bluuebunny/crossref_metadata_2025_split huggingface dataset:
Zymomonas diversity and potential for biofuel production
Authors: Felczak Magdalena M. , Bowers Robert M. , Woyke Tanja , TerAvest Michaela A. 
Published: May 2021

Abstract
Background
Zymomonas mobilis is an aerotolerant α-proteobacterium, which has been genetically engineered for industrial purposes for decades. However, a comprehensive comparison of existing strains on the genomic level in conjunction with phenotype analysis has yet to be carried out. We here performed whole-genome comparison of 17 strains including nine that were sequenced in this study. We then compared 15 available Zymomonas strains for their natural abilities to perform under conditions relevant to biofuel synthesis. We tested their growth in anaerobic rich media, as well as growth, ethanol production and xylose utilization in lignocellulosic hydrolysate. We additionally compared their tolerance to isobutanol, flocculation characteristics, and ability to uptake foreign DNA by electroporation and conjugation.

Results
Using clustering based on 99% average nucleotide identity (ANI), we classified 12 strains into four clusters based on sequence similarity, while five strains did not cluster with any other strain. Strains belonging to the same 99% ANI cluster showed similar performance while significant variation was observed between the clusters. Overall, conjugation and electroporation efficiencies were poor across all strains, which was consistent with our finding of coding potential for several DNA defense mechanisms, such as CRISPR and restriction–modification systems, across all genomes. We found that strain ATCC31821 (ZM4) had a more diverse plasmid profile than other strains, possibly leading to the unique phenotypes observed for this strain. ZM4 also showed the highest growth of any strain in both laboratory media and lignocellulosic hydrolysate and was among the top 3 strains for isobutanol tolerance and electroporation and conjugation efficiency.

Conclusions
Our findings suggest that strain ZM4 has a unique combination of genetic and phenotypic traits that are beneficial for biofuel production and propose investing future efforts in further engineering of ZM4 for industrial purposes rather than exploring new Zymomonas isolates.
Soluble guanylate cyclase stimulator reduced the gastrointestinal fibrosis in bleomycin-induced mouse model of systemic sclerosis
Authors: Yamamoto Yuzuru , Okano Takaichi , Yamada Hirotaka , Akashi Kengo , Sendo Sho , Ueda Yo , Morinobu Akio , Saegusa Jun 
Published: May 2021

AbstractBackgroundSystemic sclerosis (SSc) is a chronic autoimmune-mediated connective tissue disorder. Although the etiology of the disease remains undetermined, SSc is characterized by fibrosis and proliferative vascular lesions of the skin and internal organs. SSc involves the gastrointestinal tract in more than 90 % of patients. Soluble guanylate cyclase (sGC) stimulator is used to treat pulmonary artery hypertension (PAH) and has been shown to inhibit experimental skin fibrosis.MethodsFemale C57BL/6J mice were treated with BLM or normal saline by subcutaneous implantation of osmotic minipump. These mice were sacrificed on day 28 or day 42. Gastrointestinal pathologies were examined by Masson Trichrome staining. The expression of fibrosis-related genes in gastrointestinal tract was analyzed by real-time PCR, and the levels of collagen in the tissue were measured by Sircol collagen assay. To evaluate peristaltic movement, the small intestinal transport (ITR%) was calculated as [dyeing distance × (duodenum − appendix)] − 1 × 100 (%). We treated BLM-treated mice with sGC stimulator or DMSO orally and analyzed them on day 42.ResultsHistological examination revealed that fibrosis from lamina propria to muscularis mucosa in the esophagus was significantly increased in BLM-treated mice, suggesting that BLM induces esophageal hyperproliferative and prefibrotic response in C57BL/6J mice. In addition, the gene expression levels of Col3a1, CCN2, MMP-2, MMP-9, TIMP-1, and TIMP-2 in the esophagus were significantly increased in BLM-treated mice. More severe hyperproliferative and prefibrotic response was observed in the mice sacrificed on day 42 than the mice sacrificed on day 28. The ITR% was found to be significantly lower in BLM-treated mice, suggesting that gastrointestinal peristaltic movement was reduced in BLM-treated mice. Furthermore, we demonstrated that sGC stimulator treatment significantly reduced hyperproliferative and prefibrotic response of esophagus and intestine in BLM-treated mice, by histological examination and Sircol collagen assay.ConclusionsThese findings suggest that BLM induces gastrointestinal hyperproliferative and prefibrotic response in C57BL/6J mice, and treatment with sGC stimulator improves the BLM-induced gastrointestinal lesion.
Intestinal parasites among intellectually disabled individuals in Iran: a systematic review and meta-analysis
Authors: Abbaszadeh Afshar Mohammad Javad , Mohebali Mehdi , Mohtasebi Sina , Teimouri Aref , Sedaghat Bahareh , Saberi Reza 
Published: May 2021

Abstract
Background
Poor self-care skills and personal hygiene resulted from limitations in learning and understanding, put intellectually disabled individuals at greater risk for intestinal parasitic infections (IPIs). Despite several regional reports in Iran, the overall burden on IPIs among intellectually disabled individuals is poorly understood. Hence, the present study aimed to estimate the pooled prevalence of IPIs among intellectually disabled individuals in Iran.

Methods
Using the PRISMA guidelines, we conducted a systematic review and meta-analysis of data retrieved from seven electronic databases (PubMed, Web of Science, Scopus, Embase, and ProQuest for English articles, as well as SID and Magiran for Persian) from their inception up to December 2020. Pooled prevalence was estimated using a random-effects model with a 95% confidence interval (CI) and depicted as a forest plot, while heterogeneity was evaluated using Cochran’s Q-test.

Results
Exactly 1263 of the 3004 intellectually disabled individuals examined by 14 studies across 10 provinces of Iran were positive for IPIs. Overall pooled prevalence estimate was 41% (95% CI 29–53%) with a range of 21% (95% CI 10–32%) to 68% (95% CI 55–80%) across sub-groups. Entamoeba coli (16.2%; 95% CI 10.3–22%), Blastocystis spp. (12.2%; 95% CI 7.2–17.2%), and Giardia duodenalis (11.9%; 95% CI 7.4–16.3%) were the most prevalent protozoan species. In terms of helminthic agents, the most prevalent species were Enterobius vermicularis (11.3%; 95% CI 6.3–16.3%) followed by Strongyloides stercoralis (10.9%; 95% CI 5.0–16.9%) and Hymenolepis nana (2.8%; 95% CI 0.4–5.2%)

Conclusion
IPIs are highly prevalent among intellectually disabled individuals in Iran. Improving the health status and implementing infectious disease prevention strategies in rehabilitation centers, health promotion interventions to improve personal hygiene of intellectually disabled individuals, as well as utilize sensitive diagnostic methods besides routine stool examination techniques, and treatment of infected individuals will help in the control of these infections among intellectually disabled individuals.
Investigating the relationship between BMI across adulthood and late life brain pathologies
Authors: Lane Christopher A. , Barnes Josephine , Nicholas Jennifer M. , Baker John W. , Sudre Carole H. , Cash David M. , Parker Thomas D. , Malone Ian B. , Lu Kirsty , James Sarah-Naomi , Keshavan Ashvini , Buchanan Sarah , Keuss Sarah , Murray-Smith Heidi , Wong Andrew , Gordon Elizabeth , Coath William , Modat Marc , Thomas David , Hardy Rebecca , Richards Marcus , Fox Nick C. , Schott Jonathan M. 
Published: May 2021

Abstract
Background
In view of reported associations between high adiposity, particularly in midlife and late-life dementia risk, we aimed to determine associations between body mass index (BMI), and BMI changes across adulthood and brain structure and pathology at age 69–71 years.

Methods
Four hundred sixty-five dementia-free participants from Insight 46, a sub-study of the British 1946 birth cohort, who had cross-sectional T1/FLAIR volumetric MRI, and florbetapir amyloid-PET imaging at age 69–71 years, were included in analyses. We quantified white matter hyperintensity volume (WMHV) using T1 and FLAIR 3D-MRI; β-amyloid (Aβ) positivity/negativity using a SUVR approach; and whole brain (WBV) and hippocampal volumes (HV) using 3D T1-MRI. We investigated the influence of BMI, and BMI changes at and between 36, 43, 53, 60–64, 69 and 71 years, on late-life WMHV, Aβ-status, WBV and mean HV. Analyses were repeated using overweight and obese status.

Results
At no time-point was BMI, change in BMI or overweight/obese status associated with WMHV or WBV at age 69–71 years. Decreasing BMI in the 1–2 years before imaging was associated with an increased odds of being β-amyloid positive (OR 1.45, 95% confidence interval 1.09, 1.92). There were associations between being overweight and larger mean HV at ages 60–64 (β = 0.073 ml, 95% CI 0.009, 0.137), 69 (β = 0.076 ml, 95% CI 0.012, 0.140) and 71 years (β = 0.101 ml, 95% CI 0.037, 0.165). A similar, albeit weaker, trend was seen with obese status.

Conclusions
Using WMHV, β-amyloid status and brain volumes as indicators of brain health, we do not find evidence to explain reported associations between midlife obesity and late-life dementia risk. Declining BMI in later life may reflect preclinical Alzheimer’s disease.
Thrombosed left ventricular pseudoaneurysm following myocardial infarction: a case report
Authors: Zouari Fatma , Tlili Rami , Azaiez Fares , Zayed Sofien , Ben Romdhane Rim , Ziadi Jalel , Ben Ameur Youssef 
Published: May 2021

Abstract
Background
Pseudoaneurysm of inferior wall of the left ventricle is an uncommon complication of myocardial infarction with high mortality.

Case presentation
We report the case of a 63-year-old Tunisian man, diagnosed with a thrombosed left ventricular pseudoaneurysm and a pericardial effusion after 1 week of angina.

Conclusions
Left ventricular pseudoaneurysm is a serious complication of myocardial infarction that has atypical presentations. Diagnosis is generally established by transthoracic echocardiography but confirmed by magnetic resonance imaging. Urgent surgery is the treatment choice given the risk of embolization and rupture.
Reduction en masse of inguinal hernia after self-reduction: a case report
Authors: Najjari Khosrow , zabihi Mahmoudabadi Hossein , Seyedjavadeyn Seyed Zeynab , Hajebi Reza 
Published: May 2021

Abstract
Background
Reduction en mass (REM) is one of the rare complications of inguinal hernia reduction. Although REM can be detected on the basis of specific computed tomography (CT) scan findings, many radiologists are not familiar with its radiological appearance because of the scarcity of this complication, which may cause a delay in diagnosis.

Case presentation
The patient reported in this article was a 50-year-old Persian man with a history of inguinal hernia, who had been referred with the periumbilical pain that radiated to the right lower quadrant and developed following hernia replacement by the patient himself. REM diagnosis was based on clinical examination and CT scan findings, and surgical treatment was performed by the Lichtenstein repair and mesh implantation.

Conclusions
Although REM usually occurs after reduction with compression in the inguinal hernia, this unique case report highlighted the possibility of REM after self-reduction. Surgeons and radiologists should consider REM in patients with a history of inguinal hernia presenting with intestinal obstruction symptoms, even without any apparent signs of hernia in the physical examination.
Deep learning integration of molecular and interactome data for protein–compound interaction prediction
Authors: Watanabe Narumi , Ohnuki Yuuto , Sakakibara Yasubumi 
Published: May 2021

Abstract
Motivation
Virtual screening, which can computationally predict the presence or absence of protein–compound interactions, has attracted attention as a large-scale, low-cost, and short-term search method for seed compounds. Existing machine learning methods for predicting protein–compound interactions are largely divided into those based on molecular structure data and those based on network data. The former utilize information on proteins and compounds, such as amino acid sequences and chemical structures; the latter rely on interaction network data, such as protein–protein interactions and compound–compound interactions. However, there have been few attempts to combine both types of data in molecular information and interaction networks.

Results
We developed a deep learning-based method that integrates protein features, compound features, and multiple types of interactome data to predict protein–compound interactions. We designed three benchmark datasets with different difficulties and applied them to evaluate the prediction method. The performance evaluations show that our deep learning framework for integrating molecular structure data and interactome data outperforms state-of-the-art machine learning methods for protein–compound interaction prediction tasks. The performance improvement is statistically significant according to the Wilcoxon signed-rank test. This finding reveals that the multi-interactome data captures perspectives other than amino acid sequence homology and chemical structure similarity and that both types of data synergistically improve the prediction accuracy. Furthermore, experiments on the three benchmark datasets show that our method is more robust than existing methods in accurately predicting interactions between proteins and compounds that are unseen in training samples.
Increased dietary availability of selenium in rainbow trout (Oncorhynchus mykiss) improves its plasma antioxidant capacity and resistance to infection with Piscirickettsia salmonis
Authors: Pérez-Valenzuela Javiera , Mejías Madelaine , Ortiz Daniela , Salgado Pablo , Montt Liliana , Chávez-Báez Ignacio , Vera-Tamargo Francisca , Mandakovic Dinka , Wacyk Jurij , Pulgar Rodrigo 
Published: May 2021

AbstractSalmonid Rickettsial Septicaemia (SRS), caused by Piscirickettsia salmonis, is the most important infectious disease in the Chilean salmon farming industry. An opportunity to control this disease is to use functional micronutrients to modulate host mechanisms of response to the infection. Since P. salmonis may affect the host antioxidant system in salmonids, particularly that dependent on selenium (Se), we hypothesized that fish’s dietary selenium supplementation could improve the response to the bacterial infection. To address this, we defined a non-antibiotic, non-cytotoxic concentration of selenium to evaluate its effect on the response to in vitro infections of SHK-1 cells with P. salmonis. The results indicated that selenium supplementation reduced the cytopathic effect, intracellular bacterial load, and cellular mortality of SHK-1 by increasing the abundance and activity of host glutathione peroxidase. We then prepared diets supplemented with selenium up to 1, 5, and 10 mg/kg to feed juvenile trout for 8 weeks. At the end of this feeding period, we obtained their blood plasma and evaluated its ability to protect SHK-1 cells from infection with P. salmonis in ex vivo assays. These results recapitulated the observed ability of selenium to protect against infection with P. salmonis by increasing the concentration of selenium and the antioxidant capacity in fish’s plasma. To the best of our knowledge, this is the first report of the protective capacity of selenium against P. salmonis infection in salmonids, becoming a potential effective host-directed dietary therapy for SRS and other infectious diseases in animals at a non-antibiotic concentration.
Cerebral organoids and their potential for studies of brain diseases in domestic animals
Authors: Pain Bertrand , Baquerre Camille , Coulpier Muriel 
Published: May 2021

AbstractThe brain is a complex organ and any model for studying it in its normal and pathological aspects becomes a tool of choice for neuroscientists. The mastering and dissemination of protocols allowing brain organoids development have paved the way for a whole range of new studies in the field of brain development, modeling of neurodegenerative or neurodevelopmental diseases, understanding tumors as well as infectious diseases that affect the brain. While studies are so far limited to the use of human cerebral organoids, there is a growing interest in having similar models in other species. This review presents what is currently developed in this field, with a particular focus on the potential of cerebral organoids for studying neuro-infectious diseases in human and domestic animals.
Media forensics on social media platforms: a survey
Authors: Pasquini Cecilia , Amerini Irene , Boato Giulia 
Published: May 2021

AbstractThe dependability of visual information on the web and the authenticity of digital media appearing virally in social media platforms has been raising unprecedented concerns. As a result, in the last years the multimedia forensics research community pursued the ambition to scale the forensic analysis to real-world web-based open systems. This survey aims at describing the work done so far on the analysis of shared data, covering three main aspects: forensics techniques performing source identification and integrity verification on media uploaded on social networks, platform provenance analysis allowing to identify sharing platforms, and multimedia verification algorithms assessing the credibility of media objects in relation to its associated textual information. The achieved results are highlighted together with current open issues and research challenges to be addressed in order to advance the field in the next future.
Group signature with time-bound keys and unforgeability of expiry time for smart cities
Authors: Fang Junli , Feng Tao 
Published: May 2021

AbstractInternet of Things (IoT) lays the foundation for the various applications in smart cities, yet resource-constrained IoT devices are prone to suffer from devastating cyberattacks and privacy leak threats, thus are inevitability supposed as the weakest link of the systems in smart cities. Mitigating the security risks of data and the computing limitation of edge devices, especially identity authentication and key validity management of group devices are essential for IoT system security. In order to tackle the issues of anonymity, traceability, unforgeability of expiry time as well as efficient membership revocation for life-cycle management of devices in IoT setting, we presented a dynamic time-bound group signature with unforgeability of expiry time. Unforgeability of expiry time disables a revoked signer to create a valid signature by means of associating the signing key with an expiry time. The anonymity and traceability of the proposed scheme contribute to the identity privacy of the entities and supervision for authority agency. Moreover, our proposal is feasible in the resource-constrained setting for efficient computational cost of signing and verification algorithms.
M-ary nonlinear sine chirp spread spectrum for underwater acoustic communication based on virtual time-reversal mirror method
Authors: Liu Songzuo , Zuberi Habib Hussain , Lou Yi , Farooq Muhmmad Bilal , Shaikh Shahabuddin , Raza Waleed 
Published: May 2021

AbstractLinear chirp spread spectrum technique is widely used in underwater acoustic communication because of their resilience to high multipath and Doppler shift. Linear frequency modulated signal requires a high spreading factor to nearly reach orthogonality between two pairs of signals. On the other hand, nonlinear chirp spread spectrum signals can provide orthogonality at a low spreading factor. As a result, it improves spectral efficiency and is more insensitive to Doppler spread than the linear counterpart. To achieve a higher data rate, we propose two variants (half cycle sine and full cycle sine) of the M-ary nonlinear sine chirp spread spectrum technique based on virtual time-reversal mirror (VTRM). The proposed scheme uses different frequency bands to transmit chirp, and VTRM is used to improve the bit error rate due to high multipath. Its superior Doppler sensitivity makes it suitable for underwater acoustic communication. Furthermore, the proposed method uses a simple, low-power bank of matched filters; thus, it reduces the overall system complexity. Simulations are performed in different underwater acoustic channels to verify the robustness of the proposed scheme.
Results on the approximate controllability of fractional hemivariational inequalities of order $1< r<2$
Authors: Mohan Raja M. , Vijayakumar V. , Huynh Le Nhat , Udhayakumar R. , Nisar Kottakkaran Sooppy 
Published: May 2021

AbstractIn this paper, we investigate the approximate controllability of fractional evolution inclusions with hemivariational inequalities of order$1< r<2$1<r<2. The main results of this paper are verified by using the fractional theories, multivalued analysis, cosine families, and fixed-point approach. At first, we discuss the existence of the mild solution for the class of fractional systems. After that, we establish the approximate controllability of linear and semilinear control systems. Finally, an application is presented to illustrate our theoretical results.
A new conformable nabla derivative and its application on arbitrary time scales
Authors: Segi Rahmat Mohamad Rafi , Noorani M. Salmi M. 
Published: May 2021

AbstractIn this article, we introduce a new type of conformable derivative and integral which involve the time scale power function $\widehat{\mathcal{G}}_{\eta }(t, a)$

G
ˆ

η

(
t
,
a
)
for $t,a\in \mathbb{T}$
t
,
a
∈
T
. The time scale power function takes the form $(t-a)^{\eta }$

(
t
−
a
)

η

for $\mathbb{T}=\mathbb{R}$
T
=
R
which reduces to the definition of conformable fractional derivative defined by Khalil et al. (2014). For the discrete time scales, it is completely novel, where the power function takes the form $(t-a)^{(\eta )}$

(
t
−
a
)

(
η
)

which is an increasing factorial function suitable for discrete time scales analysis. We introduce a new conformable exponential function and study its properties. Finally, we consider the conformable dynamic equation of the form $\bigtriangledown _{a}^{\gamma }y(t)=y(t, f(t))$

▽
a
γ

y
(
t
)
=
y
(
t
,
f
(
t
)
)
, and study the existence and uniqueness of the solution. As an application, we show that the conformable exponential function is the unique solution to the given dynamic equation. We also examine the analogue of Gronwall’s inequality and its application on time scales.
On nontrivial solutions of nonlinear Schrödinger equations with sign-changing potential
Authors: Chen Wei , Wu Yue , Jhang Seongtae 
Published: May 2021

AbstractIn this paper, we consider the superlinear Schrödinger equation with bounded potential well. The potential here is allowed to be sign-changing. Without assuming the Ambrosetti–Rabinowitz-type condition, we prove the existence of a nontrivial solution and multiplicity results.