bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-Term Storage Does Not Affect the Expression Profiles of mRNA and Long Non-Coding RNA in Vitrified-Warmed Human Embryos
Authors: Li Jingyu , Zhu Ling , Huang Jin , Liu Weiwei , Han Wei , Huang Guoning
Published: February 2022

Although vitrification has been widely applied in assisted reproductive technology, it is unknown whether storage time has any impact on the mRNA and lncRNA expression profiles in human embryos. Eleven women (aged 23–35 years) who had undergone in vitro fertilization treatment were recruited for this study. The transcriptomes of 3 fresh eight-cell embryos and 8 surviving vitrified-warmed eight-cell embryos (4 embryos were cryostored for 3 years, and the others were cryostored for 8 years) were analyzed through single-cell RNA-Seq. No differentially expressed mRNAs or lncRNAs were identified between the 3-years group and 8-years group. A total of 128 mRNAs and 365 lncRNAs were differentially expressed in the 8 vitrified-warmed embryos compared with the fresh embryos. The vitrification-warming impact was moderate, and it was mainly related to the pathways of metabolism, stress response, apoptosis, cell cycle, cell adhesion, and signaling for TFG-β and Hippo. The analysis of target mRNAs suggested that lncRNAs might contribute to the regulation of mRNAs after vitrification-warming. Our findings indicated that long-term storage after vitrification does not affect the mRNA and lncRNA expression profiles in human embryos, however, the procedure of vitrification-warming would lead to minor alteration of transcriptome.
Genome Sequencing for Genetics Diagnosis of Patients With Intellectual Disability: The DEFIDIAG Study
Authors: Binquet Christine , Lejeune Catherine , Faivre Laurence , Bouctot Marion , Asensio Marie-Laure , Simon Alban , Deleuze Jean-François , Boland Anne , Guillemin Francis , Seror Valérie , Delmas Christelle , Espérou Hélène , Duffourd Yannis , Lyonnet Stanislas , Odent Sylvie , Heron Delphine , Sanlaville Damien , Frebourg Thierry , Gerard Bénédicte , Dollfus Hélène
Published: February 2022

Introduction:Intellectual Disability (ID) is the most common cause of referral to pediatric genetic centers, as it affects around 1–3% of the general population and is characterized by a wide genetic heterogeneity. The Genome Sequencing (GS) approach is expected to achieve a higher diagnostic yield than exome sequencing given its wider and more homogenous coverage, and, since theoretically, it can more accurately detect variations in regions traditionally not well captured and identify structural variants, or intergenic/deep intronic putatively pathological events. The decreasing cost of sequencing, the progress in data-management and bioinformatics, prompted us to assess GS efficiency as the first line procedure to identify the molecular diagnosis in patients without obvious ID etiology. This work is being carried out in the framework of the national French initiative for genomic medicine (Plan France Médecine Génomique 2025).

Methods and Analysis:This multidisciplinary, prospective diagnostic study will compare the diagnostic yield of GS trio analysis (index case, father, mother) with the French core minimal reference strategy (Fragile-X testing, chromosomal microarray analysis and Gene Panel Strategy of 44 selected ID genes). Both strategies are applied in a blinded fashion, in parallel, in the same population of 1275 ID index cases with no obvious diagnosis (50% not previously investigated). Among them, a subgroup of 196 patients are randomized to undergo GS proband analysis in addition to GS trio analysis plus the French core minimal reference strategy, in order to compare their efficiency. The study also aims to identify the most appropriate strategy according to the clinical presentation of the patients, to evaluate the impact of deployment of GS on the families’ diagnostic odyssey and the modification of their care, and to identify the advantages/difficulties for the patients and their families.

Ethics Statement:The protocol was approved by the Ethics Committee Sud Méditerranée I and the French data privacy commission (CNIL, authorization 919361).

Trial Registration:ClinicalTrials.govidentifier NCT04154891 (07/11/2019).
Canada’s Internet-Connected Ocean
Authors: Moran Kate , Juniper S. Kim , Bligh Sandy , Loock Daniela , Kulin Ian , Paulson Meghan , Pirenne Benoît
Published: February 2022

Over fifteen years ago, Ocean Networks Canada (ONC) began with the world’s first large-scale, interactive, real-time portal into the ocean, bringing continuous, real-time data to the surface for applications in scientific research, societal benefits, and supporting Canada’s ocean industry. This marked the dawn of the Internet-connected ocean, enabling a more fulsome understanding of the ocean through ocean intelligence. These open data have improved our ability to monitor and understand our changing ocean offshore all three coasts of Canada, thanks to diversity of sensor systems to monitor earthquakes and tsunamis, deep sea biodiversity, whales, hydrothermal vents, neutrinos, ocean noise, ocean acidification, forensics experiments, and the impact of climate change, including sea ice thinning in the Arctic. This pioneering approach began in the late 1990s, when scientists began developing a new way of doing ocean science that was no longer limited by weather and ship-time. They imagined a permanent presence in the ocean of sensors to allow a continuous flow of ocean data via the Internet. This big science began to take shape early this century, when a partnership between United States and Canadian institutions was established. ONC evolved out of this international collaboration with seed funding from the Canada Foundation for Innovation, while in the United States, the Ocean Observatories Initiative (OOI) was funded. ONC works closely with OOI on that span the countries’ west coast border. Recently similar observing initiatives in Europe have begun, led by EMSO, which now has a close collaboration with ONC as an Associate Member.
Preventive Vitamin A Supplementation Improves Striatal Function in 6-Hydroxydopamine Hemiparkinsonian Rats
Authors: Marie Anaïs , Leroy Julien , Darricau Morgane , Alfos Serge , De Smedt-Peyrusse Veronique , Richard Emmanuel , Vancassel Sylvie , Bosch-Bouju Clementine
Published: February 2022

Background

The mechanisms leading to a loss of dopaminergic (DA) neurons from the substantia nigra pars compacta (SNc) in Parkinson's disease (PD) have multifactorial origins. In this context, nutrition is currently investigated as a modifiable environmental factor for the prevention of PD. In particular, initial studies revealed the deleterious consequences of vitamin A signaling failure on dopamine-related motor behaviors. However, the potential of vitamin A supplementation itself to prevent neurodegeneration has not been established yet.

Objective

The hypothesis tested in this study is that preventive vitamin A supplementation can protect DA neurons in a rat model of PD.

Methods

The impact of a 5-week preventive supplementation with vitamin A (20 IU/g of diet) was measured on motor and neurobiological alterations induced by 6-hydroxydopamine (6-OHDA) unilateral injections in the striatum of rats. Rotarod, step test and cylinder tests were performed up to 3 weeks after the lesion. Post-mortem analyses (retinol and monoamines dosages, western blots, immunofluorescence) were performed to investigate neurobiological processes.

Results

Vitamin A supplementation improved voluntary movements in the cylinder test. In 6-OHDA lesioned rats, a marked decrease of dopamine levels in striatum homogenates was measured. Tyrosine hydroxylase labeling in the SNc and in the striatum was significantly decreased by 6-OHDA injection, without effect of vitamin A. By contrast, vitamin A supplementation increased striatal expression of D2 and RXR receptors in the striatum of 6-OHDA lesioned rats.

Conclusions

Vitamin A supplementation partially alleviates motor alterations and improved striatal function, revealing a possible beneficial preventive approach for PD.
Pro-Inflammatory and Pro-Oxidative Changes During Nilotinib Treatment in CML Patients: Results of a Prospective Multicenter Front-Line TKIs Study (KIARO Study)
Authors: Sicuranza Anna , Ferrigno Ilaria , Abruzzese Elisabetta , Iurlo Alessandra , Galimberti Sara , Gozzini Antonella , Luciano Luigiana , Stagno Fabio , Russo Rossi Antonella , Sgherza Nicola , Cattaneo Daniele , Zuanelli Brambilla Corrado , Marzano Cristina , Fava Carmen , Mulas Olga , Cencini Emanuele , Santoni Adele , Sammartano Vincenzo , Gozzetti Alessandro , Puccetti Luca , Bocchia Monica
Published: February 2022

Tyrosine kinase inhibitors (TKI) may offer a normal life expectancy to Chronic Myeloid Leukemia (CML) patients. However, a higher than expected incidence of arterial occlusive events (AOEs) was observed during treatment with nilotinib. We previously showed an “inflammatory status” during nilotinib that may explain the increased incidence of AOEs. Thus, we conducted this prospective KIARO study involving 186 CML patients (89 imatinib, 59 nilotinib, 38 dasatinib). Interleukin 6 (IL6), interleukin 10 (IL10), Tumor Necrosis Factor-α (TNFα), oxLDL, and high-sensitivity C-reactive protein (hs-CRP) plasma levels were measured at diagnosis and during treatment, with the aim to investigate changes in the inflammatory status favoring AOEs of each patient. Clinical and biochemical pro-atherothrombotic profiles and the 10-year SCORE chart were also evaluated. We showed a pro-inflammatory/pro-oxidative milieu increasing along treatment with nilotinib compared with imatinib or dasatinib, as demonstrated by higher hs-CRP and oxLDL levels and increased IL6/IL10 and TNFα/IL10 ratios only in nilotinib cohort. After median follow-up of 23.3 months starting from TKI, 10/186 patients (5.4%) suffered an AOE. Approximately 5/10 (50%) AOEs occurred during nilotinib treatment despite a lower 10-year SCORE and a lower median age in this subgroup. A longer follow-up is needed to further confirm the active role of nilotinib in AOEs pathogenesis.
Sodium-Glucose Co-Transporter 2 Inhibitors Use Improves the Satisfaction With Anti-diabetic Agent Treatment: A Questionnaire-based Propensity Score-matched Study
Authors: Shi Fang-Hong , Yue Jiang , Jiang Yi-Hong , Yang Ming-Lan , Gu Zhi-Chun , Ma Jing , Li Hao
Published: February 2022

Background: Specific safety issues with sodium-glucose co-transporter-2 (SGLT2) inhibitors such as infection, fractures, worsening of renal function and euglycemic ketoacidosis have been raised. Concerns about adverse events might limit the use of this drug class. The satisfaction with SGLT2 inhibitors treatment in Chinese patients with type 2 diabetes mellitus (T2DM) is unknown.

Material and Methods: Patients with T2DM who visited the hospital between October 2019 and June 2020 were included in this retrospective analysis. Patients were divided into SGLT2 inhibitors used group or not. The Satisfaction with Oral Anti-Diabetic Agent Scale (SOADAS) questionnaire and self-reported AEs were obtained at 3 months of follow-up. Propensity score matching (PSM) was performed to adjust for confounding factors. Univariate and multivariable linear regression models were used to explore potential risk factors associated with overall satisfaction.

Results: A total of 145 T2DM patients were included, with 76 SGLT2 inhibitors users and 69 non-users. Patients administered with SGLT2 inhibitors presented with increased overall satisfaction (mean [SE]: 22.8 [0.67] vs. 20.6 [0.64], p = 0.016) and overall satisfaction rate (n [%]: 40 [52.6%] vs 21 [30.4%], p = 0.007) when compared to other anti-diabetic agents. The use of SGLT2 inhibitors significantly improved satisfaction of glycemic control ability (mean [SE]:3.9 [0.12] vs. 3.5 [0.12], p = 0.027), diabetic symptom’s control ability (3.5 [0.15] vs. 3.0 [0.15], p = 0.027), glycemic control speed (3.9 [0.11] vs. 3.4 [0.12], p = 0.011), medication tolerability (3.9 [0.10] vs. 3.5 [0.12], p = 0.012), and overall satisfaction (4.0 [0.11] vs. 3.6 [0.12], p = 0.037), but it did not improve satisfaction of medication effect on bodyweight (3.8 [0.11] vs. 3.4 [0.11], p = 0.166). After adjusting confounding factors (47 patients for each group), consistent results were obtained. No significant differences of self-reported clinical AEs were observed between SGLT2 inhibitors users and non-users. Multivariable regression analyses verified that the use of SGLT2 inhibitors was associated with increased levels of satisfaction.

Conclusions: The use of SGLT2 inhibitors was associated with increased levels of satisfaction in T2DM patients, but not associated with overall clinical safety. Self-reported AEs were not related to the satisfaction with the use of anti-diabetic agents.
Agronomical and Physiological Behavior of Spanish Hazelnut Selection “Negret-N9” Grafted on Non-suckering Rootstocks
Authors: Rovira Mercè , Hermoso J. Francisco , Rufat Josep , Cristofori Valerio , Silvestri Cristian , Romero Agustí
Published: February 2022

“Negret” is the most widely planted hazelnut cultivar in Northeastern Spain, where it is highly appreciated by the local kernel marked for its favorable nut traits. Its main disadvantages are the high suckers emission, causing large maintenance costs every year, and its medium-to-low vigor and susceptibility to iron chlorosis. In 2000, a trial to select new vigorous and non-suckering rootstocks for hazelnut was established at IRTA Mas Bové (Spain). The “Negret N-9” selection was grafted onto four clonal rootstocks (“Dundee” and “Newberg” two selections of open-pollinatedCorylus colurnaseedlings, the low suckering cultivar “Tonda Bianca” and the local selection “IRTA MB-69”) and compared to the self-rooted “Negret N-9” as a control. The trial was designed as a randomized complete block with 10 replications and one tree per plot (10 trees per treatment). Plant vigor, suckers emission, yield, and nut and kernel traits have been evaluated over 10 years (2003–2012). During the 2006 to 2010 growing seasons, the qualitative traits of kernels, such as kernel skin color, oil content, and fatty acid profiles, were added to the characterization. Physiological data, such as steam water potential, stomatal conductance, and leaf chlorophyll content, were also evaluated during the 2015 growing season. The results showed that clonal rootstocks had a strong influence on vigor and yield of “Negret N-9.” The “Dundee,” “Newberg,” and “IRTA MB-69” rootstocks showed the highest vegetative growth and the lower suckers emission. The yield was highest in trees grafted on “Dundee” rootstock. In terms of the qualitative traits of kernel which are important to the hazelnut industry, rootstocks increased the oil stability and induced a brown light color in the kernel pellicle versus the brown dark color observed in nuts collected from self-rooted “Negret N-9.” The fatty acids profile was also influenced by the grafting combination. Finally, physiological traits indicated a higher overall performances for “Dundee” rootstock, which was generally found to be the best rootstock for “Negret N-9” in the experimental environment.
The Cassava NBS-LRR Genes Confer Resistance to Cassava Bacterial Blight
Authors: Zhang He , Ye Zi , Liu Zhixin , Sun Yu , Li Xinyu , Wu Jiao , Zhou Guangzhen , Wan Yinglang
Published: February 2022

Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (Xam) seriously affects cassava yield. Genes encoding nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains are among the most important disease resistance genes in plants that are specifically involved in the response to diverse pathogens. However, the in vivo roles of NBS-LRR remain unclear in cassava (Manihot esculenta). In this study, we isolated four MeLRR genes and assessed their expression under salicylic acid (SA) treatment and Xam inoculation. Four MeLRR genes positively regulate cassava disease general resistance against Xam via virus-induced gene silencing (VIGS) and transient overexpression. During cassava-Xam interaction, MeLRRs positively regulated endogenous SA and reactive oxygen species (ROS) accumulation and pathogenesis-related gene 1 (PR1) transcripts. Additionally, we revealed that MeLRRs positively regulated disease resistance in Arabidopsis. These pathogenic microorganisms include Pseudomonas syringae pv. tomato, Alternaria brassicicola, and Botrytis cinerea. Our findings shed light on the molecular mechanism underlying the regulation of cassava resistance against Xam inoculation.
MrMYB44-Like Negatively Regulates Anthocyanin Biosynthesis and Causes Spring Leaf Color of Malus ‘Radiant’ to Fade From Red to Green
Authors: Meng Jia-Xin , Wei Jun , Chi Ru-Fei , Qiao Yu-Hang , Zhou Jing , Wang Yi-Lin , Wang Han , Li Hou-Hua
Published: February 2022

The “Spring-red-leaf” crabapple cultivar has young red leaves and mature green leaves. However, the mechanism of anthocyanin biosynthesis in crabapple leaves in spring remains unknown. In this study, Illumina RNA sequencing (RNA-Seq) was performed on Malus ‘Radiant’ leaf tissues in different stages of development. Twenty-two genes in the anthocyanin biosynthesis pathway and 44 MYB transcription factors (TFs) were significantly enriched among differentially expressed genes (DEGs). Three R2R3-MYB TFs in subgroup 22 of the MYB TF family, MrMYB44-like1, MrMYB44-like2, and MrMYB44-like3, were highly expressed in green leaves according to RNA-Seq and quantitative real-time quantitative PCR results. Their expression levels were negatively correlated with anthocyanin content. In transient assays, overexpression of MrMYB44-like1, MrMYB44-like2, or MrMYB44-like3 inhibited anthocyanin accumulation and reduced pigment in leaf disks of M. ‘Radiant’ and fruit peels of M. domestica ‘Fuji.’ When the conserved region of the three MrMYB44-likes was silenced, the anthocyanin biosynthesis pathway was activated and pigments increased in both tissues. Moreover, bimolecular fluorescence complementation assays showed MrMYB44-likes interacted with MrWRKY6 to form protein complexes that regulated anthocyanin biosynthesis.
Goats (Capra hircus) From Different Selection Lines Differ in Their Behavioural Flexibility
Authors: Nawroth Christian , Rosenberger Katrina , Keil Nina M. , Langbein Jan
Published: February 2022

Given that domestication provided animals with more stable environmental conditions, artificial selection by humans has likely affected animals' ability to learn novel contingencies and their ability to adapt to changing environments. In addition, the selection for specific traits in domestic animals might have an additional impact on subjects' behavioural flexibility, but also their general learning performance, due to a re-allocation of resources towards parameters of productivity. To test whether animals bred for high productivity would experience a shift towards lower learning performance, we compared the performance of dwarf goats (not selected for production, 15 subjects) and dairy goats (selected for high milk yield, 18 subjects) in a visual discrimination learning and reversal learning task. Goats were tested individually in a test compartment and were rewarded by choosing either a white or a black cup presented by the experimenter on a sliding board behind a crate. Once they reached a designated learning criterion in the initial learning task, they were transferred to the reversal learning task. To increase the heterogeneity of our test sample, data was collected by two experimenters at two research stations following a similar protocol. Goats of both selection lines did not differ in the initial discrimination learning task in contrast to the subsequent reversal learning task. Dairy goats reached the learning criterion slower compared to dwarf goats (dairy goats = 9.18 sessions; dwarf goats = 7.74 sessions; P = 0.016). Our results may indicate that the selection for milk production might have affected behavioural flexibility in goats. These differences in adapting to changing environmental stimuli might have an impact on animal welfare e.g., when subjects have to adapt to new environments or changes in housing and management routines.
The Chinese Inventory of Psychosocial Balance Short-Form Questionnaire for the Older Adults: Validity and Reliability Study
Authors: Chen Pei-Yun , Ho Wen-Chao , Lo Chyi , Yeh Tzu-Pei
Published: February 2022

Background

Drawing from Erikson’s theory, Domino and Affonso constructed the Inventory of Psychosocial Balance (IPB), a scale with satisfactory reliability and validity. However, the lack of a credible Chinese version of the scale may hinder research on ego development in Taiwan. The aim of the present study was to construct a short form Chinese IPB. In addition, factor analysis was employed to shorten the original 120-item scale to make it suitable for application in the older adults in the future.

Methods

The study involved three steps: The first step was to establish the 120-items of the Chinese Inventory of Psychosocial Balance (C-IPB), and we conducted translation, back-translation, expert validity, and reliability of pilot study for this step. Following the first step was to construct the short-form C-IPB (CIPB-SF) in the second step, and the CIPB-SF was developed via item analysis and factor analysis. Finally, we assessed the reliability and validity of the CIPB-SF via structural equation model in the third step.

Results

Three hundred eight older adults without cognitive disorder completed the IPB. The 40-item CIPB-SF was completed through item analysis and factor analysis. The internal consistency test of CIPB-SF and the eight stages were good (Cronbach’s α = 0.81–0.89). The CIPB-SF had acceptable validity, except in the intimacy and identity stages, in which validity was only fair. Compared with the IPB, the CIPB-SF had good reliability and acceptable validity. However, because of its conciseness, the 40-item CIPB-SF was more suited for application among the Chinese elderly population because its application avoids physical overload.

Conclusion

The CIPB-SF served as a concise scale for assessing ego development in our study. This scale can also serve as a useful tool for convenient screening in the future.
The Highly Accurate Relation Between the Radius and Mass of the White Dwarf Star From Zero to Finite Temperature
Authors: Pei Ting-Hang
Published: February 2022

In this research, first considering the electron–electron interaction in the high-density Fermi electron gas at T = 0 K, this interaction causes the pressure 2/137 time less than the original value. However, the pressure of the Fermi electron gas should have something to do with temperature. Then, we estimate the temperature effect using statistical mechanics and find that the complicated form of the pressure p depends on temperature at the given particle number N and volume V. According to this, the central density–mass (ρc-M), central density–radius (ρc-R), and mass–radius (M-R) relations of the white dwarf star are obtained by considering the equation of state (EOS). Traditional formula gives the problematic mass–radius relation R∝M−1/3 for the low-density white dwarf stars because it leads to R→∞ and p→0 when M→0. We correct this relation and obtain two reasonable relations in the relativistic and nonrelativistic regions. In our EOS calculations, the central density is divided into the high-, middle-, and low-density regions. All three relations are almost unchanged until 108 K in the high-density region. The temperature effect mainly affects the middle- and low-density regions, and it becomes explicitly above 107 K. Our calculations can explain Sloan Digital Sky Survey observations where some white dwarf stars with a radius of more than 8 × 103 km have larger mass than the predictions by the relativistic EOS at T = 0 K. This result tells us that the temperature effect is important for the low and middle central-density white dwarf star and also useful to estimate the inner temperature of a white dwarf star.
Role of Fractalkine-CX3CR1 Axis in Acute Rejection of Mouse Heart Allografts Subjected to Ischemia Reperfusion Injury
Authors: Kanzawa Taichi , Tokita Daisuke , Saiga Kan , Yamakawa Takafumi , Ishigooka Hidetoshi , Fukuda Hironori , Katsumata Haruki , Miyairi Satoshi , Ishii Rumi , Hirai Toshihito , Imai Toshio , Okumi Masayoshi , Tanabe Kazunari
Published: February 2022

Transplantation outcomes are affected by the increase in rejection associated with ischemia reperfusion injury (IRI). Fractalkine (FKN), a chemokine for recruitment of CX3CR1+leukocytes, contributes to the pathogenesis of various inflammatory diseases. Herein, we evaluated the importance of the FKN-CX3CR1 axis during IRI-related rejections using a mouse heterotopic heart transplantation model. FKN expression and graft survival was compared between wild-type C57BL/6 recipients transplanted with BALB/c hearts preserved for 8 (WT-IRI) and 0.5 h (WT-control) at 4°C. Graft survival of WT-IRI was shorter than that of WT-control. FKN was expressed on the vascular endothelium in WT-IRI allografts, but minimally in WT-control. The role of the FKN-CX3CR1 axis in IRI-related rejection was directly investigated using the transplant model with CX3CR1-deficient recipients (CX3CR1 KO-IRI) or treatment with anti-mouse FKN monoclonal antibodies. Graft survival of CX3CR1 KO-IRI was longer than that of WT-IRI; antibody treatment prolonged graft survival. The contribution of CX3CR1+monocytes to IRI-related rejection was evaluated by adoptive transfer to CX3CR1 KO-IRI. Adoptive transfer of CX3CR1+monocytes attenuated the effect of prolonged graft survival in CX3CR1 KO-IRI. Overall, the FKN-CX3CR1 axis plays a major role during IRI-related rejection; its blockade has the potential to improve the outcomes of deceased donor transplantation.
Using Explainable Machine Learning to Explore the Impact of Synoptic Reporting on Prostate Cancer
Authors: Janssen Femke M. , Aben Katja K. H. , Heesterman Berdine L. , Voorham Quirinus J. M. , Seegers Paul A. , Moncada-Torres Arturo
Published: January 2022

Machine learning (ML) models have proven to be an attractive alternative to traditional statistical methods in oncology. However, they are often regarded as black boxes, hindering their adoption for answering real-life clinical questions. In this paper, we show a practical application of explainable machine learning (XML). Specifically, we explored the effect that synoptic reporting (SR; i.e., reports where data elements are presented as discrete data items) in Pathology has on the survival of a population of 14,878 Dutch prostate cancer patients. We compared the performance of a Cox Proportional Hazards model (CPH) against that of an eXtreme Gradient Boosting model (XGB) in predicting patient ranked survival. We found that the XGB model (c-index = 0.67) performed significantly better than the CPH (c-index = 0.58). Moreover, we used Shapley Additive Explanations (SHAP) values to generate a quantitative mathematical representation of how features—including usage of SR—contributed to the models’ output. The XGB model in combination with SHAP visualizations revealed interesting interaction effects between SR and the rest of the most important features. These results hint that SR has a moderate positive impact on predicted patient survival. Moreover, adding an explainability layer to predictive ML models can open their black box, making them more accessible and easier to understand by the user. This can make XML-based techniques appealing alternatives to the classical methods used in oncological research and in health care in general.
Comparative Study on the Physio-Biochemical Responses of Spring and Winter Barley Genotypes under Vernalized and Greenhouse Conditions
Authors: Rasheed Adeela , Feng Qidong , Adil Muhammad Faheem , Ahsan Muhammad , Han Zhigang , Zeng Fanrong , Shamsi Imran Haider
Published: January 2022

In barley (Hordeum vulgare L.) breeding, heading date is one of the most important agricultural traits that is essential for the completion of its life cycle. Certain endogenous and environmental factors regulate floral transition, morphing the complex genetic mechanism of the heading phase, which could serve as a premise of orchestration for improved yields. To elaborate the network of genetic and environmental signals, a hydroponic experiment was carried out using two spring (i.e., DM65 and DM70) and two winter barley genotypes (i.e., DM269 and DM385). Our results confirmed that the vernalized environment produced a substantial reduction in plant height, biomass and photosynthetic activity compared with the control plants. A noticeable increase in oxidative stress was exhibited by DM65 and DM70 plants compared with their respective controls at 20 °C, while no significant difference was observed for any genotype grown in the greenhouse (25 °C). Simultaneously, increased antioxidant enzyme activity in winter barley genotypes showed a defensive mechanism under vernalized conditions (4 °C). Furthermore, the expression of key regulatory flowering genes revealed that the vernalization gene (HvVRN1) is the key regulator of floral induction after cold exposure, whereas Photoperiod Response Locus 1 (HvPpd-H1) had significantly higher expression under greenhouse conditions, along with Phytochrome C (HvPHY-C), validating their involvement as upstream heading time regulators. These findings contribute to enriching the study of environmental signals that substantially modulate the complex mechanism of barley heading date.
A Simple, Semi-Automated, Gravimetric Method to Simulate Drought Stress on Plants
Authors: Liyanage Dilrukshi Kombala , Chathuranga Ishan , Mori Boyd A. , Thilakarathna Malinda S.
Published: January 2022

Drought is a major constraint of global crop production. Given that drought-induced crop losses can threaten world food security, it has been and continues to be the focus of a large body of interdisciplinary research. Most drought experiments are conducted under controlled environmental conditions, where maintaining accurate soil moisture content is critical. In this study, we developed a simple, Arduino microcontroller-based, semi-automated, lysimeter that uses the gravimetric method to adjust soil moisture content in pot experiments. This method employs an Arduino microcontroller interfaced with a balance as part of a portable lysimeter and irrigation system which can weigh and record the mass of plants growing in pots, determine water loss due to evapotranspiration, and adjust soil moisture automatically to a desired relative soil water content. The system was validated with a greenhouse pot experiment using a panel of 50 early-maturity Canadian soybean varieties. Drought was induced in the experiment by adjusting soil moisture content to 30% field capacity while maintaining control pots at 80%. Throughout the experiment, the two moisture levels were efficiently maintained using the Arduino-based lysimeter. Plant physiological responses confirmed that plants in the drought treatment were under physiological stress. This semi-automated lysimeter is low-cost, portable, and easy to handle, which allows for high-throughput screening.
Overimitation in Dogs: Is There a Link to the Quality of the Relationship with the Caregiver?
Authors: Huber Ludwig , Kubala Denise , Cimarelli Giulia
Published: January 2022

Overimitation, the copying of causally irrelevant or non-functional actions, is well-known from humans but completely absent in other primates. Recent studies from our lab have provided evidence for overimitation in canines. Previously, we found that half of tested pet dogs copied their human caregiver’s irrelevant action, while only few did so when the action was demonstrated by an unfamiliar experimenter. Therefore, we hypothesized that dogs show overimitation as a result of socio-motivational grounds. To test this more specifically, here we investigated how the relationship with the caregiver influenced the eagerness to overimitate. Given the high variability in the tendency to overimitate their caregiver, we hypothesized that not only familiarity but also relationship quality influences whether dogs faithfully copy their caregiver. For this purpose, on the one hand we measured the overimitation tendency (with the same test as in the two studies before) and on the other hand the relationship quality between the dogs and their caregivers. Although we found no significant correlation between the two test results, our data might suggest that, on average, dogs who overimitated seemed to show more referential and affiliative behaviours towards the owner than dogs who showed less or no copying of the irrelevant action. Notably, as a group, those dogs that showed the highest level of copying accuracy of the irrelevant action showed the highest level of gazing and synchronization towards the owner.
The Use of Multilayer Perceptron Artificial Neural Networks to Detect Dairy Cows at Risk of Ketosis
Authors: Bauer Edyta A. , Jagusiak Wojciech
Published: January 2022

Subclinical ketosis is one of the most dominant metabolic disorders in dairy herds during lactation. Cows suffering from ketosis experience elevated ketone body levels in blood and milk, including β-hydroxybutyric acid (BHB), acetone (ACE) and acetoacetic acid. Ketosis causes serious financial losses to dairy cattle breeders and milk producers due to the costs of diagnosis and management as well as animal welfare reasons. Recent years have seen a growing interest in the use of artificial neural networks (ANNs) in various fields of science. ANNs offer a modeling method that enables the mapping of highly complex functional relationships. The purpose of this study was to determine the relationship between milk composition and blood BHB levels associated with subclinical ketosis in dairy cows, using feedforward multilayer perceptron (MLP) artificial neural networks. The results were verified based on the estimated sensitivity and specificity of selected network models, an optimum cut-off point was identified for the receiver operating characteristic (ROC) curve and the area under the ROC curve (AUC). The study demonstrated that BHB, ACE and lactose (LAC) levels, as well as the fat-to-protein ratio in milk, were important input variables in the network training process. For the identification of cows at risk of subclinical ketosis, variables such as BHB and ACE levels in milk were of particular relevance, with a sensitivity and specificity of 0.84 and 0.61, respectively. It was found that the back propagation algorithm offers opportunities to integrate artificial intelligence and dairy cattle welfare within a computerized decision support tool.
Genetic Evaluation of Body Weights and Egg Production Traits Using a Multi-Trait Animal Model and Selection Index in Thai Native Synthetic Chickens (Kaimook e-san2)
Authors: Chomchuen Kitsadee , Tuntiyasawasdikul Veeraya , Chankitisakul Vibuntita , Boonkum Wuttigrai
Published: January 2022

To improve the genetics of both growth and egg production, which are limitations in purebred native chickens, new genetic lines can be developed using an appropriate genetic approach. The data used in this study included 2713 body weight (BW0, BW4, BW6, BW8, and BW10), breast circumference (BrC6), chicken age at first egg (AFE), and egg production (240EP, 270EP, 300EP, and 365EP) records covering the period 2015 to 2020. A multi-trait animal model with the average information-restricted maximum likelihood (AI-REML) and a selection index was used to estimate the variance components, genetic parameters, and breeding values. The results showed that males had significantly higher weights than females (p < 0.05) from 4 to 10 weeks of age and that this difference increased over the generations. The differences between BW0 and BrC6 by sex and generation were not significant (p > 0.05). The estimated heritability of body weight ranged from 0.642 (BW0) to 0.280 (BW10); meanwhile, the estimated heritability of BrC6 was moderate (0.284). For egg production traits, the estimated heritability of 240EP, 270EP, 300EP, and 365EP was 0.427, 0.403, 0.404, and 0.426, respectively, while the estimated heritability of AFE was 0.269. The genetic and phenotypic correlations among the growth traits (BW0 to BW10) were low to highly positive. The genetic and phenotypic correlations between growth (BW0 to BW10) and BrC6 traits were positive, and the genetic correlations between BW6 (0.80), BW8 (0.84), BW10 (0.93), and BrC6 were strongly positive. Genetic correlations among the egg production traits (240EP, 270EP, 300EP, and 365EP) were low to highly positive and ranged from 0.04 to 0.86. The genetic correlations between AFE and all egg production traits were low to moderately negative and ranged from −0.14 to −0.29. The positive genetic correlations between body weight (BW6, BW8, and BW10) and egg production traits were found only in 240EP. The average genetic progress of body weight traits ranged from −0.38 to 30.12 g per generation for BW0 to BW10 (p < 0.05); the genetic progress was 0.28 cm per generation for BrC6 (p > 0.05). The average genetic progress of cumulative egg production traits ranged from 4.25 to 12.42 eggs per generation for 240EP to 365EP (p < 0.05), while the average genetic progress of AFE was −7.12 days per generation (p < 0.05). In conclusion, our study suggests that the body weight at six weeks of age (BW6), breast circumference at six weeks of age (BrC6), cumulative egg production at 240 days of age (240EP), and age at first egg (AFE) are the traits that should be used as selection criteria, as they have a positive effect on the development of growth and egg production.
Molecular Detection of Avipoxvirus in Wild Birds in Central Italy
Authors: Bertelloni Fabrizio , Ceccherelli Renato , Marzoni Margherita , Poli Alessandro , Ebani Valentina Virginia
Published: January 2022

Avipoxviruses (APVs) are important pathogens of both domestic and wild birds. The associated disease is characterized by skin proliferative lesions in the cutaneous form or by lesions of the first digestive and respiratory tracts in the diphtheritic form. Previous studies investigated these infections in symptomatic wild birds worldwide, including Italy, but data about the circulation of APVs in healthy avian wildlife are not available. The present study tested spleen samples from 300 wild birds without typical lesions to detect Avipoxvirus DNA. Overall, 43.33% of the samples scored positive. Aquatic birds were more frequently infected (55.42%) than other animals (26.40%), and in Anseriformes, high positivity was found (52.87%). The obtained results suggest that wild birds could be asymptomatic carriers of Avipoxviruses, opening new possible epidemiological scenarios.
The Effects of Lemon Balm (Melissa officinalis L.) Essential Oil on the Stress Response, Anti-Oxidative Ability, and Kidney Metabolism of Sea Bass during Live Transport
Authors: Wang Qi , Mei Jun , Xie Jing
Published: January 2022

This study was conducted to enhance the viability and alleviate the oxidative stress response using MO for sea bass during live transport. Six experimental groups were designed, and the effects of the physiological responses of MO were evaluated in comparison with MS-222 and eugenol. The physiological stress levels, proprotein convertase subtilisin/kexin type 9 (PCSK-9), antioxidant enzyme activities, and kidney parameters of blood serum were determined. It was found that cortisol level, glucose (Glu), lactic acid (LD), heat shock proteins (HSPs), catalase (CAT), myeloperoxidase (MPO), glutathione peroxidase (GSH-Px), uric acid (UA), and urea nitrogen (BUN) in the MO-treated samples were lower than that of the control (133.72 ng/L); however, the total antioxidant capacity (T-AOC) was higher after 72 h of the simulated live transport. The ability to resist oxidative stress increased along with the increase in the MO concentration in the water during live transport, which was similar to the results of MS-222 and eugenol treatment. In conclusion, MO, acting as a kind of novel sedative and anesthetic, can be used to improve the oxidative system and survival rate during live transport. The results of this study provide a reference for enhancing animal welfare and anti-oxidative stress ability, reducing mortality and the stress response during live fish transport.
ESBL-Producing Moellerella wisconsensis—The Contribution of Wild Birds in the Dissemination of a Zoonotic Pathogen
Authors: Athanasakopoulou Zoi , Sofia Marina , Giannakopoulos Alexios , Papageorgiou Konstantinos , Chatzopoulos Dimitris C. , Spyrou Vassiliki , Petridou Evanthia , Petinaki Efthymia , Billinis Charalambos
Published: January 2022

Moellerella wisconsensis is an Enterobacteriaceae with unclarified dispersion and pathogenicity. During an ongoing investigation about antimicrobial resistance in Greece, the occurrence of M. wisconsensis was evaluated among wild birds and humans. A total of 445 wild bird and 2000 human fecal samples were collected and screened for the presence of the organism. Subsequently, all M. wisconsensis strains were phenotypically and molecularly characterized regarding their antimicrobial resistance characteristics. Four M. wisconsensis were isolated from a common pheasant (Phasianus colchicus), two Eurasian magpies (Pica pica) and a great white-fronted goose (Anser albifrons). Among these four strains, the three latter presented resistance to 3rd generation cephalosporins, were phenotypically confirmed to produce ESBLs and were found to harbor blaCTX-M-1. The three ESBL isolates additionally exhibited resistance to tetracyclines, while resistance to aminoglycosides was detected in two of them and to trimethoprim/sulfamethoxazole in one. No Moellerella wisconsensis strains were retrieved from the human samples tested. This is the first report that provides evidence of M. wisconsensis dissemination among wild birds in Greece, describing CTX-M-1 production in multidrug resistant wild birds’ isolates of this bacterial species.
Multidrug-Resistant and Genetic Characterization of Extended-Spectrum Beta-Lactamase-Producing E. coli Recovered from Chickens and Humans in Egypt
Authors: Badr Heba , Reda Reem M. , Hagag Naglaa M. , Kamel Essam , Elnomrosy Sara M. , Mansour Amal I. , Shahein Momtaz A. , Ali Samah F. , Ali Hala R.
Published: February 2022

Colonization of food chain animals such as chickens with extended-spectrum β-lactamases (ESBL) poses a major health threat to human. The current study aimed to determine the phenotypic and genotypic relationship between ESBL-producing E. coli from diseased human and chickens in Egypt. A total of 56 out of 120 chicken farms (46.7%) and 9 human samples (100%) were phenotypically and genotypically identified with at least one ESBL-phenotype/gene. Chicken isolates showed a high proportion of beta lactamase from CTX-M group 9 > TEM > PER families, followed by CTX-M group 1 > SHV > GES > OXA group10 > VEB > OXA group2 families, while human isolates only contained the CTX-M family. A high incidence of ESBL genes from the CTX-M family was recognized in both human and chicken isolates. Furthermore, nucleotide identity showed high similarity between chicken and human isolates. In conclusion, the current study traced phenotypes and genotypes of ESBL-producing E. coli from chickens and human samples in Egypt, reporting degrees of similarity that suggest potential zoonotic transmission. Our data highlighted the significant importance of chicken as a major food source not only in Egypt but all over the world in the spreading of ESBL-producing E. coli to human.
Mutual Links between the Endocannabinoidome and the Gut Microbiome, with Special Reference to Companion Animals: A Nutritional Viewpoint
Authors: Schiano Moriello Aniello , Di Marzo Vincenzo , Petrosino Stefania
Published: February 2022

There is growing evidence that perturbation of the gut microbiome, known as “dysbiosis”, is associated with the pathogenesis of human and veterinary diseases that are not restricted to the gastrointestinal tract. In this regard, recent studies have demonstrated that dysbiosis is linked to the pathogenesis of central neuroinflammatory disorders, supporting the existence of the so-called microbiome-gut-brain axis. The endocannabinoid system is a recently recognized lipid signaling system and termed endocannabinoidome monitoring a variety of body responses. Accumulating evidence demonstrates that a profound link exists between the gut microbiome and the endocannabinoidome, with mutual interactions controlling intestinal homeostasis, energy metabolism and neuroinflammatory responses during physiological conditions. In the present review, we summarize the latest data on the microbiome-endocannabinoidome mutual link in health and disease, focalizing the attention on gut dysbiosis and/or altered endocannabinoidome tone that may distort the bidirectional crosstalk between these two complex systems, thus leading to gastrointestinal and metabolic diseases (e.g., idiopathic inflammation, chronic enteropathies and obesity) as well as neuroinflammatory disorders (e.g., neuropathic pain and depression). We also briefly discuss the novel possible dietary interventions based not only on probiotics and/or prebiotics, but also, and most importantly, on endocannabinoid-like modulators (e.g., palmitoylethanolamide) for intestinal health and beyond.
Alterations of Cortisol and Melatonin Production by the Theca Interna Cells of Porcine Cystic Ovarian Follicles
Authors: Qin Yusheng , Bai Jiahua , Dai Jiage , Zhou Jianhui , Zhang Taipeng , Zhang Silong , Xu Xiaoling , Liu Yan
Published: February 2022

(1) Background: Cortisol and melatonin (MT) act in regulating follicular development. We hypothesized that abnormal levels of cortisol, MT, and steroids in theca interna cells might be involved in the development of follicular cysts in sows. (2) Methods: To test this hypothesis, we measured the mRNA levels of enzymes involved in steroid hormone synthesis, the glucocorticoid receptor (GR), and melatonin receptors (MTRs) in theca interna cells of cystic and normal porcine follicles. (3) Results: The concentrations of estradiol, progesterone, and cortisol were greater in cystic follicles than in control ones (p = 0.034, p = 0.020, p = 0.000), but the concentration of MT was significantly lower (p = 0.045). The levels of GR, 11β-HSD1, and 11β-HSD2 were higher in cystic follicles than in control l follicles. MT types 1 and 2 were significantly lower in cystic follicles (p < 0.05). The mRNA expression levels of genes encoding the steroid hormone synthesis enzymes, steroidogenic acute regulatory protein (StAR), recombinant cytochrome P45011A1 (CYP11A1), and 3β-hydroxysteroid dehydrogenase (3β-HSD) in theca interna cells of cystic follicles were significantly higher than in control follicles. Thus, there was disruption of hormone secretion in the fluid of cystic follicles in sows. (4) Conclusions: The levels of steroid hormones, cortisol and MT are disrupted in porcine cystic follicles.