bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental optimization of lensless digital holographic microscopy with rotating diffuser-based coherent noise reduction
Authors: Arcab Piotr , Mirecki Bartosz , Stefaniuk Marzena , Pawłowska Monika , Trusiak Maciej
Published: September 2022

Laser-based lensless digital holographic microscopy (LDHM) is often spoiled by considerable coherent noise factor. We propose a novel LDHM method with significantly limited coherent artifacts, e.g., speckle noise and parasitic interference fringes. It is achieved by incorporating a rotating diffuser, which introduces partial spatial coherence and preserves high temporal coherence of laser light, crucial for credible in-line hologram reconstruction. We present the first implementation of the classical rotating diffuser concept in LDHM, significantly increasing the signal-to-noise ratio while preserving the straightforwardness and compactness of the LDHM imaging device. Prior to the introduction of the rotating diffusor, we performed LDHM experimental hardware optimization employing 4 light sources, 4 cameras, and 3 different optical magnifications (camera-sample distances). It was guided by the quantitative assessment of numerical amplitude/phase reconstruction of test targets, conducted upon standard deviation calculation (noise factor quantification), and resolution evaluation (information throughput quantification). Optimized rotating diffuser LDHM (RD-LDHM) method was successfully corroborated in technical test target imaging and examination of challenging biomedical sample (60 µm thick mouse brain tissue slice). Physical minimization of coherent noise (up to 50%) was positively verified, while preserving optimal spatial resolution of phase and amplitude imaging. Coherent noise removal, ensured by proposed RD-LDHM method, is especially important in biomedical inference, as speckles can falsely imitate valid biological features. Combining this favorable outcome with large field-of-view imaging can promote the use of reported RD-LDHM technique in high-throughput stain-free biomedical screening.
Self-adjusting inverse design method for nanophotonic devices
Authors: Liu Haida , Wang Qianqian , Xiang Zhengxin , Teng Geer , Zhao Yu , Liu Ziyang , Wei Kai , Dai Fengtong , Lv Linji , Zhao Kuo , Yang Chenyi
Published: September 2022

Nanophotonic devices, which consist of multiple cell structures of the same size, are easy to manufacture. To avoid the optical proximity effect in the ultraviolet lithography process, the cell structures must be maintained at a distance from one another. In the inverse design process, the distance is maintained by limiting the optimized range of the location. However, this implementation can weaken the performance of the devices designed during transmission. To solve this problem, a self-adjusting inverse design method based on the adjoint variable method is developed. By introducing artificial potential field method, the location of one cell structure is modified only when the distances between this cell structure and other cell structures are smaller than a threshold. In this case, the range of the location can be expanded, and thus the performance of the designed devices can be improved. A wavelength demultiplexer with a channel spacing of 1.6 nm is designed to verify the performance of the proposed method. The experiment reveals that the transmission of the designed devices can be improved by 20%, and the self-adjusting inverse design process is 100 times faster than the inverse-design process based on the genetic algorithm.
BoxCARS 2D IR spectroscopy with pulse shaping
Authors: Al-Mualem Ziareena A. , Chen Xiaobing , Shirley Joseph C. , Xu Cong , Baiz Carlos R.
Published: September 2022

BoxCARS and pump-probe geometries are common implementations of two-dimensional infrared (2D IR) spectroscopy. BoxCARS is background-free, generally offering greater signal-to-noise ratio, which enables measuring weak vibrational echo signals. Pulse shapers have been implemented in the pump-probe geometry to accelerate data collection and suppress scatter and other unwanted signals by precise control of the pump-pulse delay and carrier phase. Here, we introduce a 2D-IR optical setup in the BoxCARS geometry that implements a pulse shaper for rapid acquisition of background-free 2D IR spectra. We show a signal-to-noise improvement using this new fast-scan BoxCARS setup versus the pump-probe geometry within the same configuration.
Triggerless data acquisition in asynchronous optical-sampling terahertz time-domain spectroscopy based on a dual-comb system
Authors: Okano Makoto , Watanabe Shinichi
Published: September 2022

By using two mutually phase-locked optical frequency combs with slightly different repetition rates, we demonstrate asynchronous optical-sampling terahertz time-domain spectroscopy (ASOPS THz-TDS) without using any trigger signals or optical delay lines. Due to a tight stabilization of the repetition frequencies, it was possible to accumulate the data over 48 minutes in a triggerless manner without signal degradation. The fractional frequency stability of the measured terahertz signal is evaluated to be ∼8.0 × 10−17 after 730 s. The frequency accuracy of the obtained terahertz spectrum is ensured by phase-locking the two frequency combs to a frequency standard. To clarify the performance of our system, we characterized the absorption line of water vapor around 0.557 THz. The good agreement of the measured center frequency and linewidth with the values predicted from the HITRAN database verifies the suitability of our ASOPS THz-TDS system for precise measurements.
Bi-directional ultra-violet communication with self-interference
Authors: Zhang Yubo , Gong Chen , Xu Zhengyuan
Published: September 2022

We investigate the self-interference characterization, achievable rate, signal detection and parameter estimation for bi-directional ultra-violet (UV) communication. We firstly characterize and experimentally demonstrate the self-interference of UV communication, which is non-negligible as the angle between the transmission and receiver directions is blow 60°. Then, we present the achievable rate and symbol detection under self-interference, which show that the offset between self-interference and desirable symbols can increase the achievable rate and decrease the symbol detection error probability. We propose the practical system design with parameter estimation under self-interference. Finally, we experimentally evaluate the receiver-side signal detection with self-interference generated by Field Programmable Gate Array, and the signal detection of a real bidirectional UV communication system. Lower symbol detection error probability can also be observed as the offset between desirable symbols and self-interference symbols increases to half-symbol length from both system-level simulation and real experiments, which further validates the theoretical results.
High-performance multi-parameter fiber sensor by grating-enhanced Mach–Zehnder interference
Authors: Li Boyao , Liang Yaoyao , Xie Zhongye , Sun Jinghua
Published: September 2022

A multi-parameter dual-core fiber sensor is proposed to realize highly sensitive detection of illumination, temperature, and humidity, separately. Through partial grating etching of a one-side core, the interaction between the core and the external environment is enhanced. Then, combining the Mach–Zehnder effect of the dual core, a higher sensing sensitivity is obtained. Experimental results show the temperature sensitivity is higher than 6.1952 nm/°C. Besides, the humidity and illumination resolution can reach as accurate as 0.041 relative humidity (RH) and 0.025 light units, respectively. To have better multi-parameter sensing and demodulation, the deep learning algorithm of a one-dimensional convolutional neural network (1D-CNN) is used to reach an accuracy of 99.05% with ∼2.00 root mean square error (RMSE). We envision such an excellent multi-parameter sensor can be promising in environmental monitoring and intelligent manufacturing.
Design of immunogens for eliciting antibody responses that may protect against SARS-CoV-2 variants
Authors: Wang Eric , Chakraborty Arup K.
Published: September 2022

The rise of SARS-CoV-2 variants and the history of outbreaks caused by zoonotic coronaviruses point to the need for next-generation vaccines that confer protection against variant strains. Here, we combined analyses of diverse sequences and structures of coronavirus spikes with data from deep mutational scanning to design SARS-CoV-2 variant antigens containing the most significant mutations that may emerge. We trained a neural network to predict RBD expression and ACE2 binding from sequence, which allowed us to determine that these antigens are stable and bind to ACE2. Thus, they represent viable variants. We then used a computational model of affinity maturation (AM) to study the antibody response to immunization with different combinations of the designed antigens. The results suggest that immunization with a cocktail of the antigens is likely to promote evolution of higher titers of antibodies that target SARS-CoV-2 variants than immunization or infection with the wildtype virus alone. Finally, our analysis of 12 coronaviruses from different genera identified the S2’ cleavage site and fusion peptide as potential pan-coronavirus vaccine targets.
Prostaglandins and calprotectin are genetically and functionally linked to the Inflammatory Bowel Diseases
Authors: Karaky Mohamad , Boucher Gabrielle , Mola Saraï , Foisy Sylvain , Beauchamp Claudine , Rivard Marie-Eve , Burnette Melanie , Gosselin Hugues ,   iGenoMed Consortium, Bitton Alain , Charron Guy , Goyette Philippe , Rioux John D.
Published: September 2022

Background

Genome wide association studies (GWAS) have identified and validated more than 200 genomic loci associated with the inflammatory bowel disease (IBD), although for most the causal gene remains unknown. Given the importance of myeloid cells in IBD pathogenesis, the current study aimed to uncover the role of genes within IBD genetic loci that are endogenously expressed in this cell lineage.

Methods

The open reading frames (ORF) of 42 genes from IBD-associated loci were expressed via lentiviral transfer in the THP-1 model of human monocytes and the impact of each of these on the cell’s transcriptome was analyzed using a RNA sequencing-based approach. We used a combination of genetic and pharmacologic approaches to validate our findings in the THP-1 line with further validation in human induced pluripotent stem cell (hiPSC)-derived-monocytes.

Results

This functional genomics screen provided evidence that genes in four IBD GWAS loci (PTGIR, ZBTB40, SLC39A11 and NFKB1) are involved in controlling S100A8 and S100A9 gene expression, which encode the two subunits of calprotectin (CP). We demonstrated that increasing PTGIR expression and/or stimulating PTGIR signaling resulted in increased CP expression in THP-1.

This was further validated in hiPSC-derived monocytes. Conversely, knocking-down PTGIR endogenous expression and/or inhibiting PTGIR signaling led to decreased CP expression. These analyses were extended to the known IBD gene PTGER4, whereby its specific agonist also led to increased CP expression. Furthermore, we demonstrated that the PTGIR and PTGER4 mediated control of CP expression was dependent on signaling via adenylate cyclase and STAT3. Finally, we demonstrated that LPS-mediated increases in CP expression could be potentiated by agonists of PTGIR and PTGER4, and diminished by their antagonists.

Conclusion

Our results support a causal role for the PTGIR, PTGER4, ZBTB40, SLC39A11 and NFKB1 genes in IBD, with all five genes regulating the expression of CP in myeloid cells, as well as potential roles for the prostacyclin/prostaglandin biogenesis and signaling pathways in IBD susceptibility and pathogenesis.
Effects of replication domains on genome-wide UV-induced DNA damage and repair
Authors: Huang Yanchao , Azgari Cem , Yin Mengdie , Chiou Yi-Ying , Lindsey-Boltz Laura A. , Sancar Aziz , Hu Jinchuan , Adebali Ogun
Published: September 2022

Nucleotide excision repair is the primary repair mechanism that removes UV-induced DNA lesions in placentals. Unrepaired UV-induced lesions could result in mutations during DNA replication. Although the mutagenesis of pyrimidine dimers is reasonably well understood, the direct effects of replication fork progression on nucleotide excision repair are yet to be clarified. Here, we applied Damage-seq and XR-seq techniques and generated replication maps in synchronized UV-treated HeLa cells. The results suggest that ongoing replication stimulates local repair in both early and late replication domains. Additionally, it was revealed that lesions on lagging strand templates are repaired slower in late replication domains, which is probably due to the imbalanced sequence context. Asymmetric relative repair is in line with the strand bias of melanoma mutations, suggesting a role of exogenous damage, repair, and replication in mutational strand asymmetry.
Passive epidemiological surveillance in wildlife in Costa Rica identifies pathogens of zoonotic and conservation importance
Authors: Aguilar-Vargas Fernando , Solorzano-Scott Tamara , Baldi Mario , Barquero-Calvo Elías , Jiménez-Rocha Ana , Jiménez Carlos , Piche-Ovares Marta , Dolz Gaby , León Bernal , Corrales-Aguilar Eugenia , Santoro Mario , Alfaro-Alarcón Alejandro
Published: September 2022

Epidemiological surveillance systems for pathogens in wild species have been proposed as a preventive measure for epidemic events. These systems can minimize the detrimental effects of an outbreak, but most importantly, passive surveillance systems are the best adapted to countries with limited resources. Therefore, this research aimed to evaluate the technical and infrastructural feasibility of establishing this type of scheme in Costa Rica by implementing a pilot program targeting the detection of pathogens of zoonotic and conservation importance in wildlife. Between 2018 and 2020, 85 carcasses of free-ranging vertebrates were admitted for post-mortem and microbiology analysis. However, we encountered obstacles mainly related to the initial identification of cases and limited local logistics capacity. Nevertheless, this epidemiological surveillance scheme allowed us to estimate the general state of health of the country’s wildlife by establishing the causes of death according to pathological findings. For instance, 60% (51/85) of the deaths were not directly associated with an infectious agent. Though in 37.6% (32/85) of these cases an infectious agent associated or not with disease was detected. In 27.1% (23/85) of the cases, death was directly related to infectious agents. Furthermore, 12.9% (11/85), the cause of death was not determined. Likewise, this wildlife health monitoring program allowed the detection of relevant pathogens such as Canine Distemper Virus, Klebsiella pneumoniae, Angiostrongylus spp., Baylisascaris spp., among others. Our research demonstrated that this passive surveillance scheme is cost-effective and feasible in countries with limited resources. This passive surveillance can be adapted to the infrastructure dedicated to monitoring diseases in productive animals according to the scope and objectives of monitoring wildlife specific to each region. The information generated from the experience of the initial establishment of a WHMP is critical to meeting the challenges involved in developing this type of scheme in regions with limited resources and established as hotspots for emerging infectious diseases.
Latent classes of men’s intimate partner violence perpetration and attitudes towards gender norms: A UN multi-country, cross-sectional study in Asia and the Pacific
Authors: Willie Tiara C. , Katague Marina , Halim Nafisa , Gupta Jhumka
Published: September 2022

Objective

To examine distinct patterns of IPV perpetration and examined gender equitable attitudes as a correlate of these patterns among men from six countries in Asia and the Pacific.

Design

2011–12 UN Multi-country Study on Men and Violence cross-sectional study.

Setting

Households in Bangladesh, Cambodia, China, Indonesia, Sri Lanka and Papua New Guinea.

Participants

10,178 men aged 18–49 years residing in Bangladesh, Cambodia, China, Indonesia, Sri Lanka and Papua New Guinea.

Primary outcomes measure

Our primary outcome was distinct patterns of IPV perpetration which were derived from multilevel latent class analyses.

Results

The odds of being assigned to the Low All Forms of IPV Perpetration class than the High All Forms of IPV Perpetration class was lower for men in the middle tertile group than men in the high tertile group for gender equitable attitudes. The odds of being assigned to the High Emotional IPV Perpetration class than the High All Forms of IPV Perpetration class was greater for men in the low tertile group than men in the high tertile group for gender equitable attitudes. The odds of being assigned to the High Physical/Emotional/Economic IPV Perpetration class than the High All Forms of IPV Perpetration class was lower for men in the low tertile group than men in the high tertile group for gender equitable attitudes.

Conclusions

Gender transformative interventions that use an adaptive, personalized approach to men’s typology of IPV perpetration may be beneficial to reduce violence against for women in the Asia-Pacific region.
Photosymbiont associations persisted in planktic foraminifera during early Eocene hyperthermals at Shatsky Rise (Pacific Ocean)
Authors: Davis Catherine V. , Shaw Jack O. , D’haenens Simon , Thomas Ellen , Hull Pincelli M.
Published: September 2022

Understanding the sensitivity of species-level responses to long-term warming will become increasingly important as we look towards a warmer future. Here, we examine photosymbiont associations in planktic foraminifera at Shatsky Rise (ODP Site 1209, Pacific Ocean) across periods of global warming of differing magnitude and duration. We compare published data from the Paleocene-Eocene Thermal Maximum (PETM; ~55.9 Ma) with data from the less intense Eocene Thermal Maximum 2 (ETM2; ~54.0 Ma), and H2 events (~53.9 Ma). We use a positive relationship between test size and carbon isotope value (size-δ13C) in foraminifera shells as a proxy for photosymbiosis in Morozovella subbotinae and Acarinina soldadoensis, and find no change in photosymbiont associations during the less intense warming events, in contrast with PETM records indicating a shift in symbiosis in A. soldadoensis (but not M. subbotinae). Declines in abundance and differing preservation potential of the asymbiotic species Subbotina roesnaesensis along with sediment mixing likely account for diminished differences in δ13C between symbiotic and asymbiotic species from the PETM and ETM2. We therefore conclude that photosymbiont associations were maintained in both A. soldadoensis and M. subbotinae across ETM2 and H2. Our findings support one or both of the hypotheses that 1) changing symbiotic associations in response to warming during the PETM allowed A. soldadoensis and perhaps other acarininids to thrive through subsequent hyperthermals or 2) some critical environmental threshold value was not reached in these less intense hyperthermals.
The effect of domain and framing on elicited risk aversion
Authors: Espinosa María Paz , Ezquerra Lara
Published: September 2022

Experimental literature has found that risk attitudes are not robust to different elicitation techniques. However, most comparisons across elicitation methods involve different rewards and framings simultaneously. Our experimental design helps to disentangle the effect of these two factors. We consider two different personal rewards (money domain and grade domain) and two different scenarios while keeping the reward constant (lottery framing and exam framing). We find no differences in elicited risk aversion between the two domains. However, framing matters: elicited risk aversion is lower in the exam framing.
Comparative assessment of the cost-effectiveness of Tuberculosis (TB) active case-finding interventions: A systematic analysis of TB REACH wave 5 projects
Authors: Gomes Isabella , Dong Chaoran , Vandewalle Pauline , Khan Amera , Creswell Jacob , Dowdy David , Sohn Hojoon
Published: September 2022

Purpose

Interventions that can help streamline and reduce gaps in the tuberculosis (TB) care cascade can play crucial roles in TB prevention and care, but are often operationally complex and resource intensive, given the heterogenous settings in which they are implemented. In this study, we present a comparative analysis on cost-effectiveness of TB REACH Wave 5 projects with diverse programmatic objectives to inform future decisions regarding funding, strategic adoption, and scale-up.

Methods

We comprehensively reviewed project reports and financial statements from TB REACH Wave 5, a funding mechanism for interventions that aimed to strengthen the TB care cascade in diverse settings. Two independent reviewers abstracted cost (in 2017 US dollars) and key programmatic data, including project type (case-finding only; case-finding and linkage-to-care; or case-finding, linkage-to-care and patient support), operational setting (urban or rural), and project outputs (numbers of people with TB diagnosed, started on treatment, and successfully completing treatment). Cost-effectiveness ratios for each project were calculated as ratios of apportioned programmatic expenditures to corresponding project outputs.

Results

Of 32 case finding and patient support projects funded through TB REACH Wave 5, 29 were included for analysis (11 case-finding only; 9 case-finding and linkage-to-care; and 9 case-finding, linkage-to-care and patient support). 21 projects (72%) were implemented in either Africa or Southeast Asia, and 19 (66%) focused on serving urban areas. Average cost-effectiveness was $184 per case diagnosed (range: $30-$10,497), $332 per diagnosis and treatment initiation ($123-$10,608), and $40 per patient treatment supported ($8-$160). Cost per case diagnosed was lower for case-finding-only projects ($132) than projects including linkage-to-care ($342) or linkage-to-care and patient support ($254), and generally increased with the corresponding country’s per-capita GDP ($543 per $1000 increase, 95% confidence interval: -$53, $1138).

Conclusion

The costs and cost-effectiveness of interventions to strengthen the TB care cascade were heterogenous, reflecting differences in context and programmatic objective. Nevertheless, many such interventions are likely to offer good value for money. Systematic collection and analysis of cost-effectiveness data can help improve comparability, monitoring, and evaluation.
Acute melanization of silkworm hemolymph by peptidoglycans of the human commensal bacterium Cutibacterium acnes
Authors: Matsumoto Yasuhiko , Sato Eri , Sugita Takashi
Published: September 2022

Cutibacterium acnes is a pathogenic bacterium that cause inflammatory diseases of the skin and intervertebral discs. The immune activation induced by C. acnes requires multiple cellular responses in the host. Silkworm, an invertebrate, generates melanin by phenoloxidase upon recognizing bacterial or fungal components. Therefore, the melanization reaction can be used as an indicator of innate immune activation. A silkworm infection model was developed for evaluating the virulence of C. acnes, but a system for evaluating the induction of innate immunity by C. acnes using melanization as an indicator has not yet been established. Here we demonstrated that C. acnes rapidly causes melanization of the silkworm hemolymph. On the other hand, Staphylococcus aureus, a gram-positive bacterium identical to C. acnes, does not cause immediate melanization. Even injection of heat-killed C. acnes cells caused melanization of the silkworm hemolymph. DNase, RNase, and protease treatment of the heat-treated C. acnes cells did not decrease the silkworm hemolymph melanization. Treatment with peptidoglycan-degrading enzymes, such as lysostaphin and lysozyme, however, decreased the induction of melanization by the heat-treated C. acnes cells. These findings suggest that silkworm hemolymph melanization may be a useful indicator to evaluate innate immune activation by C. acnes and that C. acnes peptidoglycans are involved in the induction of innate immunity in silkworms.
Low rate of SARS-CoV-2 incident infection identified by weekly screening PCR in a prospective year-long cohort study
Authors: Harrington Whitney E. , Yeung Winnie , Beck Ingrid A. , Mast Fred D. , Houck John , Styrchak Sheila , Miller Leslie R. , Li Song , Haglund Micaela , Jiang Yonghou , Armistead Blair , Wallner Jackson , Nguyen Tina , Ko Daisy , Hardy Samantha , Oldroyd Alyssa , Gervassi Ana , Aitchison John D. , Frenkel Lisa M.
Published: September 2022

Background

Asymptomatic and pre-symptomatic SARS-CoV-2 infections may contribute to ongoing community transmission, however, the benefit of routine screening of asymptomatic individuals in low-risk populations is unclear.

Methods

To identify SARS-CoV-2 infections 553 seronegative individuals were prospectively followed for 52 weeks. From 4/2020-7/2021, participants submitted weekly self-collected nasal swabs for rtPCR and completed symptom and exposure surveys.

Results

Incident SARS2-CoV-2 infections were identified in 9/553 (1.6%) participants. Comparisons of SARS2-CoV-2(+) to SARS2-CoV-2(-) participants revealed significantly more close contacts outside the household (median: 5 versus 3; p = 0.005). The incidence of infection was higher among unvaccinated/partially vaccinated than among fully vaccinated participants (9/7,679 versus 0/6,845 person-weeks; p = 0.004). At notification of positive test result, eight cases were symptomatic and one pre-symptomatic.

Conclusions

These data suggest that weekly SARS2-CoV2 surveillance by rtPCR did not efficiently detect pre-symptomatic infections in unvaccinated participants.
Identification of circulating metabolites associated with wooden breast and white striping
Authors: Lake Juniper A. , Yan Yiren , Dekkers Jack C. M. , Qiu Jing , Brannick Erin M. , Abasht Behnam
Published: September 2022

Current diagnostic methods for wooden breast and white striping, common breast muscle myopathies of modern commercial broiler chickens, rely on subjective examinations of the pectoralis major muscle, time-consuming microscopy, or expensive imaging technologies. Further research on these disorders would benefit from more quantitative and objective measures of disease severity that can be used in live birds. To this end, we utilized untargeted metabolomics alongside two statistical approaches to evaluate plasma metabolites associated with wooden breast and white striping in 250 male commercial broiler chickens. First, mixed linear modeling was employed to identify metabolites with a significant association with these muscle disorders and found 98 metabolites associated with wooden breast and 44 metabolites associated with white striping (q-value < 0.05). Second, a support vector machine was constructed using stepwise feature selection to determine the smallest subset of metabolites with the highest categorization accuracy for wooden breast. The final support vector machine achieved 94% accuracy using only 6 metabolites. The metabolite 3-methylhistidine, which is often used as an index of myofibrillar breakdown in skeletal muscle, was the top metabolite for both wooden breast and white striping in our mixed linear model and was also the metabolite with highest marginal prediction accuracy (82%) for wooden breast in our support vector machine. Overall, this study identified a candidate set of metabolites for an objective measure of wooden breast or white striping severity in live birds and expanded our understanding of these muscle disorders.
Association of poorly controlled HbA1c with increased risk of progression to end-stage kidney disease and all-cause mortality in patients with diabetes and chronic kidney disease
Authors: Chen Sheng-Jen , Chiang Hsiu-Yin , Chen Pei-Shan , Chang Shih-Ni , Chen Sheng-Hsuan , Wu Min-Yen , Yeh Hung-Chieh , Ting I-Wen , Tsai Hsiu-Chen , Chen Pei-Chun , Kuo Chin-Chi
Published: September 2022

Glycosylated hemoglobin (HbA1c) targets for patients with chronic kidney disease (CKD) and type 2 diabetes remain controversial. To evaluate whether baseline HbA1cand HbA1ctrajectories are associated with the risk of end-stage kidney disease (ESKD) and all-cause mortality, we recruited adult patients with CKD and type 2 diabetes from a “Pre-ESKD Program” at a medical center in Taiwan from 2003 to 2017. Group-based trajectory modeling was performed to identify distinct patient groups that contained patients with similar longitudinal HbA1c patterns. Cox proportional hazard models were used to estimate hazard ratios (HRs) of ESKD and mortality associated with baseline HbA1clevels and HbA1ctrajectories. In the analysis related to baseline HbA1c(n= 4543), the adjusted HRs [95% confidence interval (CI)] of all-cause mortality were 1.06 (0.95–1.18) and 1.25 (95% CI, 1.07–1.46) in patients with an HbA1clevel of 7%–9% (53–75 mmol/mol) and >9% (>75 mmol/mol), respectively, as compared with those with an HbA1c level < 7% (<53 mmol/mol). In the trajectory analysis(n= 2692), three distinct longitudinal HbA1ctrajectories were identified: nearly optimal (55.9%), moderate to stable (34.2%), and poor control (9.9%). Compared with the “nearly optimal” HbA1ctrajectory group, the “moderate-to-stable” group did not have significantly higher mortality, but the “poorly controlled” group had 35% higher risk of mortality (adjusted HR = 1.35, 95% CI = 1.06–1.71). Neither baseline levels of HbA1cnor trajectories were associated with ESKD risk. In conclusion, in patients with CKD and type 2 diabetes, poor glycemic control was associated with an elevated risk of mortality but not associated with a risk of progression to ESKD.
Maximizing economic prosperity, strengthening military, or developing social bonds? Study protocol for research on the relationship between regulatory focus and preferences for the direction of societal development
Authors: Roczniewska Marta , Marszałek Magdalena , Kaffka-Skierka Kamila , Kryś Kuba , Gasiorowska Agata
Published: September 2022

Recent research has pointed to cross-cultural differences with regard to preferences for the directions that societies should take in their development. From an individual’s perspective, these directions might be understood as ‘goals’, i.e., internal representations of desired end states. To date, research on individual differences that determine preferences for such directions is scarce. However, people’s motivational concerns, i.e., what they fundamentally value, may shape their views about the desired paths for their country’s future. The role of such motivational concerns has been described by regulatory focus theory, which distinguishes between promotion concerns related to advancement needs and prevention concerns linked with security needs. The overall aim of this project is to map the different pathways of societal development with regulatory focus concerns. This will be achieved in two studies. In Study 1, a group concept mapping method will be employed, and leading psychologists will assess the extent to which various societal development goals represent promotion and prevention goals. Based on these ratings, a two-dimensional map of the goals will be created and presented to the same experts, who will be asked to create goal clusters based on their proximity with regard to promotion and prevention ratings. This study will reveal which societal development directions have promotion concerns that outweigh prevention concerns (and vice versa) and which are both high (or low) on these dimensions. This initial mapping will be corroborated in correlational Study 2 with representative samples from two countries differing in dominating regulatory orientations (Poland vs. USA). Here, the roles of individual promotion and prevention orientations in preferences for specific societal development directions will be evaluated. This project will provide new insights into the roles of individual motivational systems in preferences for goals that might be pursued in country development.
The presence of spin in systematic reviews focused on diabetic neuropathy: A cross-sectional analysis
Authors: Khan Ali , Riley Haley , Ottwell Ryan , Arthur Wade , Greiner Benjamin , Shapiro Ekaterina , Wright Drew , Hartwell Micah , Chen Suhao , Miao Zhuqi , Chronister Stacy , Vassar Matt
Published: September 2022

Background

Spin—the misrepresentation of a study’s actual results—has the potential to alter a clinician’s interpretation of the study’s findings and therefore could affect patient care. Studies have shown spin frequently occurs in abstracts of systematic reviews from a variety of other medical disorders and specialties.

Aims

Our primary aim was to evaluate whether the nine most severe types of spin occurred in systematic review abstracts’ concerning diabetic neuropathy treatments. Secondly, we aimed to determine whether spin presence was associated with the methodological quality of a systematic review.

Methods

A search of MEDLINE and Embase collected 1297 articles focused on diabetic neuropathy treatments, of which we included 114 systematic reviews for spin assessment. Each included study was evaluated for the nine most severe types of spin as defined by Yachitz et al. The methodological quality of a systematic review was determined by using the AMSTAR-2 instrument. All screening and data extraction were conducted in a masked, duplicate fashion. Since the final sample size of 114 was not sufficiently powered to do multivariable logistic regression, we calculated unadjusted odds ratios which evaluated relationships between spin presence within abstracts and study characteristics.

Results

From the 114 articles reviewed, spin was present in 7.9% of the studies (9/114), with spin type 5: “conclusion claims the beneficial effect of the experimental treatment despite the high risk of bias in the included primary studies” as the most frequent in our study. Spin types 1, 2, 6, and 8 were not identified. No association was observed between the study characteristics and spin presence, including the methodological quality of a systematic review.

Conclusions

Overall, spin is infrequently observed in abstracts of systematic reviews covering diabetic neuropathy treatments. When comparing our results to other fields of medicine, the field of diabetic neuropathy research publishes systematic reviews whose abstracts mostly portray the findings of the review’s full-text to reflect the results adequately.
Comparing the long non-coding RNA expression profiles of skeletal muscle and kidney tissues from patients with diabetes
Authors: Kim Young-Kook
Published: September 2022

Background

Diabetes causes the dysregulation of several organs, and these effects are often closely associated with changes in the expression of long non-coding RNAs (lncRNAs), a group of non-coding RNAs, within these tissues. Previous studies have described a variety of changes in the expression profile of several lncRNAs from different organs in response to the pathogenesis of diabetes. However, none of these studies compared the expression profiles of these lncRNAs between these organs. This study was designed to identify common and specific lncRNAs involved in the progression of diabetes in the skeletal muscles and kidneys.

Methods

Publicly available RNA sequencing data of diabetic patients was obtained from the Gene Expression Omnibus database. By analyzing the expression of lncRNAs in these datasets, differentially expressed lncRNAs in each tissue between non-diabetic and diabetic patients were identified. To identify any lncRNAs changed in common in both kidney and muscle tissues, those lncRNAs that are significantly dysregulated in both datasets were selected.

Results

These evaluations identified a series of novel lncRNAs unique to each organ and several transcripts that were common to both skeletal muscle and kidney tissues in these patients. Interestingly, the genomic location of these lncRNAs suggests that they reside in close proximity to several protein-coding genes known to be related to diabetes suggesting that these lncRNAs may have a regulatory relationship with their neighboring genes.

Conclusion

These results offer valuable insights into the role of lncRNAs during the pathogenesis of diabetes.
Habitat amount or landscape configuration: Emerging HotSpot analysis reveals the importance of habitat amount for a grassland bird in South Dakota
Authors: Harsh Sprih , Lonsinger Robert C. , Gregory Andrew J.
Published: September 2022

Habitat loss and fragmentation are two important drivers of biodiversity decline. Understanding how species respond to landscape composition and configuration in dynamic landscapes is of great importance for informing the conservation and management of grassland species. With limited conservation resources, prescribed management targeted at the appropriate landscape process is necessary for the effective management of species. We used pheasants (Phasianus colchicus) across South Dakota, USA as a model species to identify environmental factors driving spatiotemporal variation in population productivity. Using an emerging Hotspot analysis, we analyzed annual count data from 105 fixed pheasant brood routes over a 24-year period to identify high (HotSpot) and low (ColdSpot) pheasant population productivity areas. We then applied classification and regression tree modeling to evaluate landscape attributes associated with pheasant productivity among spatial scales (500 m and 1000 m). We found that the amount of grassland at a local spatial scale was the primary factor influencing an area being a HotSpot. Our results also demonstrated non-significant or weak effects of fragmentationper seon pheasant populations. These findings are in accordance with the habitat amount hypothesis highlighting the importance of habitat amount in the landscape for maintaining and increasing the pheasant population. We, therefore, recommend that managers should focus on increasing the total habitat area in the landscape and restoring degraded habitats. Our method of identifying areas of high productivity across the landscape can be applied to other species with count data.
Intention to obtain a COVID-19 vaccine among Brazilian immigrant women in the U.S.
Authors: Allen Jennifer D. , Priebe Rocha Leticia , Rose Raviv , Hoch Annmarie , Porteny Thalia , Fernandes Adriana , Galvão Heloisa
Published: September 2022

Background

COVID-19 has disproportionately impacted low-income immigrant communities. There is concern that the current uptake of COVID-19 vaccines is suboptimal and that this may be contributing to COVID-19 inequities. However, little is known about the acceptability of COVID-19 vaccines among immigrants in the U.S. Our goal was to gauge COVID-19 vaccine intentions among Brazilian immigrant women living in the U.S.

Methods

We conducted an online survey between July and August 2020 offered in Portuguese and English languages among a convenience sample of Brazilian immigrant women ages 18 years and older. Women were recruited through online advertisements by community-based organizations and social media groups to complete a survey that assessed intention to get a COVID-19 vaccine, attitudes toward vaccines, and perceptions about the pandemic.

Results

Of the total sample (N = 353), most (70.8%) indicated they intended to get a COVID-19 vaccine. In bivariate analyses, vaccine intentions were significantly associated with perceptions about the severity of the pandemic, trusted sources of health information, and the number of years lived in the U.S. Multinomial logistic regression models revealed that those who did not intend to be vaccinated had lived a longer time in the U.S. (OR: -0.12 95% CI: -0.19, -0.05), perceived the pandemic to be a minor issue (OR: 1.52, 95% CI: 0.62, 2.42), and trusted information from social networks (OR: -1.94, 95% CI: -3.25, -0.63) or private news sources (OR: -1.71, 95% CI: -2.78, -0.63).

Conclusions

While most women reported they would get a COVID-19 vaccine, efforts to reach those who may be hesitant should target those who have lived in the U.S. for longer periods of time and do not perceive the pandemic to be a major crisis. Healthcare providers may be particularly suited to deliver this information given high levels of trust.
Hcmv-miR-UL148D regulates the staurosporine-induced apoptosis by targeting the Endoplasmic Reticulum to Nucleus signaling 1(ERN1)
Authors: Pandeya Abhishek , Khalko Raj Kumar , Singh Sukhveer , Kumar Manish , Gosipatala Sunil Babu
Published: September 2022

The propensity of viruses to co-opt host cellular machinery by reprogramming the host’s RNA-interference machinery has been a major focus of research, however, regulation of host defense mechanisms by virus-encoded miRNA, is an additional regulatory realm gaining momentum in the arena of host-viral interactions. The Human Cytomegalovirus (HCMV) miRNAs, regulate many cellular pathways alone or in concordance with HCMV proteins, thereby paving a conducive environment for successful infection in the human host. We show that HCMV miRNA, hcmv-miR-UL148D inhibits staurosporine-induced apoptosis in HEK293T cells. We establish that ERN1 mRNA is a bonafide target of hcmv-miR-UL148D and its encoded protein IRE1α is translationally repressed by the overexpression of hcmv-miR-UL148D resulting in the attenuation of apoptosis. Unlike the host microRNA seed sequence (6–8 nucleotides), hcmv-miR-UL148D has long complementarity to 3’ UTR of ERN1 mRNA resulting in mRNA degradation. The repression of IRE1α by the hcmv-miR-UL148D further downregulates Xbp1 splicing and c-Jun N-terminal kinase phosphorylation thus regulating ER-stress and ER-stress induced apoptotic pathways. Strikingly, depletion of ERN1 attenuates staurosporine-induced apoptosis which further suggests that hcmv-miR-UL148D functions through regulation of its target ERN1. These results uncover a role for hcmv-miR-UL148D and its target ERN1 in regulating ER stress-induced apoptosis.
Multi-scale fusion framework via retinex and transmittance optimization for underwater image enhancement
Authors: Li Tie , Zhou Tianfei
Published: September 2022

Low contrast, poor color saturation, and turbidity are common phenomena of underwater sensing scene images obtained in highly turbid oceans. To address these problems, we propose an underwater image enhancement method by combining Retinex and transmittance optimized multi-scale fusion framework. Firstly, the grayscale of R, G, and B channels are quantized to enhance the image contrast. Secondly, we utilize the Retinex color constancy to eliminate the negative effects of scene illumination and color distortion. Next, a dual transmittance underwater imaging model is built to estimate the background light, backscattering, and direct component transmittance, resulting in defogged images through an inverse solution. Finally, the three input images and corresponding weight maps are fused in a multi-scale framework to achieve high-quality, sharpened results. According to the experimental results and image quality evaluation index, the method combined multiple advantageous algorithms and improved the visual effect of images efficiently.
A glimpse into the genotype and clinical importance of non tuberculous mycobacteria among pulmonary tuberculosis patients: The case of Ethiopia
Authors: Alemayehu Alem , Kebede Abebaw , Neway Sebsib , Tesfaye Efrem , Zerihun Betselot , Getu Melak , Petros Beyene
Published: September 2022

Laboratory identification of nontuberculous mycobacteria (NTM) species is not regularly performed while, they have a public health importance with a prevalence of more than 5% among pulmonary tuberculosis (PTB) patients in Ethiopia. Hence, this study aimed to identify the NTM species and their clinical significance among PTB patients. A retrospective study was conducted at the Ethiopian Public Health Institution’s (EPHI’s) national TB referral laboratory. Stored NTM isolates were genotyped using GenoType Mycobacterium CM/AS kit (Hain Life science, Germany). Data pertinent to the study was extracted from the EPHI’s database and patients’ medical records. Between January 2 & December 28 of 2017, a total of 3,834 samples were processed from 698 TB patients of whom 50% were female. Among 3,317 samples with mycobacterial culture results 7.3% were NTM and majority of them were identified from smear negative TB patients. M. simiae was the /predominant NTM among the genotyped isolates. All the studied NTM species were not clinically important however, considering the similarity of clinical and radiologic findings between NTM and MTBC infected patients, integrating NTM species identification in the routine TB laboratory diagnosis may augment clinicians’ decision particularly in DR-TB patients. Additional similar prospective study with a larger sample size is recommended. Moreover, urgent improvements on patients’ record keeping practice are required in the studied hospitals.
Mouse models of COVID-19 recapitulate inflammatory pathways rather than gene expression
Authors: Bishop Cameron R. , Dumenil Troy , Rawle Daniel J. , Le Thuy T. , Yan Kexin , Tang Bing , Hartel Gunter , Suhrbier Andreas
Published: September 2022

How well mouse models recapitulate the transcriptional profiles seen in humans remains debatable, with both conservation and diversity identified in various settings. Herein we use RNA-Seq data and bioinformatics approaches to analyze the transcriptional responses in SARS-CoV-2 infected lungs, comparing 4 human studies with the widely used K18-hACE2 mouse model, a model where hACE2 is expressed from the mouse ACE2 promoter, and a model that uses a mouse adapted virus and wild-type mice. Overlap of single copy orthologue differentially expressed genes (scoDEGs) between human and mouse studies was generally poor (≈15–35%). Rather than being associated with batch, sample treatment, viral load, lung damage or mouse model, the poor overlaps were primarily due to scoDEG expression differences between species. Importantly, analyses of immune signatures and inflammatory pathways illustrated highly significant concordances between species. As immunity and immunopathology are the focus of most studies, these mouse models can thus be viewed as representative and relevant models of COVID-19.
What Are the Benefits and Pitfalls of Innovation Ecosystems? : Lessons Learned From Tungsram’s Ecosystem
Authors: Horváth Klaudia Gabriella
Published: September 2022

Whereas innovation ecosystems became widely popular lately, our knowledge is quite limited on the practical implementation of the relevant ecosystem models, specifically in Hungary. Hence, the aim of this paper is to analyse an innovation ecosystem as a case study related to one of the biggest Hungarian multinational company, called Tungsram. The research is considered to be a qualitative research, as the methodology incorporates document analysis and 26 semi-structured interviews with the ecosystem’s participants. The results show that the main benefits of participating in ecosystems are: new value creation by resource and knowledge sharing, networking and minimizing the cost of innovation. Meanwhile, the pitfalls of cooperation are closely related to the credibility of the ecosystem leader, to the formulation of the ecosystem’s strategy and to the quality of the absorptive capacity of the partners.
Diseño de espacios educativos que favorecen el aprendizaje y la creatividad
Authors: López Siro
Published: September 2022

¿Influye el diseño de los espacios educativos en el comportamiento, aprendizaje y creatividad? ¿Qué criterios pedagógicos hemos de tener en cuenta para mejorar la calidad educativa? En el artículo se señalan únicamente tres aspectos que requieren muy poco presupuesto: descubrir la importancia de la gestión de la iluminación, cuidar la neutralidad de los espacios y evitar la sobreestimulación, y naturalizar la escuela con el fin de potenciar la salud, la curiosidad, la motivación, el aprendizaje y la creatividad.