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Inhibitory cueing effects following manual and saccadic responses to arrow cues

Ding Y, He T, Satel J, Wang Z

Atten Percept Psychophys, 2016 05;78(4):1020-9.
PMID: 26956560 DOI: 10.3758/s13414-016-1079-6

With two cueing tasks, in the present study we examined output-based inhibitory cueing effects (ICEs) with manual responses to arrow targets following manual or saccadic responses to arrow cues. In all experiments, ICEs were observed when manual localization responses were required to both the cues and targets, but only when the cue-target onset asynchrony (CTOA) was 2,000 ms or longer. In contrast, when saccadic responses were made in response to the cues, ICEs were only observed with CTOAs of 2,000 ms or less-and only when an auditory cue-back signal was used. The present study also showed that the magnitude of ICEs following saccadic responses to arrow cues decreased with time, much like traditional inhibition-of-return effects. The magnitude of ICEs following manual responses to arrow cues, however, appeared later in time and had no sign of decreasing even 3 s after cue onset. These findings suggest that ICEs linked to skeletomotor activation do exist and that the ICEs evoked by oculomotor activation can carry over to the skeletomotor system.
Fulltext Use of the uroflow study in the diagnosis of bladder outlet obstruction in elderly men

Ding YY, Lieu PK, Choo PWJ

Med J Malaysia, 1998 Sep;53(3):209-16.
PMID: 10968155

The uroflow and pressure-flow data of 67 men aged 65 years or more were compared. At best, the uroflow study applying the Liverpool nomogram (25th percentile) and Bristol nomogram (OSD) diagnosed bladder outlet obstruction with sensitivity of 62.5% and 62.5% and specificity of 48.8% and 74.4% respectively. Using the 50th percentile of the Liverpool nomogram as the cut-off resulted in a negative predictive value of 100.0% allowing about 10% of men to have this diagnosis ruled out. We conclude that the uroflow study is inaccurate in diagnosing bladder outlet obstruction in elderly men. However, it can be used to rule out this condition in the small subset of men with maximum flow rates above the 50th percentile of the Liverpool nomogram.
Fulltext MRI Evaluation of Complete Response of Locally Advanced Rectal Cancer After Neoadjuvant Therapy: Current Status and Future Trends

Xu Q, Xu Y, Sun H, Jiang T, Xie S, Ooi BY, et al.

Cancer Manag Res, 2021;13:4317-4328.
PMID: 34103987 DOI: 10.2147/CMAR.S309252

Complete tumor response can be achieved in a certain proportion of patients with locally advanced rectal cancer, who achieve maximal response to neoadjuvant therapy (NAT). For these patients, a watch-and-wait (WW) or nonsurgical strategy has been proposed and is becoming widely practiced in order to avoid unnecessary surgical complications. Therefore, a non-invasive, reliable diagnostic tool for accurately evaluating complete tumor response is needed. Magnetic resonance imaging (MRI) plays a crucial role in both primary staging and restaging tumor response to NAT in rectal cancer without relying on resected specimen. In recent years, numerous efforts have been made to research the value of MRI in predicting and evaluating complete response in rectal cancer. Current MRI evaluation is mainly based on morphological and functional images. Morphologic MRI yields high soft tissue resolution, multiplanar images, and provides detailed depictions of rectal cancer and its surrounding structures. Functional MRI may help to distinguish residual tumor from fibrosis, therefore improving the diagnostic performance of morphologic MRI in identifying complete tumor response. Both morphologic and functional MRI have several promising parameters that may help accurately evaluate and/or predict complete response of rectal cancer. However, these parameters still have limitations and the results remain inconsistent. Recent development of new techniques, such as textural analysis, radiomics analysis and deep learning, demonstrate great potential based on MRI-derived parameters. This article aimed to review and help better understand the strengths, limitations, and future trends of these MRI-derived methods in evaluating complete response in rectal cancer.
How does government efficiency affect carbon emission intensity? A comprehensive empirical study

Ding Y, Chin L, Taghizadeh-Hesary F, Abdul-Rahim AS, Deng P

Environ Sci Pollut Res Int, 2023 Dec;30(59):123067-123082.
PMID: 37979120 DOI: 10.1007/s11356-023-31069-4

This study utilized panel data from 132 countries spanning from 1996 to 2019 to examine the effect of government efficiency on carbon emission intensity. Using a fixed effect model, the study found that stronger government efficiency is associated with a significant decrease in carbon emission intensity. Robustness tests were performed, the results of which consistently supported the main findings. Additionally, the study investigated the mechanisms underlying the linkage between government efficiency and carbon emission intensity, revealing that improved government efficiency can inhibit carbon emission intensity by fostering environmental innovation and promoting renewable energy consumption. Finally, the study examined the moderating effects of national income level, economic freedom, democracy, and ruling party ideology on the nexus of government efficiency and carbon emission intensity, and found empirical evidence supporting these moderating effects. These results provide new insights for governments seeking to reduce carbon emission intensity.
Extended-Spectrum β-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans

Ding Y, Saw WY, Tan LWL, Moong DKN, Nagarajan N, Teo YY, et al.

Appl Environ Microbiol, 2021 09 28;87(20):e0048821.
PMID: 34347523 DOI: 10.1128/AEM.00488-21

Multidrug-resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and 6 different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analyzed the genetic context of the resistance genes and found that composite transposons played important roles in the cotransfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome single nucleotide polymorphisms (SNPs) shared by these isolates, we identified possible clonal transmission of an MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. IMPORTANCE The human gut can harbor both antibiotic-resistant and virulent Escherichia coli which may subsequently cause infections. In this study, we found that multidrug-resistant (MDR) E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes and are highly diverse. By comparing their genomes with the extended-spectrum β-lactamase (ESBL)-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected an MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia, and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.
Legume protein fermented by lactic acid bacteria: Specific enzymatic hydrolysis, protein composition, structure, and functional properties

Du Q, Li H, Tu M, Wu Z, Zhang T, Liu J, et al.

Colloids Surf B Biointerfaces, 2024 Jun;238:113929.
PMID: 38677155 DOI: 10.1016/j.colsurfb.2024.113929

In recent years, with increasing emphasis on healthy, green, and sustainable consumption concepts, plant-based foods have gained popularity among consumers. As widely sourced plant-based raw materials, legume proteins are considered sustainable and renewable alternatives to animal proteins. However, legume proteins have limited functional properties, which hinder their application in food products. LAB fermentation is a relatively natural processing method that is safer than chemical/physical modification methods and can enrich the functional properties of legume proteins through biodegradation and modification. Therefore, changes in legume protein composition, structure, and functional properties and their related mechanisms during LAB fermentation are described. In addition, the specific enzymatic hydrolysis mechanisms of different LAB proteolytic systems on legume proteins are also focused in this review. The unique proteolytic systems of different LAB induce specific enzymatic hydrolysis of legume proteins, resulting in the production of hydrolysates with diverse functional properties, including solubility, emulsibility, gelability, and foamability, which are determined by the composition (peptide/amino acid) and structure (secondary/tertiary) of legume proteins after LAB fermentation. The correlation between LAB-specific enzymatic hydrolysis, protein composition and structure, and protein functional properties will assist in selecting legume protein raw materials and LAB strains for legume plant-based food products and expand the application of legume proteins in the food industry.
Fulltext Characterization of SARS-CoV-2 worldwide transmission based on evolutionary dynamics and specific viral mutations in the spike protein

Liu J, Chen X, Liu Y, Lin J, Shen J, Zhang H, et al.

Infect Dis Poverty, 2021 Aug 21;10(1):112.
PMID: 34419160 DOI: 10.1186/s40249-021-00895-4

BACKGROUND: The coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) is pandemic. However, the origins and global transmission pattern of SARS-CoV-2 remain largely unknown. We aimed to characterize the origination and transmission of SARS-CoV-2 based on evolutionary dynamics.
METHODS: Using the full-length sequences of SARS-CoV-2 with intact geographic, demographic, and temporal information worldwide from the GISAID database during 26 December 2019 and 30 November 2020, we constructed the transmission tree to depict the evolutionary process by the R package "outbreaker". The affinity of the mutated receptor-binding region of the spike protein to angiotensin-converting enzyme 2 (ACE2) was predicted using mCSM-PPI2 software. Viral infectivity and antigenicity were tested in ACE2-transfected HEK293T cells by pseudovirus transfection and neutralizing antibody test.
RESULTS: From 26 December 2019 to 8 March 2020, early stage of the COVID-19 pandemic, SARS-CoV-2 strains identified worldwide were mainly composed of three clusters: the Europe-based cluster including two USA-based sub-clusters; the Asia-based cluster including isolates in China, Japan, the USA, Singapore, Australia, Malaysia, and Italy; and the USA-based cluster. The SARS-CoV-2 strains identified in the USA formed four independent clades while those identified in China formed one clade. After 8 March 2020, the clusters of SARS-CoV-2 strains tended to be independent and became "pure" in each of the major countries. Twenty-two of 60 mutations in the receptor-binding domain of the spike protein were predicted to increase the binding affinity of SARS-CoV-2 to ACE2. Of all predicted mutants, the number of E484K was the largest one with 86 585 sequences, followed by S477N with 55 442 sequences worldwide. In more than ten countries, the frequencies of the isolates with E484K and S477N increased significantly. V367F and N354D mutations increased the infectivity of SARS-CoV-2 pseudoviruses (P
Fulltext Helminth infection promotes colonization resistance via type 2 immunity

Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, et al.

Science, 2016 Apr 29;352(6285):608-12.
PMID: 27080105 DOI: 10.1126/science.aaf3229

Increasing incidence of inflammatory bowel diseases, such as Crohn's disease, in developed nations is associated with changes to the microbial environment, such as decreased prevalence of helminth colonization and alterations to the gut microbiota. We find that helminth infection protects mice deficient in the Crohn's disease susceptibility gene Nod2 from intestinal abnormalities by inhibiting colonization by an inflammatory Bacteroides species. Resistance to Bacteroides colonization was dependent on type 2 immunity, which promoted the establishment of a protective microbiota enriched in Clostridiales. Additionally, we show that individuals from helminth-endemic regions harbor a similar protective microbiota and that deworming treatment reduced levels of Clostridiales and increased Bacteroidales. These results support a model of the hygiene hypothesis in which certain individuals are genetically susceptible to the consequences of a changing microbial environment.
Fulltext The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone

Chen SL, Ding Y, Apisarnthanarak A, Kalimuddin S, Archuleta S, Omar SFS, et al.

Sci Rep, 2019 09 13;9(1):13245.
PMID: 31519972 DOI: 10.1038/s41598-019-49467-5

The ST131 multilocus sequence type (MLST) of Escherichia coli is a globally successful pathogen whose dissemination is increasing rates of antibiotic resistance. Numerous global surveys have demonstrated the pervasiveness of this clone; in some regions ST131 accounts for up to 30% of all E. coli isolates. However, many regions are underrepresented in these published surveys, including Africa, South America, and Asia. We collected consecutive bloodstream E. coli isolates from three countries in Southeast Asia; ST131 was the most common MLST type. As in other studies, the C2/H30Rx clade accounted for the majority of ST131 strains. Clinical risk factors were similar to other reported studies. However, we found that nearly all of the C2 strains in this study were closely related, forming what we denote the SEA-C2 clone. The SEA-C2 clone is enriched for strains from Asia, particularly Southeast Asia and Singapore. The SEA-C2 clone accounts for all of the excess resistance and virulence of ST131 relative to non-ST131 E. coli. The SEA-C2 strains appear to be locally circulating and dominant in Southeast Asia, despite the intuition that high international connectivity and travel would enable frequent opportunities for other strains to establish themselves.
Fulltext Author Correction: The higher prevalence of extended spectrum beta-lactamases among Escherichia coli ST131 in Southeast Asia is driven by expansion of a single, locally prevalent subclone

Chen SL, Ding Y, Apisarnthanarak A, Kalimuddin S, Archuleta S, Omar SFS, et al.

Sci Rep, 2021 Apr 14;11(1):8563.
PMID: 33854114 DOI: 10.1038/s41598-021-87312-w
ACORN (A Clinically-Oriented Antimicrobial Resistance Surveillance Network) II: protocol for case based antimicrobial resistance surveillance

Mo Y, Ding Y, Cao Y, Hopkins J, Ashley EA, Waithira N, et al.

Wellcome Open Res, 2023;8:179.
PMID: 37854055 DOI: 10.12688/wellcomeopenres.19210.2

Background: Antimicrobial resistance surveillance is essential for empiric antibiotic prescribing, infection prevention and control policies and to drive novel antibiotic discovery. However, most existing surveillance systems are isolate-based without supporting patient-based clinical data, and not widely implemented especially in low- and middle-income countries (LMICs). Methods: A Clinically-Oriented Antimicrobial Resistance Surveillance Network (ACORN) II is a large-scale multicentre protocol which builds on the WHO Global Antimicrobial Resistance and Use Surveillance System to estimate syndromic and pathogen outcomes along with associated health economic costs. ACORN-healthcare associated infection (ACORN-HAI) is an extension study which focuses on healthcare-associated bloodstream infections and ventilator-associated pneumonia. Our main aim is to implement an efficient clinically-oriented antimicrobial resistance surveillance system, which can be incorporated as part of routine workflow in hospitals in LMICs. These surveillance systems include hospitalised patients of any age with clinically compatible acute community-acquired or healthcare-associated bacterial infection syndromes, and who were prescribed parenteral antibiotics. Diagnostic stewardship activities will be implemented to optimise microbiology culture specimen collection practices. Basic patient characteristics, clinician diagnosis, empiric treatment, infection severity and risk factors for HAI are recorded on enrolment and during 28-day follow-up. An R Shiny application can be used offline and online for merging clinical and microbiology data, and generating collated reports to inform local antibiotic stewardship and infection control policies. Discussion: ACORN II is a comprehensive antimicrobial resistance surveillance activity which advocates pragmatic implementation and prioritises improving local diagnostic and antibiotic prescribing practices through patient-centred data collection. These data can be rapidly communicated to local physicians and infection prevention and control teams. Relative ease of data collection promotes sustainability and maximises participation and scalability. With ACORN-HAI as an example, ACORN II has the capacity to accommodate extensions to investigate further specific questions of interest.

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