemical entities and known heterogeneous network
Authors: Zhou Deshan , Xu Zhijian , Li WenTao , Xie Xiaolan , Peng Shaoliang
Published: June 2021

Motivation

Predicting new drug–target interactions is an important step in new drug development, understanding of its side effects and drug repositioning. Heterogeneous data sources can provide comprehensive information and different perspectives for drug–target interaction prediction. Thus, there have been many calculation methods relying on heterogeneous networks. Most of them use graph-related algorithms to characterize nodes in heterogeneous networks for predicting new drug–target interactions (DTI). However, these methods can only make predictions in known heterogeneous network datasets, and cannot support the prediction of new chemical entities outside the heterogeneous network, which hinder further drug discovery and development.

Results

To solve this problem, we proposed a multi-modal DTI prediction model named ‘MultiDTI’ which uses our proposed joint learning framework based on heterogeneous networks. It combines the interaction or association information of the heterogeneous network and the drug/target sequence information, and maps the drugs, targets, side effects and disease nodes in the heterogeneous network into a common space. In this way, ‘MultiDTI’ can map the new chemical entity to this learned common space based on the chemical structure of the new entity. That is, bridging the gap between new chemical entities and known heterogeneous network. Our model has strong predictive performance, and the area under the receiver operating characteristic curve of the model is 0.961 and the area under the precision recall curve is 0.947 with 10-fold cross validation. In addition, some predicted new DTIs have been confirmed by ChEMBL database. Our results indicate that ‘MultiDTI’ is a powerful and practical tool for predicting new DTI, which can promote the development of drug discovery or drug repositioning.

Availability and implementation

Python codes and dataset are available at https://github.com/Deshan-Zhou/MultiDTI/.

Supplementary information

Supplementary data are available at Bioinformatics online.
Linear functional organization of the omic embedding space
Authors: Xenos A , Malod-Dognin N , Milinković S , Pržulj N
Published: June 2021

Motivation

We are increasingly accumulating complex omics data that capture different aspects of cellular functioning. A key challenge is to untangle their complexity and effectively mine them for new biomedical information. To decipher this new information, we introduce algorithms based on network embeddings. Such algorithms represent biological macromolecules as vectors in d-dimensional space, in which topologically similar molecules are embedded close in space and knowledge is extracted directly by vector operations. Recently, it has been shown that neural networks used to obtain vectorial representations (embeddings) are implicitly factorizing a mutual information matrix, called Positive Pointwise Mutual Information (PPMI) matrix. Thus, we propose the use of the PPMI matrix to represent the human protein–protein interaction (PPI) network and also introduce the graphlet degree vector PPMI matrix of the PPI network to capture different topological (structural) similarities of the nodes in the molecular network.

Results

We generate the embeddings by decomposing these matrices with Nonnegative Matrix Tri-Factorization. We demonstrate that genes that are embedded close in these spaces have similar biological functions, so we can extract new biomedical knowledge directly by doing linear operations on their embedding vector representations. We exploit this property to predict new genes participating in protein complexes and to identify new cancer-related genes based on the cosine similarities between the vector representations of the genes. We validate 80% of our novel cancer-related gene predictions in the literature and also by patient survival curves that demonstrating that 93.3% of them have a potential clinical relevance as biomarkers of cancer.

Availability and implementation

Code and data are available online at https://gitlab.bsc.es/axenos/embedded-omics-data-geometry/.

Supplementary information

Supplementary data are available at Bioinformatics online.
CStreet: a computed

C

ell

S

tate

tr

ajectory inf

e

r

e

nce method for

t

ime-series single-cell RNA sequencing data
Authors: Zhao Chengchen , Xiu Wenchao , Hua Yuwei , Zhang Naiqian , Zhang Yong
Published: June 2021

Motivation

The increasing amount of time-series single-cell RNA sequencing (scRNA-seq) data raises the key issue of connecting cell states (i.e. cell clusters or cell types) to obtain the continuous temporal dynamics of transcription, which can highlight the unified biological mechanisms involved in cell state transitions. However, most existing trajectory methods are specifically designed for individual cells, so they can hardly meet the needs of accurately inferring the trajectory topology of the cell state, which usually contains cells assigned to different branches.

Results

Here, we present CStreet, a computed Cell State trajectory inference method for time-series scRNA-seq data. It uses time-series information to construct the k-nearest neighbor connections between cells within each time point and between adjacent time points. Then, CStreet estimates the connection probabilities of the cell states and visualizes the trajectory, which may include multiple starting points and paths, using a force-directed graph. By comparing the performance of CStreet with that of six commonly used cell state trajectory reconstruction methods on simulated data and real data, we demonstrate the high accuracy and high tolerance of CStreet.

Availability and implementation

CStreet is written in Python and freely available on the web at https://github.com/TongjiZhanglab/CStreet and https://doi.org/10.5281/zenodo.4483205

Supplementary information

Supplementary data are available at Bioinformatics online.
Chemerin as a modulator of angiogenesis and apoptosis processes in the corpus luteum of pigs: an in vitro study
Authors: Rytelewska Edyta , Kiezun Marta , Zaobidna Ewa , Gudelska Marlena , Kisielewska Katarzyna , Dobrzyn Kamil , Kaminski Tadeusz , Smolinska Nina
Published: June 2021

The corpus luteum (CL) undergoes rapid changes, and its functional capabilities are influenced by processes such as angiogenesis and apoptosis. According to the literature, chemerin-a protein that participates in the regulation of energy homeostasis and the immune response, may also affect angiogenesis and apoptosis. Therefore, the aim of this study was to investigate the in vitro effect of chemerin on angiogenesis and apoptosis in porcine luteal cells (Lc) during specific phases related to CL physiology. Luteal cells were harvested from gilts during the early-, mid-, and late-luteal phases of the estrous cycle. The cells were preincubated for 48 h and incubated for 24 h with chemerin or a serum-free medium (controls). The abundance of angiogenesis- and apoptosis-related proteins was determined by enzyme-linked immunosorbent assay (ELISA) in spent culture media, or by ELISA and Western blot in protein extracts. The current study demonstrated that chemerin stimulates the production of vascular endothelial growth factor A (VEGF-A) and basic fibroblast growth factor (bFGF) by porcine Lc and increases the protein abundance of angiogenic factors’ receptors (VEGFR1, VEGFR2, VEGFR3, FGFR1, FGFR2) in these cells. The study also revealed that chemerin exerts a modulatory effect (stimulatory/inhibitory, depending on the phase of the cycle) on the protein abundance of first apoptosis signal (Fas), Fas ligand, B-cell lymphoma 2, and caspase-3 in porcine Lc. These results imply that chemerin may affect angiogenesis and apoptosis processes in the porcine CL, as evidenced by its modulatory effect of chemerin on the protein abundance of crucial angiogenesis- and apoptosis-related factors, observed in an in vitro study of porcine Lc.
Characterization of transcriptional activity during ZGA in mammalian SCNT embryo
Authors: Deng Mingtian , Chen Baobao , Yang Yingnan , Wan Yongjie , Liu Zifei , Fu Jun , Wang Feng
Published: June 2021

Developmental arrest of somatic cell nuclear transfer (SCNT) embryos first occurs at zygotic/embryonic genome activation (ZGA/EGA), which is critical for preimplantation development. However, study on transcriptome of SCNT embryos during ZGA/EGA is limited. In the present study, we performed RNA sequencing (RNA-seq) of the eight-cell SCNT embryos in goat and provide cross-species analysis of transcriptional activity of SCNT embryos during ZGA/EGA in mice, human, bovine, and goat. RNA-seq data revealed 3966 differentially expressed genes (DEGs) failed to be reprogrammed or activated during EGA of SCNT embryos in goat. Series test of cluster analysis showed four clusters of DEGs and similar changes of the clusters in the four species. Specifically, genes in cluster 3 were somehow upregulated compared with the donor cells and the in vitro fertilization embryo. Moreover, the histone methylation key players and N6-methyladenosine modifiers (SUV39H1, SETDB1, SETD2, KDM5B, IGF2BP1, and YTHDF2) were differentially expressed in SCNT embryos of all species. Finally, we identified three modules correlated with the development of SCNT embryos in mice and screened 288 genes (such as BTG4, WEE1, KLF3, and USP21) that are likely critical for SCNT reprogramming using weighted gene correlation network analysis. Our data will broaden the current understanding of transcriptome activity during stochastic reprogramming events and provide an excellent source for future studies.
The potential role of stress and sex steroids in heritable effects of sevoflurane
Authors: Martynyuk Anatoly E , Ju Ling-Sha , Morey Timothy E
Published: June 2021

Most surgical procedures require general anesthesia, which is a reversible deep sedation state lacking all perception. The induction of this state is possible because of complex molecular and neuronal network actions of general anesthetics (GAs) and other pharmacological agents. Laboratory and clinical studies indicate that the effects of GAs may not be completely reversible upon anesthesia withdrawal. The long-term neurocognitive effects of GAs, especially when administered at the extremes of ages, are an increasingly recognized health concern and the subject of extensive laboratory and clinical research. Initial studies in rodents suggest that the adverse effects of GAs, whose actions involve enhancement of GABA type A receptor activity (GABAergic GAs), can also extend to future unexposed offspring. Importantly, experimental findings show that GABAergic GAs may induce heritable effects when administered from the early postnatal period to at least young adulthood, covering nearly all age groups that may have children after exposure to anesthesia. More studies are needed to understand when and how the clinical use of GAs in a large and growing population of patients can result in lower resilience to diseases in the even larger population of their unexposed offspring. This minireview is focused on the authors’ published results and data in the literature supporting the notion that GABAergic GAs, in particular sevoflurane, may upregulate systemic levels of stress and sex steroids and alter expressions of genes that are essential for the functioning of these steroid systems. The authors hypothesize that stress and sex steroids are involved in the mediation of sex-specific heritable effects of sevoflurane.
A Clinical Prediction Model for Unsuccessful Pulmonary Tuberculosis Treatment Outcomes
Authors: Peetluk Lauren S , Rebeiro Peter F , Ridolfi Felipe M , Andrade Bruno B , Cordeiro-Santos Marcelo , Kritski Afranio , Durovni Betina , Calvacante Solange , Figueiredo Marina C , Haas David W , Liu Dandan , Rolla Valeria C , Sterling Timothy R ,   Regional Prospective Observational Research in Tuberculosis (RePORT)-Brazil Network, Spener-Gomes Renata , de Souza Alexandra Brito , Silva Jesus Jaquelane , Benjamin Aline , Marinho Sant’Anna Flavia , Peixoto Ignácio Francine , Cristina Lourenço Maria , Gomes-Silva Adriano , de Oliveira Jamile G , Moreira Adriana S R , Calçada Carvalho Anna Cristina , Silva Elisangela C , Mello Mayla , Rocha Michael S , Nogueira Betania , Nascimento Vanessa , Nery Saulo , Andrade Alice M S , Malta-Santos Hayna , Rebouças-Silva Jéssica , Ramos André M C , Melo Sayonara , Cubillos-Angulo Juan M , de Moraes Laise
Published: June 2021

Background

Despite widespread availability of curative therapy, tuberculosis (TB) treatment outcomes remain suboptimal. Clinical prediction models can inform treatment strategies to improve outcomes. Using baseline clinical data, we developed a prediction model for unsuccessful TB treatment outcome and evaluated the incremental value of human immunodeficiency virus (HIV)–related severity and isoniazid acetylator status.

Methods

Data originated from the Regional Prospective Observational Research for Tuberculosis Brazil cohort, which enrolled newly diagnosed TB patients in Brazil from 2015 through 2019. This analysis included participants with culture-confirmed, drug-susceptible pulmonary TB who started first-line anti-TB therapy and had ≥12 months of follow-up. The end point was unsuccessful TB treatment: composite of death, treatment failure, regimen switch, incomplete treatment, or not evaluated. Missing predictors were imputed. Predictors were chosen via bootstrapped backward selection. Discrimination and calibration were evaluated with c-statistics and calibration plots, respectively. Bootstrap internal validation estimated overfitting, and a shrinkage factor was applied to improve out-of-sample prediction. Incremental value was evaluated with likelihood ratio–based measures.

Results

Of 944 participants, 191 (20%) had unsuccessful treatment outcomes. The final model included 7 baseline predictors: hemoglobin, HIV infection, drug use, diabetes, age, education, and tobacco use. The model demonstrated good discrimination (c-statistic = 0.77; 95% confidence interval, .73–.80) and was well calibrated (optimism-corrected intercept and slope, –0.12 and 0.89, respectively). HIV-related factors and isoniazid acetylation status did not improve prediction of the final model.

Conclusions

Using information readily available at treatment initiation, the prediction model performed well in this population. The findings may guide future work to allocate resources or inform targeted interventions for high-risk patients.
Conditional Cash Transfers to Incentivize Tuberculosis Screening: Description of a Novel Strategy for Contact Investigation in Rural South Africa
Authors: Baik Yeonsoo , Hanrahan Colleen F , Mmolawa Lesego , Nonyane Bareng A S , Albaugh Nicholas W , Lebina Limakatso , Siwelana Tsundzukani , Martinson Neil , Dowdy David W
Published: June 2021

Background

Providing incentives to screen close contacts for tuberculosis (TB) is an alternative to household-based contact investigation. We aimed to characterize patients and contexts where this incentive-based strategy might be preferred.

Methods

This is a secondary analysis of a cluster randomized trial of TB contact investigation in Limpopo District, South Africa, conducted between 2016 and 2020. Twenty-eight clinics were randomly allocated to household-based vs incentive-based contact investigation. In the incentive-based arm, index participants and contacts received transport reimbursement and incentives for TB screening and microbiological diagnosis of contacts. We estimated differences in mean number of contacts per index participant with household-based vs incentive-based contact investigation overall and within subgroups of index participants.

Results

A total of 3776 contacts (1903 in the incentive-based and 1873 in the household-based arm) were referred by 2501 index participants. A higher proportion of contacts in the incentive-based than household-based arm were adults (72% vs 59%), reported chronic TB symptoms (25% vs 16%) or ever smoking (23% vs 11%). Index participants who walked or bicycled to a clinic referred 1.03 more contacts per index (95% confidence interval [CI], .48 to 1.57) through incentive-based than household-based investigation. Index participants living with >5 household members referred 0.48 more contacts per index (95% CI, .03 to .94) through household-based than incentive-based investigation.

Conclusions

Relative to household-based investigation, incentive-based investigation identifies contacts likely at higher risk for active TB. Incentive-based investigation may be more appropriate for index participants who can easily access clinics, versus household-based investigation for patients with large households.

Clinical Trials Registration. NCT02808507.
Learning Representation From Concurrence-Words Graph For Aspect Sentiment Classification
Authors: Lu Guangquan , Huang Jihong
Published: June 2021

Aspect sentiment classification is an important research topic in natural language processing and computational linguistics, assisting in automatically review analysis and emotional tendency judgement. Different from extant methods that focus on text sequence representations, this paper presents a network framework to learn representation from concurrence-words relation graph (LRCWG), so as to improve the Macro-F1 and accuracy. The LRCWG first employs the multi-head attention mechanism to capture the sentiment representation from the sentences which can learn the importance of text sequence representation. And then, it leverages the priori sentiment dictionary information to construct the concurrence relations of sentiment words with Graph Convolution Network (GCN). This assists in that the learnt context representation can keep both the semantics integrity and the features of sentiment concurrence-words relations. The designed algorithm is experimentally evaluated with all the five benchmark datasets and demonstrated that the proposed aspect sentiment classification can significantly improve the prediction performance of learning task.
The Progenetix oncogenomic resource in 2021
Authors: Huang Qingyao , Carrio-Cordo Paula , Gao Bo , Paloots Rahel , Baudis Michael
Published: June 2021

In cancer, copy number aberrations (CNAs) represent a type of nearly ubiquitous and frequently extensive structural genome variations. To disentangle the molecular mechanisms underlying tumorigenesis as well as identify and characterize molecular subtypes, the comparative and meta-analysis of large genomic variant collections can be of immense importance. Over the last decades, cancer genomic profiling projects have resulted in a large amount of somatic genome variation profiles, however segregated in a multitude of individual studies and datasets. The Progenetix project, initiated in 2001, curates individual cancer CNA profiles and associated metadata from published oncogenomic studies and data repositories with the aim to empower integrative analyses spanning all different cancer biologies. During the last few years, the fields of genomics and cancer research have seen significant advancement in terms of molecular genetics technology, disease concepts, data standard harmonization as well as data availability, in an increasingly structured and systematic manner. For the Progenetix resource, continuous data integration, curation and maintenance have resulted in the most comprehensive representation of cancer genome CNA profiling data with 138 663 (including 115 357 tumor) copy number variation (CNV) profiles. In this article, we report a 4.5-fold increase in sample number since 2013, improvements in data quality, ontology representation with a CNV landscape summary over 51 distinctive National Cancer Institute Thesaurus cancer terms as well as updates in database schemas, and data access including new web front-end and programmatic data access.

Database URL: progenetix.org
Minimally invasive oesophagectomy in the prone versus lateral decubitus position: a systematic review and meta-analysis
Authors: Schizas Dimitrios , Papaconstantinou Dimitrios , Krompa Anastasia , Athanasiou Antonios , Triantafyllou Tania , Tsekrekos Andrianos , Ruurda Jelle P , Rouvelas Ioannis
Published: June 2021

The thoracic phase of minimally invasive esophagectomy was initially performed in the lateral decubitus position (LDP); however, many experts have gradually transitioned to a prone position (PP) approach. The aim of the present systematic review and meta-analysis is to quantitatively compare the two approaches. A systematic literature search of the MEDLINE, Embase, Google Scholar, Web of Knowledge, China National Knowledge Infrastructure and ClinicalTrials.gov databases was undertaken for studies comparing outcomes between patients undergoing minimally invasive esophageal surgery in the PP versus the LDP. In total, 15 studies with 1454 patients (PP; n = 710 vs. LDP; n = 744) were included. Minimally invasive esophagectomy in the PP provides statistically significant reduction in postoperative respiratory complications (Risk ratios 0.5, 95% confidence intervals [CI] 0.34–0.76, P < 0.001), blood loss (weighted mean differences [WMD] –108.97, 95% CI –166.35 to −51.59 mL, P < 0.001), ICU stay (WMD –0.96, 95% CI –1.7 to −0.21 days, P = 0.01) and total hospital stay (WMD –2.96, 95% CI –5.14 to −0.78 days, P = 0.008). In addition, prone positioning increases the overall yield of chest lymph node dissection (WMD 2.94, 95% CI 1.54–4.34 lymph nodes, P < 0.001). No statistically significant difference in regards to anastomotic leak rate, mortality and 5-year overall survival was encountered. Subgroup analysis revealed that the protective effect of prone positioning against pulmonary complications was more pronounced for patients undergoing single-lumen tracheal intubation. A head to head comparison of minimally invasive esophagectomy in the prone versus the LDP reveals superiority of the former method, with emphasis on the reduction of postoperative respiratory complications and reduced length of hospitalization. Long-term oncologic outcomes appear equivalent, although validation through prospective studies and randomized controlled trials is still necessary.
Urbanisation and the Onset of Modern Economic Growth
Authors: Brunt Liam , García-Peñalosa Cecilia
Published: June 2021

A large literature characterises urbanisation as resulting from productivity growth attracting rural workers to cities. Incorporating economic geography elements into a growth model, we suggest that causation runs the other way: when rural workers move to cities, the resulting urbanisation produces technological change and productivity growth. Urban density leads to knowledge exchange and innovation, thus creating a positive feedback loop between city size and productivity that initiates sustained economic growth. This model is consistent with the fact that urbanisation rates in western Europe, most notably England, reached unprecedented levels by the mid-eighteenth century, the eve of the Industrial Revolution.
Adaptation of the Communities That Care Youth Survey for use in Brazil: A pilot study
Authors: de Oliveira Corrêa Arthur , Brown Eric C , Murta Sheila Giardini , Briney John S
Published: June 2021

Substance use and violence are serious problems affecting Brazilian youth, prompting local authorities to invest in adapting and implementing evidence-based prevention programs developed abroad. To ensure that interventions are effective, valid and reliable measures of risk factors for substance use and violence are needed. We conducted a pilot examination of the measurement properties of risk factors in the Communities That Care Youth Survey (CTCYS), a school-based survey developed in the United States. The Brazilian-adapted CTCYS included 25 risk factors as well as measures of substance use and antisocial behaviors. The survey was translated into Brazilian Portuguese and adapted for use in Brazil, incorporating suggestions from local experts. The survey was administered to 926 students in one Brazilian community. Results indicate that scale internal consistency was acceptable for all but two scales: (i) Academic Failure and (ii) Rebelliousness. Confirmatory factor analyses suggested good model fit for most measurement models albeit with minor modifications for most scales. Findings from this pilot study provide a foundation for the use of the CTCYS in Brazil to assess community levels of adolescent risk and evaluate prevention programs.
Integrative DNA Methylation and Gene Expression Analysis in the Prefrontal Cortex of Mexicans Who Died by Suicide
Authors: Romero-Pimentel Ana L , Almeida Daniel , Muñoz-Montero Said , Rangel Claudia , Mendoza-Morales Roberto , Gonzalez-Saenz Eli E , Nagy Corina , Chen Gary , Aouabed Zahia , Theroux Jean-Francois , Turecki Gustavo , Martinez-Levy Gabriela , Walss-Bass Consuelo , Monroy-Jaramillo Nancy , Fernández-Figueroa Edith A , Gómez-Cotero Amalia , García-Dolores Fernando , Morales-Marin Mirna E , Nicolini Humberto
Published: June 2021

Background

Suicide represents a major health concern, especially in developing countries. While many demographic risk factors have been proposed, the underlying molecular pathology of suicide remains poorly understood. A body of evidence suggests that aberrant DNA methylation and expression is involved. In this study, we examined DNA methylation profiles and concordant gene expression changes in the prefrontal cortex of Mexicans who died by suicide.

Methods

In collaboration with the coroner’s office in Mexico City, brain samples of males who died by suicide (n = 35) and age-matched sudden death controls (n = 13) were collected. DNA and RNA were extracted from prefrontal cortex tissue and analyzed with the Infinium Methylation480k and the HumanHT-12 v4 Expression Beadchips, respectively.

Results

We report evidence of altered DNA methylation profiles at 4430 genomic regions together with 622 genes characterized by differential expression in cases vs controls. Seventy genes were found to have concordant methylation and expression changes. Metacore-enriched analysis identified 10 genes with biological relevance to psychiatric phenotypes and suicide (ADCY9, CRH, NFATC4, ABCC8, HMGA1, KAT2A, EPHA2, TRRAP, CD22, and CBLN1) and highlighted the association that ADCY9 has with various pathways, including signal transduction regulated by the cAMP-responsive element modulator, neurophysiological process regulated by the corticotrophin-releasing hormone, and synaptic plasticity. We therefore went on to validate the observed hypomethylation of ADCY9 in cases vs control through targeted bisulfite sequencing.

Conclusion

Our study represents the first, to our knowledge, analysis of DNA methylation and gene expression associated with suicide in a Mexican population using postmortem brain, providing novel insights for convergent molecular alterations associated with suicide.
Genome-Wide Correlation of DNA Methylation and Gene Expression in Postmortem Brain Tissues of Opioid Use Disorder Patients
Authors: Liu Andi , Dai Yulin , Mendez Emily F , Hu Ruifeng , Fries Gabriel R , Najera Katherine E , Jiang Shan , Meyer Thomas D , Stertz Laura , Jia Peilin , Walss-Bass Consuelo , Zhao Zhongming
Published: June 2021

Background

Opioid use disorder (OUD) affects millions of people, causing nearly 50 000 deaths annually in the United States. While opioid exposure and OUD are known to cause widespread transcriptomic and epigenetic changes, few studies in human samples have been conducted. Understanding how OUD affects the brain at the molecular level could help decipher disease pathogenesis and shed light on OUD treatment.

Methods

We generated genome-wide transcriptomic and DNA methylation profiles of 22 OUD subjects and 19 non-psychiatric controls. We applied weighted gene co-expression network analysis to identify genetic markers consistently associated with OUD at both transcriptomic and methylomic levels. We then performed functional enrichment for biological interpretation. We employed cross-omics analysis to uncover OUD-specific regulatory networks.

Results

We found 6 OUD-associated co-expression gene modules and 6 co-methylation modules (false discovery rate <0.1). Genes in these modules are involved in astrocyte and glial cell differentiation, gliogenesis, response to organic substance, and response to cytokine (false discovery rate <0.05). Cross-omics analysis revealed immune-related transcription regulators, suggesting the role of transcription factor-targeted regulatory networks in OUD pathogenesis.

Conclusions

Our integrative analysis of multi-omics data in OUD postmortem brain samples suggested complex gene regulatory mechanisms involved in OUD-associated expression patterns. Candidate genes and their upstream regulators revealed in astrocyte, and glial cells could provide new insights into OUD treatment development.
Activity of meropenem/vaborbactam and comparators against Gram-negative isolates from Eastern and Western European patients hospitalized with pneumonia including ventilator-associated pneumonia (2014–19)
Authors: Shortridge Dee , Carvalhaes Cecilia , Deshpande Lalitagauri , Castanheira Mariana
Published: June 2021

Objectives

Meropenem/vaborbactam has been approved in Europe for the treatment of hospital-acquired bacterial pneumonia, ventilator-associated pneumonia (VAP) and bacteraemia among other indications. Vaborbactam is an inhibitor of class A and C β-lactamases, including Klebsiella pneumoniae carbapenemase (KPC) enzymes, but not class B or D carbapenemases. We analysed the activity of meropenem/vaborbactam and comparators against 6846 Enterobacterales and 3567 Pseudomonas aeruginosa isolates from patients hospitalized with pneumonia (PHP), including VAP.

Methods

Isolates from PHP were consecutively collected during 2014–19 from 42 European hospitals located in 21 countries and susceptibility tested using the broth microdilution method. Carbapenem-resistant Enterobacterales (CRE) isolates were molecularly characterized to identify their carbapenem-resistance mechanisms. EUCAST (2020) interpretive criteria were used.

Results

The most common Gram-negative pathogens isolated from PHP were P. aeruginosa (n = 3567), K. pneumoniae (n = 1877) and Escherichia coli (n = 1646). Overall, 98.0% of Enterobacterales and 82.1% of P. aeruginosa were susceptible to meropenem/vaborbactam, with 99.8% of Enterobacterales and 89.7% of P. aeruginosa in Western Europe (WE) and 92.7% of Enterobacterales and 69.1% of P. aeruginosa in Eastern Europe (EE). CRE were more common in EE (15.1%) than WE (2.1%). KPC was the most common carbapenemase in WE, while OXA-48-like was the most common carbapenemase in EE. Meropenem/vaborbactam susceptibility was 63.0% for all CRE (92.2% in WE and 51.5% in EE). Meropenem/vaborbactam inhibited 99.1% of KPC-producing isolates and 40.5% of OXA-48-like-producing isolates.

Conclusions

These in vitro data demonstrate that meropenem/vaborbactam has potent activity against isolates from PHP, including isolates producing KPC, and may be a useful treatment option for PHP, including VAP.
Effect of plane of nutrition during the first 12 weeks of life on growth, metabolic and reproductive hormone concentrations, and testicular relative mRNA abundance in preweaned Holstein Friesian bull calves
Authors: Coen Stephen P , Keogh Kate , Byrne Colin J , Lonergan Pat , Fair Sean , Crowe Mark A , Kenny David A
Published: June 2021

The objective of this study was to examine the effect of nutrition during the first 12 wk of life on aspects of the physiological and transcriptional regulation of testicular and overall sexual development in the bull calf. Holstein Friesian bull calves with a mean (SD) age and bodyweight of 17.5 (2.85) d and 48.8 (5.30) kg, respectively, were assigned to either a high (HI; n = 15) or moderate (MOD; n = 15) plane of nutrition and were individually fed milk replacer and concentrate to achieve overall target growth rates of at least 1.0 and 0.5 kg/d, respectively. Throughout the trial, animal growth performance, feed intake, and systemic concentrations of metabolites, metabolic hormones, and reproductive hormones were assessed. Additionally, pulsatility of reproductive hormones (luteinizing hormone, follicle-stimulating hormone, and testosterone) was recorded at 15-min intervals during a 10-h period at 10 wk of age. At 87 ± 2.14 d of age, all calves were euthanized, testes were weighed, and testicular tissue was harvested. Differential expression of messenger ribonucleic acid (mRNA) candidate genes involved in testicular development was examined using quantitative polymerase chain reaction assays. All data were analyzed using the MIXED procedure in Statistical Analysis Software using terms for treatment as well as time for repeated measures. Blood metabolites and metabolic hormones generally reflected the improved metabolic status of the calves on the HI plane of nutrition though the concentrations of reproductive hormones were not affected by diet. Calves on the HI diet had greater mean (SED) slaughter weight (112.4 vs. 87.70 [2.98] kg; P < 0.0001) and testicular tissue weight (29.2 vs. 20.1 [2.21] g; P = 0.0003) than those on the MOD diet. Relative mRNA abundance data indicated advanced testicular development through upregulation of genes involved in cellular metabolism (SIRT1; P = 0.0282), cholesterol biosynthesis (EBP; P = 0.007), testicular function (INSL3; P = 0.0077), and Sertoli cell development (CLDN11; P = 0.0054) in HI compared with MOD calves. In conclusion, results demonstrate that offering dairy-bred male calves a high plane of nutrition during the first 3 mo of life not only improves growth performance and metabolic status but also advances testicular development consistent with more precocious sexual maturation.