bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and implementation of fish freshness detection algorithm using deep learning
Authors: Anas D F , Jaya I , Nurjanah  
Published: December 2021

AbstractOrganoleptic assessment of fresh fish includes specifications for the quality of the eyes, gills, mucus, odor, texture and flesh (color and appearance). However, not everyone has knowledge about it. This research uses the tiny yolov2 to facilitate the determination of fish freshness levels (good quality, medium quality, poor quality) correctly and fast. There are a few stages in this research, included organoleptic test accompanied by taking fish eye image dataset every hour, processing organoleptic test data labeling, training, and validation. There are three types of fish used, consists ofRastrelliger, Euthynnus affinis, andChanos chanos. Detection of fish freshness level for three species was successfully carried out with the result of average precision is 72.9%, average recall is 57.5%, and accuracy is 57.5%. The factors that affect the prediction results in this study is the collection of datasets before the training process is carried out consisting of fish samples obtained from traditional markets, which are considered inadequate so that it affects the organoleptic test process itself, the organoleptic test that was carried out as a reference for image sorting was considered inaccurate because it used less than 30 untrained panelists and dataset imbalance.
Estimation of soil carbon storage under mono-specific Enhalus acoroides meadows in Pari Island, Indonesia
Authors: Rifai H , Rahmawati S , Nurdiansah D , Afdal  
Published: December 2021

Abstract
Large seagrass meadows in Indonesia are predicted to have a significant ability in capturing and storing carbon and are useful to mitigate global climate change. However, most of the available data are derived from short-term carbon storage of living biomass, whereas data on long-term carbon storage in the soil is still limited. This study, therefore, aims to measure soil carbon storage in mono-specific Enhalus acoroides meadows in Pari Island. A total of nine soil cores was collected in a 100×100 m2 area. The parameters were soil depth, dry bulk density (DBD), and Corg content. We applied a PVC corer with 7.4 cm in diameter and 80 cm in length to collect the soil. The length of the soil core varied between 8 and 67 cm. The mean (±SE) of soil dry bulk density is 0.98±0.04 gr/cm3 and the median is 1.1 gr/cm3, while Corg content is 2.1±0.1% soil DW (mean±SE) and 1.9% (median). E. acoroides vegetation in Pari Island stores around 63 Mg Corg/ha organic carbon in 8-67cm or 34cm (mean depth) of topsoil. Carbon storage of these mono-specific meadows is comparable to soil carbon storage in the seagrass ecosystems per hectare areas on national, regional, and global levels.
Additive manufacturing of cartilage-mimetic scaffolds as off-the-shelf implants for joint regeneration
Authors: Wang Bin , Chariyev-Prinz Farhad , Burdis Ross , Eichholz Kian , Kelly Daniel J 
Published: December 2021

Abstract
Biomimetic scaffolds that provide a tissue-specific environment to cells are particularly promising for tissue engineering and regenerative medicine applications. The goal of this study was to integrate emerging additive manufacturing and biomaterial design strategies to produce articular cartilage (AC) mimetic scaffolds that could be used as ‘off-the-shelf’ implants for joint regeneration. To this end alginate sulfate, a sulfated glycosaminoglycan (sGAG) mimic, was used to functionalize porous alginate-based scaffolds and to support the sustained release of transforming growth factor-β3 (TGF-β3). Covalent crosslinking dramatically improved the elasticity of the alginate/alginate sulfate scaffolds, while scaffold architecture could be tailored using a directional freezing technique. Introducing such an anisotropic architecture was found to promote mesenchymal stem cell (MSC) infiltration into the scaffold and to direct the orientation of the deposited extracellular matrix, leading to the development of cartilage tissue with a biomimetic zonal architecture. In vitro experiments also demonstrated the capacity of the sulfated scaffolds to both enhance chondrogenesis of MSCs and to control the release of TGF-β3, leading to the development of a tissue rich in sGAG and type II collagen. The scaffolds were further reinforced with a 3D printed poly(lactide-co-ϵ-caprolactone) (PLCL) framework, leading to composite implants that were more elastic than those reinforced with polycaprolactone, and which better mimicked the bulk mechanical properties of native cartilage tissue. The ability of this composite scaffold to support chondrogenesis was then confirmed within a dynamic culture system. Altogether, these findings demonstrate the potential of such biomimetic scaffolds as putative ‘single-stage’ or ‘off-the-shelf’ strategies for AC regeneration.
Fast-sweeping Langmuir probes: what happens to the I
–V trace when sweeping frequency is higher than the ion plasma frequency?
Authors: JIN Chenyao , YIP Chi-shung , ZHANG Wei , JIANG Di , XU Guosheng 
Published: December 2021

Abstract
Limited particle transit time is one of several limiting factors which determine the maximum temporal resolution of a Langmuir probe. In this work, we have revisited the known fast sweep Langmuir probe techniques in a uniform, quiescent multi-dipole confined hot cathode discharge with two operation scenarios: one in which the probe sweeping frequency f
sweep is much lower than the ion plasma frequency f
pi, another one where f
sweep is much greater than f
pi, respectively. This allows investigation into the effect of limited ion-motion on I–V traces. Serious distortions of I–V traces at high frequencies, previously claimed to be an ion-motion limitation effect, were not found unless shunt resistance is sufficiently high, despite a f
sweep/f
pi ratio of ∼3. On the other hand, evidences of sheath capacitance on the I–V traces have been observed. Distortions of I–V traces qualitatively agree with predictions of sheath capacitance response to the sweeping voltage. Additionally, techniques in fast sweep Langmuir probe are briefly discussed. The comparison between the high-speed dual Langmuir probe (HDLP) and the single probe setup shows that the capacitive response can be removed via subtracting a leakage current for the single probe setup almost as effectively as using the HDLP setup, but the HDLP setup does remain advantageous in its facilitation of better recovery of weak current signal commonly in low density plasma.
The quantum solitons atomtronic interference device
Authors: Polo Juan , Naldesi Piero , Minguzzi Anna , Amico Luigi 
Published: December 2021

Abstract
We study a quantum many-body system of attracting bosons confined in a ring-shaped potential and interrupted by a weak link. With such architecture, the system defines atomtronic quantum interference devices harnessing quantum solitonic currents. We demonstrate that the system is characterized by the specific interplay between the interaction and the strength of the weak link. In particular, we find that, depending on the operating conditions, the current can be a universal function of the relative size between the strength of the impurity and interaction. The low lying many-body states are studied through a quench dynamical protocol that is the atomtronic counterpart of Rabi interferometry. With this approach, we demonstrate how our system defines a two level system of coupled solitonic currents. The current states are addressed through the analysis of the momentum distribution.
Angular momenta in fields from a rotational mechanical antenna‡
Authors: Mao Yu , Liu Y , Lin Hai 
Published: December 2021

Abstract
Mechanic antennas provide opportunities for human portable, VLF communications, where a rotational dipole emits EM signals with angular momenta. In this paper we analytically derive the electromagnetic fields from a rotational electric dipole using Fourier transform method, and find that the radiated fields from the rotational electric dipole carries nonzero energy flow density in both orbital and spin angular momentum (AM) parts by their flux tensors. Intuitively, a dipole circulating on the transverse plane induces a longitudinal orbital angular momentum and a longitudinal spin angular momentum. And the binding force for the rotational electric dipole is then shown to result mainly from the Coulomb fields. We believe that our work will contributes to novel communication designs for portable mechanic antennas.
Prevalence and diagnostic agreement of sarcopenic obesity with different definitions among Chinese community-dwelling older adults
Authors: Mo Yi-Han , Yang Chen , Su Yi-Dong , Dong Xin , Deng Wen-Yu , Liu Bei-Bei , Yao Xue-Mei , Wang Xiu-Hua 
Published: December 2021

Abstract

Objective
this retrospective study aims to compare the prevalence and diagnostic agreement of sarcopenic obesity (SO) using different obesity diagnostic methods among Chinese community-dwelling older adults.

Methods
SO was diagnosed with sarcopenia and obesity diagnostic methods. Sarcopenia was defined using the Asian Working Group for Sarcopenia criteria 2019 (AWGS2019). Four widely used indicators were used to define obesity: body mass index (BMI), waist circumference (WC), percent of body fat (PBF) and visceral fat area (VFA). Cohen’s kappa was used to analyse the diagnosis agreement of SO between different diagnostic methods.

Results
a total of 1,050 participants were included, including 347 men (71.3 ± 7.4 years) and 703 women (69.9 ± 7.5 years). The prevalence of sarcopenia was 25% in total participants, there was no difference between men (24.2%) and women (25.5%), (P = 0.705). With different obesity diagnostic methods, the obesity prevalence ranged from 4.1 to 42.2%, the SO prevalence was 0.1–7.9%. The diagnosis agreement of SO was poor-to-moderate (κ ranged from −0.002 to 0.682). Among the four diagnostic methods, AWGS combined with BMI had the poorest agreement (κ = −0.002 with other methods), AWGS combined with VFA had the best agreement (κ = 0.641 and 0.682 with AWGS combined with PBF and with AWGS combined with WC, respectively).

Conclusion
the prevalence of SO vary considerably and the diagnostic agreement is poor-to-moderate with non-uniform diagnostic methods. BMI has the lowest sensitivity, whereas VFA has the highest sensitivity in diagnosis of SO, and VFA has a relatively good diagnostic agreement with other diagnostic methods.
Association of longitudinal trends in thyroid function with incident carotid atherosclerosis in middle-aged and older euthyroid subjects: the Tianjin Chronic Low-Grade Systemic Inflammation and Health (TCLSIH) cohort study
Authors: Gu Yeqing , Meng Ge , Zhang Qing , Liu Li , Wu Hongmei , Zhang Shunming , Wang Yawen , Zhang Tingjing , Wang Xuena , Sun Shaomei , Wang Xing , Jia Qiyu , Song Kun , Liu Qiang , Niu Kaijun 
Published: December 2021

Abstract

Background
Previous studies have posited that an association exists between thyroid function and the heart and vasculature. It remains unclear, however, whether longitudinal trends in thyroid function contribute to the development of atherosclerosis. We conducted a cohort study to examine the association of longitudinal trends in thyroid function with incident carotid atherosclerosis (CA) in middle-aged and older euthyroid subjects.

Methods
This cohort study’s participants were recruited from the Tianjin Chronic Low-grade Systemic Inflammation and Health Cohort Study in Tianjin, China. Free triiodothyronine (FT3), thyroxine (FT4) and thyroid-stimulating hormone (TSH) were measured using chemiluminescence immunoassay. CA was assessed using carotid ultrasonography. Thyroid function and ultrasonography were assessed yearly during follow-up. Multivariable Cox proportional hazards regression models were used to assess the association between thyroid function and incident CA.

Results
A total of 3,181 participants were enrolled in the cohort study. Within 7,762 person-years of follow-up, 944 participants developed CA, the incidence rate of CA was 122 per 1,000 person-years. The fully adjusted hazards ratios (95% confidence interval) of CA for per 1-unit increase in changes of FT3, FT4 and TSH were 1.34(1.22–1.47), 1.22(1.19–1.26) and 0.92 (0.77–1.09) (P &lt; 0.0001, &lt;0.0001 and = 0.32, respectively), respectively. Similar significant associations between mean levels of FT3 and FT4 and incident CA were observed. However, baseline thyroid function was not associated with incident CA.

Conclusions
These findings suggest that higher mean levels and higher values of changes in thyroid hormones were associated with a higher risk of incident CA in middle-aged and older euthyroid subjects.
III—Doxastic Wrongs, Non-Spurious Generalizations and Particularized Beliefs
Authors: Fabre Cécile 
Published: December 2021

Abstract
According to the doxastic wrongs thesis, holding certain beliefs about others can be morally wrongful. Beliefs which take the form of stereotypes based on race and gender (or sexual orientation, disability, and so on) and which turn out to be false and are negatively valenced are prime candidates for the charge of doxastic wronging: it is no coincidence that most of the cases discussed in the literature involve false beliefs. My aim in this paper is to show that the thesis of doxastic wrongs does not turn on the truth-value or valence of beliefs.
Dehydrated males are less likely to dive into the mating pool
Authors: Friesen Christopher R , Uhrig Emily J , Mason Robert T 
Published: December 2021

AbstractThe hydration state of animals vying for reproductive success may have implications for the tempo and mode of sexual selection, which may be salient in populations that experience increasing environmental fluctuations in water availability. Using red-sided garter snakes as a model system, we tested the effect of water supplementation on courtship, mating behavior, and copulatory plug (CP) production during a drought year. Over 3 days of mating trials, water-supplemented males (WET males, n = 45) outperformed a control group that was not supplemented with water (DRY males, n = 45). Over 70% of WET males mated but just 33% of DRY males did so. As a group, WET males mated 79 times versus 28 times by DRY males. On the last day of mating trials, over 70% of WET males were still courting, with 19 of them mating, whereas less than 25% of DRY males were courting and only one mated. CP deposition accounted for 4–6% of the mass lost by mating males, but hydration did not affect CP mass or water content. These findings suggest that, in years of low water availability, the number of courting males and the intensity of their courtship declines, thereby affecting sexual selection and conflict, at least within that year.
PHIST: fast and accurate prediction of prokaryotic hosts from metagenomic viral sequences
Authors: Zielezinski Andrzej , Deorowicz Sebastian , Gudyś Adam 
Published: December 2021

Abstract

Summary
Phage–Host Interaction Search Tool (PHIST) predicts prokaryotic hosts of viruses based on exact matches between viral and host genomes. It improves host prediction accuracy at species level over current alignment-based tools (on average by 3 percentage points) as well as alignment-free and CRISPR-based tools (by 14–20 percentage points). PHIST is also two orders of magnitude faster than alignment-based tools making it suitable for metagenomics studies.

Availability and implementation
GNU-licensed C++ code wrapped in Python API available at: https://github.com/refresh-bio/phist.

Supplementary information
Supplementary data are available at Bioinformatics online.
Mesenteric SParIng versus extensive mesentereCtomY in primary ileocolic resection for ileocaecal Crohn’s disease (SPICY): study protocol for randomized controlled trial
Authors: van der Does de Willebois E M L ,   SPICY study group, Bemelman W A , Buskens C J , D'Haens G R A M , D'Hoore A , Danese S , Duijvestein M , Gecse K B , Hompes R , Koot B , Indemans F , Lightner A L , Mundt M W , Spinelli A , van der Bilt J D W , van Dongen K W A , Vermeire S , Zwaveling S 
Published: December 2021

Abstract

Background
There is emerging evidence to suggest that Crohn’s disease (CD) may be a disease of the mesentery, rather than of the bowel alone. A more extensive mesenteric resection, removing an increased volume of mesentery and lymph nodes to prevent recurrence of CD, may improve clinical outcomes. This study aims to analyse whether more extensive ‘oncological’ mesenteric resection reduces the recurrence rate of CD.

Methods
This is an international multicentre randomized controlled study, allocating patients to either group 1—mesenteric sparing ileocolic resection (ICR), the current standard procedure for CD, or group 2—extensive mesenteric ICR, up to the level of the ileocolic trunk. To detect a clinically relevant difference of 25 per cent in endoscopic recurrence at 6 months, a total of 138 patients is required (including 10 per cent dropout). Patients aged over 16 with CD undergoing primary ICR are eligible. Primary outcome is 6-month postoperative endoscopic recurrence rate (modified Rutgeerts score of greater than or equal to i2b). Secondary outcomes are postoperative morbidity, clinical recurrence, quality of life, and the need for (re)starting immunosuppressive medication. For long-term results, patients will be followed up for up to 5 years to determine the reoperation rate for recurrence of disease at the anastomotic site.

Conclusion
Analysing these two treatment strategies in a head-to-head comparison will allow an objective evaluation of the clinical relevance of extensive mesenteric resection in CD. If a clinical benefit can be demonstrated, this could result in changes to guidelines which currently recommend close bowel resection.

Registration number
NCT00287612 (http://www.clinicaltrials.gov)
Physician Assistance in Dying: An Option for Christians?
Authors: Steffen Lloyd 
Published: December 2021

Abstract
Opposition to physician-assisted suicide is widespread in Christian ethics. However, on a topic as controversial as physician-assisted suicide, no one can reasonably speak for “the Christian” perspective. Natural-law and, specifically, just-war thinking are claimed in the Christian tradition, yet the natural-law contribution to a Christian ethical analysis of physician-assisted suicide requires explanation and defense. Natural-law ethical theory affirms the central role of reason in moral thinking and provides a theoretical resource in contemporary ethics to assist in analyzing specific moral issues, problems, and conflicts. This essay seeks to demonstrate how just-war thinking, derived from natural-law tradition, allows movement from the theoretical world of natural-law theory to the practical world of normative ethics. Here the case is made that the just-war model of ethics helps elucidate the moral problematic involved in physician-assisted suicide while clarifying direction on this particularly thorny and controversial problem.
Effect of Oral Streptococci Expressing Pneumococcus-like Cross-Reactive Capsule Types on World Health Organization Recommended Pneumococcal Carriage Detection Procedure
Authors: Ganaie Feroze , Branche Angela R , Peasley Michael , Rosch Jason W , Nahm Moon H 
Published: December 2021

AbstractBackgroundCarriage studies are fundamental to assessing the effects of pneumococcal vaccines. Because a large proportion of oral streptococci carry homologues of pneumococcal genes, non–culture-based detection and serotyping of upper respiratory tract (URT) samples can be problematic. In the current study, we investigated whether culture-free molecular methods could differentiate pneumococci from oral streptococci carried by adults in the URT.MethodsPaired nasopharyngeal (NP) and oropharyngeal (OP) samples were collected from 100 older adults twice a month for 1 year. Extracts from the combined NP + OP samples (n = 2400) were subjected to lytA real-time polymerase chain reaction (PCR). Positive samples were subjected to pure culture isolation, followed by species confirmation using multiple approaches. Multibead assays and whole-genome sequencing were used for serotyping.ResultsIn 20 of 301 combined NP + OP extracts with positive lytA PCR results, probable pneumococcus-like colonies grew, based on colony morphology and biochemical tests. Multiple approaches confirmed that 4 isolates were Streptococcus pneumoniae, 3 were Streptococcus pseudopneumoniae, 12 were Streptococcus mitis, and 1 were Streptococcus oralis. Eight nonpneumococcal strains carried pneumococcus-like cps loci (approximate size, 18–25 kb) that showed &gt;70% nucleotide identity with their pneumococcal counterparts. While investigating the antigenic profile, we found that some S. mitis strains (P066 and P107) reacted with both serotype-specific polyclonal (type 39 and FS17b) and monoclonal (Hyp10AG1 and Hyp17FM1) antisera, whereas some strains (P063 and P074) reacted only with polyclonal antisera (type 5 and FS35a).ConclusionThe extensive capsular overlap suggests that pneumococcal vaccines could reduce carriage of oral streptococci expressing cross-reactive capsules. Furthermore, direct use of culture-free PCR-based methods in URT samples has limited usefulness for carriage studies.
Safety and Pharmacokinetics of Exebacase in an Infant With Disseminated Staphylococcus aureus Infection
Authors: Moorthy Ganga S , Greenberg Rachel G , Hornik Chi D , Cassino Cara , Ghahramani Parviz , Kumar Karan R , Fowler Vance G , Cohen-Wolkowiez Michael 
Published: December 2021

Abstract
Exebacase, an antistaphylococcal lysin produced from a bacteriophage-encoded gene, is a promising adjunctive therapy for severe methicillin-resistant Staphylococcus aureus infections. We describe the first infant to receive exebacase, dosing, and pharmacokinetics. Exebacase may be safe and efficacious in children; however, further clinical trials are needed to optimize dosing.
Longitudinal Analysis of Memory T-Cell Responses in Survivors of Middle East Respiratory Syndrome
Authors: Shin Hyoung Shik , Kim Yeonjae , Kang Jihye , Um Jihye , Park Jun Sun , Park Wan Beom , Kim Yeon Sook , Choi Jae Phil , Rhee Ji Young , Joh Joon Sung , Cho Nam Hyuk , Yang Jeong Sun , Lee Joo Yeon , Lim Dong Gyun 
Published: December 2021

Abstract

Background
Middle East respiratory syndrome (MERS) is a highly lethal respiratory disease caused by a zoonotic betacoronavirus. The development of effective vaccines and control measures requires a thorough understanding of the immune response to this viral infection.

Methods
We investigated cellular immune responses up to 5 years after infection in a cohort of 59 MERS survivors by performing enzyme-linked immunospot assay and intracellular cytokine staining after stimulation of peripheral blood mononuclear cells with synthetic viral peptides.

Results
Memory T-cell responses were detected in 82%, 75%, 69%, 64%, and 64% of MERS survivors from 1–5 years post-infection, respectively. Although the frequency of virus-specific interferon gamma (IFN-γ)–secreting T cells tended to be higher in moderately/severely ill patients than in mildly ill patients during the early period of follow-up, there was no significant difference among the different clinical severity groups across all time points. While both CD4+ and CD8+ T cells were involved in memory T-cell responses, CD4+ T cells persisted slightly longer than CD8+ T cells. Both memory CD4+ and CD8+ T cells recognized the E/M/N proteins better than the S protein and maintained their polyfunctionality throughout the period examined. Memory T-cell responses correlated positively with antibody responses during the initial 3–4 years but not with maximum viral loads at any time point.

Conclusions
These findings advance our understanding of the dynamics of virus-specific memory T-cell immunity after MERS-coronavirus infection, which is relevant to the development of effective T cell–based vaccines.