bluuebunny/crossref_metadata_2025 huggingface dataset:
Phenotype performance of M1 generation Bima Shallot (Allium cepa var ascalonicum) result of Ethyl Methane Sulfonate induced
Authors: Zulfahmi  , Affandi D , Mahmuzar  , Gusrinaldi  , Rosmaina
Published: December 2022

The diversity of crops can be produced via mutagen induction. Its result can be utilized as a source of genetic material in the plant breeding activities to produce a high-quality variety. The purpose of this study was to investigate the phenotype performance of Bima varieties of Shallot (Allium cepa var ascalonicum) result of Ethyl Methane Sulfonate induced. This study used a randomized complete block design, with the treatment of five levels of EMS concentrations. Data obtained were analyzed of variance and if EMS treatment was significant difference that will be proceeded to Duncan Multiple ranged Test. The present study found that EMS treatment differed significantly for all parameters (p< 0.05). The first generation of Bima shallot exhibited growth inhibition and decrease of yield with increasing of EMS concentration than control. The reduction of these parameters may be caused by genetic changing and physiologically damage as consequences of EMS treatments. The EMS treatment of 100 ppm displayed a higher value for all parameters compared to 200, 300, and 400 ppm of EMS.
Information flow among farmers in the acceleration of agriculture 4.0
Authors: Widiyanti E , Utari P , Padmaningrum D
Published: December 2022

To adopt agriculture 4.0, farmers need to adapt to a new digital-based environment and the speed of its information flow. Many studies have found that the biggest obstacle to agriculture 4.0 (Smart Farming) in Indonesia is the gap in Information and Communication Technology (ICT) skills at the farmer level. However, some farmers managed to adopt agriculture 4.0. These farmers come from millennial and non-millennial generations (generation x). This study aims to analyze and describe the flow of information on agriculture 4.0 at the farmer level which enables them to adopt agriculture 4.0. Using multiple-case study approach, this study sought to reveal a holistic picture of the information flow in two cases of horticultural farmers in Ngablak, Magelang, Central Java. The cases studied were information flows among millennial farmers and non-millennial farmers. From the interactive analysis results, this study found several different flow patterns in the process of searching and distributing information related to smart farming and online marketing in both cases. This study also found the role of millennial farmers and the collaboration between millennial and non-millennial farmers in adopting agriculture 4.0. The millennial farmers serve as liaisons and information providers for non-millennial farmers.
A review on participation of cocoa smallholders in agricultural certification scheme
Authors: Rusli A L , Fatah F A
Published: December 2022

The ability of cocoa smallholders to comply with the agricultural certification scheme has led to the improvement of commodity profits in agriculture, especially cocoa crops. This study aims to determine the participation of cocoa smallholders in agricultural certification schemes. Cocoa production contributes to the national economy by generating exchange profits. Factors such as the age of smallholders, gender, training, farming experience, education, and attitude influence the smallholder’s participation in the agricultural certification scheme. Educational status had a significant positive relationship with the certification scheme. Based on the review, the multinomial logistic regression model and other methods are used to analyse smallholders’ participation in the certification. Therefore, the certification has some benefits for smallholders in terms of food safety standards. Consequently, it can improve the safety of the consumer, the livelihood of smallholders, and the quality of agricultural products. This capacity will locate the cocoa crops at the global demand linked together from top to down of the value chain process.
Establishing a co-design framework for disaster mitigation agenda in the urban context. A case study: SIBAT Solo
Authors: Setiawan A , Ramdhon A , Utami L A
Published: December 2022

One of the impacts of climate change on the urban environment is the flood cycle which is significantly difficult to predict. Along with using engineering methods, one more effort that can be conducted is to prepare communities for flood catastrophes in order to address the problem of unpredictable floods in urban settings. The correct technique and approach should be employed to involve residents in a disaster mitigation system. The objective of this study is to provide a co-design framework to assist the agenda for reducing flood disasters in urban settings. The co-design technique is being utilized as a participatory strategy to perform the work objectives of the community-based disaster preparedness community in Solo, Indonesia, according to the preliminary study findings reported in this paper. This study employed a case study method of flood disaster mitigation practices by the SIBAT community. Data analysis administered the interactive model through three stages: data reduction, data display, and conclusion drawing. Preliminary results obtained indicate that the local social and cultural context is essential in developing a co-design framework. Therefore, these findings will later become the basis for building a co-design framework for implementing the flood disaster mitigation agenda in Solo
Ecoprinting with weed plant: utilization of cacabean (ludwigia octavalvis) and ketul (biden pilosa) as ecoprint natural dyes
Authors: Pratiwi K Y , Sulistyati A N
Published: December 2022

Ecoprint is a technique that process the shape and colors of leaves, flowers, and stems into a media namely fabric. In this case, the plants used as ecoprint media are weeds. Weeds are plants that can grow in any place and its existence are often considered as a hinder due to the fact that it can interfere other cultivated plants as well as human activities. The processing of Cacabean (Ludwigia octavalvis) and Ketul (Bidens pilosa) weeds as raw materials for ecoprint natural dyes is one of huge leap in development of textile colorings which also helps increase the value of weeds. The method used for this research is a qualitative method complemented with data collection technique in the form of observation, interviews, and experiments. The result of this research indicates that Bidens pilosa can be utilized as an alternative in the manufacture of natural dyes. The dye produced from this plant can be well absorbed by the cotton fabrics and produces a yellow to brown color, while the Ludwigia octavalvis can be used as a medium for ecoprint with a really clear result and produces black color for the old leaves and green for the younger one.
Development of cilacap batik utilizing natural dyes with main motifs of marine life and Dipterocarpus littoralis (pelahlar)
Authors: Widiastuti T , Sulistyati A N , Darwoto  , Dartono F A , Handayani S R
Published: December 2022

The design of Cilacap batik was developed by batik artisan in Cilacap by utilizing its local potentials both in techniques, aesthetics, as well as its symbolic values which contained in its motifs. Cilacap batik takes main motifs of marine life and plants typical of Cilacap, namely the pelahlar tree. The added value of Cilacap batik is that it uses environmentally friendly natural dyes for its production, namely mangrove and indigofera plants. A production method with natural dyes is a form of solution made by the community in response to environmental issues, especially the issue regarding liquid waste produced from the residue of batik dyes that do not harm the environment. The research method used in this research is a qualitative method accompanied with data collection techniques in the form of observation and interviews with the local artisans and business people of Cilacap batik.
Cattle corporation village program as small-scale farmer group empowerment to support National beef self sufficiency
Authors: Suganda A , Salman D , Baba S , Fahmid I M
Published: December 2022

Government of Indonesia has implemented various programs to increase cattle population and beef production. In 2020, Directorate General of Livestock and Animal Health Services, Ministry of Agriculture has introduced Cattle Corporation Village Program (CCVP). The study aims to identify the capability of small-scale farmer group empowered by CCVP on good farming practices, availability of forage, utilization of infrastructure and colony cages, and corporate institution formed by farmers. The study was located at Cianjur District in 2022. The primary and secondary data were obtained by survey and interview that analyzed by qualitative descriptive. The results of the study indicate: (1) capability of farmer is encouraged to develop good farming practices with business scale; (2) the productivity of cattle should be supported by the sufficiency of forages and additional concentrate; (3) facilities has been provided by CCVP utilized by farmers, however the improvement of some facilities may required; and (4) CCVP is designed as profitable integrated corporation farming for small-scale farmers with upstream to downstream business integration. Through the CCVP, farmers are empowered and assisted in implementing good farming practices with business-scale. In addition, they will obtain some support from various institution and stakeholders to increase their income and welfare.
The participation of Forum Anak Surakarta in developing children-friendly public spaces into a smoke-free area
Authors: Yuliani S , Wijaya M , Supriyadi S , Setyowati R
Published: December 2022

Children Forum (Indonesian: Forum Anak) is a medium to express children’s interest in development. The availability of health and environment-friendly public spaces is one of children’s needs. This research aims to study the participation of Children Forum in developing a smoke-free public space in Surakarta City. This study is a descriptive qualitative research using case study approach. The informants were selected purposively, consisting of staff in Children Protection Division of Women Empowerment, Children Protection, and Community Empowerment Office, Head of Self-Help Group (Yayasan Kakak or Kakak Foundation), and 15 members and 1 facilitator of Children Forum in Surakarta. Data collection was carried out through observation, in-depth interview, focus group discussion, and documentation study. Data analysis was carried out using an interactive model of analysis, encompassing three stages: data reduction, data display, and conclusion drawing. The results concluded that as a part of civil society, Forum Anak Surakarta has successfully urged the ratification of smoke-free area policy but cannot ensure its effective implementation. The inhibiting factors are people’s low awareness of the hazard of cigarette smoke to children and regional government’s weak commitment to control cigarette consumption and advertisement, promotion, and sponsor.
Decrease in population of Ditylenchus dipsaci in garlic cultivation with the application of mycorrhizae and organic fertilizers
Authors: Poromarto S H , Hadiwiyono  , Subagiya  , Supyani  , Widono S , Septiriani D N , Hermawan K
Published: December 2022

Garlic is the main commodity of farmers in Tawangmangu, Central Java. The superior variety in the area is Tawangmangu Baru. Unfortunately this variety is susceptible to garlic root rot caused byFusarium oxysporumf.sp.cepae.The infection of this pathogen was increased by the presence of the nematodeDitylenchus dipsaci.Besides the loss due to single infection, this nematode can predispose garlic to be susceptible to garlic root rot disease. Therefore, population decrease ofD. capsaciis important as a component of integrated control of the two pests. Environmentally friendly control is a priority now and in the future, including biologically, such as the application of mycorrhizae and orgnically such as organic fertilizers. This paper reports a decrease in the population ofD. dipsaciin garlic cultivation with the application of mycorrhizae and organic fertilizers. This research was conducted on farmer’s land in Tawangmangu Karanganyar Central Java at an altitude of 1000 m asl and Andosol soil type. The results showed that mycorrhizae, compost, and husk charcoal could decrease the population ofD. capsaci.The effectiveness of nematode population decrease in the single treatment of mycorrhizae, compost, and husk charcoal were 18.45, 42.14, and 27.56%, respectively. While the combination of the three treatments gave the highest effectiveness value, namely 48.52%.
The effect of liquid organic fertilizer on growth of bulbil and yield of porang (Amorphophallus muelleri Blume)
Authors: Supriyono  , Syahda T N , Harsono P
Published: December 2022

Porang (Amorphophallus muelleri Blume) is a tuber plant with excellent potential because it contains nutrients and advantages. Liquid organic fertilizer (LOF) must be applied to increase porang output and maintain soil fertility. The research aimed to examine the effect of liquid organic fertilizer application and get the optimum LOF dose that has a better impact on bulbil growth and porang yields. The research was conducted from March 2021 to August 2021 at the Forest Management Unit (BKPH) Pojok in Kemadohbatur Village, Tawangharjo, Grobogan. The design of this research used a one-factor Randomized Block Design (RCBD) with four levels of treatment, namely the dose of liquid organic fertilizer, 0.375 ml/plant, 0.75 ml/plant, 1.125 ml/plant, and control, each level 6 times test. The observational parameters are; the number of bulbils, bulbil weight, fresh tuber weight, tuber diameter, dry wind weight, and tuber volume. Data analysis in this research uses ANOVA test level 5%. Regression test is used to determine the optimum dose. The results showed that the application of LOF with treatment doses has not been able to produce bulbil growth and porang yields well, and there is no optimum dose because there is no significant increase in bulbil growth and porang yields.
Growth and content of N, P, K, Fe in rice plants with liquid organic fertilizer application of moringa leaf
Authors: Rachmawatie S J , Purwanto E , Sakya A T , Dewi W S
Published: December 2022

The availability of macronutrients and micronutrients strongly influences the growth of rice plants. If the availability of nutrients in the soil is not optimal, then fertilization is necessary. Moringa leaf extract can increase plant growth because it contains minerals such as Ca, K and Fe. The study examines the effect of applying liquid organic fertilizer from Moringa leaves and golden snails with different fertilizer concentrations on rice growth. The research design used was a factorial completely randomized design, with two factors are fertilizer application (P1: Moringa leaves extract, P2: Moringa leaves fermentation, P3: Golden snail extract, P4: Golden snail fermentation, P5: Moringa and golden snail fermentation) and concentration of fertilizer application (K1: 2%, K2: 4%, K3: 6%, K4: 8%). Each treatment was repeated three times to obtain 60 experimental units. The parameters observed were nutrients in plant tissue (N, P, K, and Fe) and dry weight. Data were analyzed using analysis of variance (ANOVA), and if they were significantly different, they were further tested with DMRT with a 95% confidence level. The result showed that the highest Fe content in the P5K2 (Moringa and golden snail fermentation on 4%) was 27.42% or 90.25% more than control.
Effects of different organic fertilizers on growth and yield potential of Solanum melongena (eggplant) in Malaysia
Authors: Mahamad N I A , Samah S N A A , Khidzir M N A M
Published: December 2022

Eggplant is a vegetable crop where its growth rate and yield quality are largely influenced by fertilizer application. The application of organic fertilizer has high economic advantages when compared to inorganic fertilizer. The study aimed to determine the growth of eggplant and quantify its fruit yield based on the fresh weight as affected by different organic fertilization. The experiment was conducted in the Greenhouse 3, UiTM Malacca Branch, Campus Jasin from March to July 2022 with 4 treatments and 4 replications by using the Randomized Complete Block Design (RCBD). The treatments consisted of T0(control), T1(252g chicken dung), T2(252g vermicompost), and T3(252g biochar) with two split applications. The results showed that the application of chicken dung had significantly increased the plant height, number of leaves, leaf area, plant fresh weight and dry weight, and number of flowers compared to the other treatments. This study confirmed that chicken dung was the best organic fertilizer for eggplant’s growth and yield potential.
Networking capabilities of millennial farmers in Central Java
Authors: Riptanti E W , Harisudin M , Kusnandar  , Khomah I , Setyowati N , Qonita R A
Published: December 2022

The role of millennial farmers as the next generation is very important considering that more millennial generations are reluctant to work in agriculture sector. The Ministry of Agriculture establishes policies and programs that can attract millennials to work in agriculture. One of the dominant influencing factors is networking ability of diverse business. The purpose of the study was to determine the networking capabilities of millennial farmers. The research method uses analytical descriptive. The study was conducted in Central Java by taking a sample location of 10 selected regencies based on the proportion of millennial farmer ambassadors. The number of millennial farmer respondents was taken as many as 120 respondents by snowball sampling. The results show that the networking capabilities of millennial farmers in Central Java vary between agribusiness sub-systems, scope, main capital, and patterns. The networking pattern that is built leads to business to business. Professional associations play an important role in expanding the networking built by millennial farmers. Networking in the marketing field cannot be separated from the use of digital technology, while other fields are still limited. Networking in the marketing field is what determines business continuity compared to other networking fields.
Highly sensitive interdigitated thermistor based on PEDOT:PSS for human body temperature monitoring
Authors: Khalaf Ayatallah M , Ramírez José Luis , Mohamed Shaimaa A , Issa Hanady Hussein
Published: December 2022

This work introduces a wearable, highly sensitive human body temperature sensor. The proposed thermistor sensor employs a poly(3,4-ethylenedioxythiophene) polystyrene sulfonate (PEDOT:PSS) as a temperature sensing layer and interdigitated electrodes (IDEs) from Silver nanoparticles deposited on Polyimide (PI) and Epson glossy paper substrates. The IDEs were patterned using inkjet printer Drop-on-demand PiXDRO LP50. The PEDOT:PSS layer was added by drop casting technique. The sensitivity of fabricated sensors was tested for different IDE number of fingers to investigate their response to the temperature range of 28–50 °C. The sensors performed linearly in the tested temperature range. Repeatability has been verified for five temperature measurement cycles. The achieved sensitivities are −1.462% /°C and −3.202%/°C for Epson paper and PI substrates, respectively. The sensor bendability results highlight the capability of the proposed sensor to be utilized for the wearable human body temperature reading.
Digitizing the Epistolary: Dracula Daily and Embodied Contemporary Reading
Authors: Young Lin
Published: December 2022

This review discusses the online phenomenon of Dracula Daily, an internet substack that emails users sections of the epistolary novel Dracula in real-time, rearranged chronology. It examines the unique appeal of Dracula for virtual dissemination, examines how the epistolary format changes the context in virtual form, how readers read online, community reading, and whether or not the success of Dracula Daily can be replicated with other classic novels.
Asthma and Respiratory Infections From Birth to Young Adulthood
Authors: Belachew Abate Bekele , Rantala Aino K , Jaakkola Maritta S , Hugg Timo T , Jaakkola Jouni J K
Published: December 2022

We applied data from a population-based prospective study, the Espoo Cohort Study (n = 2,568), to identify the potential susceptibility of persons with asthma to respiratory tract infections (RTIs). Information on the occurrence of asthma and both upper respiratory tract infections (URTIs) and lower respiratory tract infections (LRTIs) was collected with a questionnaire at baseline and at the 6-year and 20-year follow-up studies, and from the Finnish national health registries. We estimated age- and sex-specific incidence rate differences (IRDs) and incidence rate ratios (IRRs) by applying negative binomial regression. Meta-regression was used to summarize the age-specific IRRs from childhood to 27 years of age. Individuals with asthma at any age during the follow-up period had increased risks of both URTIs (adjusted IRD = 72.6 (95% confidence interval (CI): 50.6, 94.7) per 100 person-years; adjusted IRR = 1.27 (95% CI: 1.20, 1.35)) and LRTIs (adjusted IRD = 25.5 (95% CI: 17.9, 33.1); adjusted IRR = 2.87 (95% CI: 2.33, 3.53)) from childhood to young adulthood. In young adulthood, the association between asthma and URTIs was stronger in women than in men, while such an association was not detected for LRTIs. This analysis provides strong evidence that persons with asthma experience more RTIs from preschool age to young adulthood than do those without asthma. Thus, they constitute a susceptible population for RTIs. Women with asthma are at especially high risk.
Changes in both top-down and bottom-up effective connectivity drive visual hallucinations in Parkinson’s disease
Authors: Thomas George E C , Zeidman Peter , Sultana Tajwar , Zarkali Angeliki , Razi Adeel , Weil Rimona S
Published: December 2022

Visual hallucinations are common in Parkinson’s disease and are associated with a poorer quality of life and a higher risk of dementia. An important and influential model that is widely accepted as an explanation for the mechanism of visual hallucinations in Parkinson’s disease and other Lewy body diseases is that these arise due to aberrant hierarchical processing, with impaired bottom-up integration of sensory information and overweighting of top-down perceptual priors within the visual system. This hypothesis has been driven by behavioural data and supported indirectly by observations derived from regional activation and correlational measures using neuroimaging. However, until now, there was no evidence from neuroimaging for differences in causal influences between brain regions measured in patients with Parkinson’s hallucinations. This is in part because previous resting-state studies focused on functional connectivity, which is inherently undirected in nature and cannot test hypotheses about the directionality of connectivity. Spectral dynamic causal modelling is a Bayesian framework that allows the inference of effective connectivity—defined as the directed (causal) influence that one region exerts on another region—from resting-state functional MRI data. In the current study, we utilize spectral dynamic causal modelling to estimate effective connectivity within the resting-state visual network in our cohort of 15 Parkinson’s disease visual hallucinators and 75 Parkinson’s disease non-visual hallucinators. We find that visual hallucinators display decreased bottom-up effective connectivity from the lateral geniculate nucleus to primary visual cortex and increased top-down effective connectivity from the left prefrontal cortex to primary visual cortex and the medial thalamus, as compared with non-visual hallucinators. Importantly, we find that the pattern of effective connectivity is predictive of the presence of visual hallucinations and associated with their severity within the hallucinating group. This is the first study to provide evidence, using resting-state effective connectivity, to support a model of aberrant hierarchical predictive processing as the mechanism for visual hallucinations in Parkinson’s disease.
Feasible IV regression without excluded instruments
Authors: Tsyawo Emmanuel Selorm
Published: December 2022

The relevance condition of integrated conditional moment (ICM) estimators is significantly weaker than the conventional instrumental variable's in at least two respects: (1) consistent estimation without excluded instruments is possible, provided endogenous covariates are nonlinearly mean-dependent on exogenous covariates, and (2) endogenous covariates may be uncorrelated with but mean-dependent on instruments. These remarkable properties notwithstanding, multiplicative-kernel ICM estimators suffer diminished identification strength, large bias, and severe size distortions even for a moderately sized instrument vector. This paper proposes a computationally fast linear ICM estimator that better preserves identification strength in the presence of multiple instruments and a test of the ICM relevance condition. Monte Carlo simulations demonstrate a considerably better size control in the presence of multiple instruments and a favourably competitive performance in general. An empirical example illustrates the practical usefulness of the estimator, where estimates remain plausible when no excluded instrument is used.
Synchronous atrioventricular sequential pacing utilizing conventional and leadless pacemakers in an elderly patient: a case report
Authors: Bodagh Neil , Cheng Kevin , Eysenck William , Wong Tom
Published: December 2022

Background

Leadless pacemakers present a viable alternative to conventional transvenous devices to mitigate the risk of lead- and/or pocket-related complications. In elderly patients who have encountered ventricular lead failures with transvenous pacemakers, this option may enable the delivery of atrioventricular synchronous pacing therapy, while obviating the requirement for lead extraction and lead-based pacemaker re-implantation.

Case summary

This case report describes the successful implantation of a leadless pacemaker in a 90-year-old who had undergone two dual-chamber permanent pacemaker implantation procedures with a failure of three of four previously implanted leads. Atrioventricular synchronous pacing was achieved, as the leadless device was able to track the atrial-paced rhythm from the pre-existing right-sided device.

Discussion

In elderly patients who have encountered issues with transvenous pacemakers, alternative approaches should be considered to mitigate the risk of future complications. Leadless pacemakers may offer a low-risk solution, enabling the delivery of atrioventricular synchronous pacing therapy in such patient groups. Future studies should be designed to delineate whether these devices could be utilized as a first-line approach in certain situations.
Association Between Handgrip Strength and Type 2 Diabetes: A Prospective Cohort Study and Systematic Review With Meta-analysis
Authors: Wu Hongmei , Gu Yeqing , Wang Xuena , Meng Ge , Rayamajhi Sabina , Thapa Amrish , Zhang Qing , Liu Li , Zhang Shunming , Zhang Tingjing , Cao Zhixia , Dong Jun , Zheng Xiaoxi , Zhang Xu , Dong Xinrong , Wang Xing , Sun Shaomei , Jia Qiyu , Song Kun , Huang Jian , Huo Junsheng , Zhang Bing , Ding Gangqiang , Niu Kaijun
Published: December 2022

Background

Both absolute (kg) and relative (kg per kg of body weight) handgrip strength (HGS) have been used as indicators of HGS. Multiple studies have explored HGS associations with type 2 diabetes (T2DM); however, prognostic values were inconsistent. We aimed to examine the associations between both absolute and relative HGS and incident T2DM.

Methods

A total of 12,957 participants aged 40 years and older (mean age 51.0 years, 58.4% men) were followed and enrolled in the Tianjin Chronic Low-grade Systemic Inflammation and Health (TCLSIH) Cohort Study. Cox proportional hazards regression models were used to examine the association of HGS with incident T2DM. Other prospective studies on HGS and risk of T2DM were identified by searching several electronic databases up to November 31, 2021. Meta-analysis was performed by combining the results from the TCLSIH study and previous prospective cohort studies.

Results

From the TCLSIH Cohort study, after adjustment, relative HGS was inversely associated with T2DM (hazard ratio per 0.1 higher relative HGS 0.667, 95% confidence interval [CI] 0.616, 0.722). However, no significant association between absolute HGS and incident T2DM was found. The meta-analyses showed that per 5 kg higher HGS was associated with a 5% (95% CI 2%, 8%) lower risk of T2DM and each 0.1 higher relative HGS was associated with a 22% (95% CI 14%, 29%) lower risk of T2DM.

Conclusion

The results from our cohort study and meta-analysis suggest that relative HGS was better than absolute HGS in predicting incident T2DM. Adiposity was an important factor that mediates the association between HGS and T2DM.
DC-SIGN and Galectin-3 individually and collaboratively regulate H5N1 and H7N9 avian influenza A virus infection via interaction with viral envelope hemagglutinin protein
Authors: Yang Zih-Syuan , Wang Wen-Hung , Lin Yu-Ting , Lin Chih-Yen , Urbina Aspiro Nayim , Thitithanyanont Arunee , Lu Po-Liang , Chen Yen-Hsu , Wang Sheng-Fan
Published: December 2022

DC-SIGN and Galectin-3 are two different lectins and have been reported to participate in regulation of several virus infections. WHO has pointed that H5N1 and H7N9 avian influenza viruses (AIVs) play continuous threats to global health. AIV hemagglutinin (HA) protein—a highly glycosylated protein—mediates influenza infection and was proposed to have DC-SIGN and Gal3 interactive domains. This study aims to address the individual and collaborative roles of DC-SIGN and Gal3 toward AIVs infection. Firstly, A549 cells with DC-SIGN expression or Gal3-knockdown, via lentiviral vector-mediated CD209 gene expression or LGALS-3 gene knockdown, respectively were generated. Quantitative reverse transcription PCR (qRT-PCR) results indicated that DC-SIGN expression and Gal3 knockdown in A549 cells significantly promoted and ameliorated HA or NP gene expression, respectively after H5N1 and H7N9-reverse genetics (RG) virus postinfections (P < 0.05). Similar results observed in immunoblotting, indicating that DC-SIGN expression significantly facilitated H5N1-RG and H7N9-RG infections (P < 0.05), whereas Gal3 knockdown significantly reduced both viral infections (P < 0.05). Furthermore, we found that DC-SIGN and Gal3 co-expression significantly enhanced infectivity of both H5N1-RG and H7N9-RG viruses (P < 0.01) and higher regulatory capabilities by DC-SIGN and Gal3 in H5N1-RG than H7N9-RG were noted. The promoting effect mainly relied on exogenous Gal3 and DC-SIGN directly interacting with the HA protein of H5N1 or H7N9 AIVs, subsequently enhancing virus infection. This study sheds light on two different lectins individually and collaboratively regulating H5N1 and H7N9 AIVs infection and suggests that inhibitors against DC-SIGN and Gal3 interacting with HA could be utilized as alternative antiviral strategies.
A sensitive method for determining UDP-glucose: ceramide glucosyltransferase (UGCG) activity in biological samples using deuterated glucosylceramide as acceptor substrate
Authors: Cas Michele Dei , Casati Sara , Roda Gabriella , Pablo Sardi Sergio , Paroni Rita , di Fonzo Alessio , Trinchera Marco
Published: December 2022

Glucosylceramide synthase (UGCG) is a key enzyme in the biosynthesis of glycosphingolipids and its activity is related to the resistance to anticancer drugs and is involved in the derangement of metabolism in various diseases. Moreover, UGCG acts as a major controller of the balanced levels of individual brain sphingolipids that may trigger neurodegeneration in Gaucher disease and in Parkinson disease associated to pathogenic variants in the glucocerebrosidase-encoding gene GBA. We have developed an effective method for determining UGCG activity in vitro using deuterated ceramide as an acceptor, and quantitation of the formed deuterated glucosylceramide by liquid chromatography coupled with tandem mass spectrometry. The method enabled us to determine the kinetic parameters of UGGC and the effect of the inhibitor GZ667161 on the enzyme activity expressed in model cells, as well as to measure UGCG specific activity in human fibroblasts using a simple crude cell homogenate. This novel approach may be useful in determining the actual UGCG activity levels in patient cells and tissues of animal models of diseases, and to study novel drugs targeting glycosphingolipid metabolism.
Past, present, and future of genetic strategies to control tolerance to the main fungal and oomycete pathogens of grapevine
Authors: Pirrello Carlotta , Magon Gabriele , Palumbo Fabio , Farinati Silvia , Lucchin Margherita , Barcaccia Gianni , Vannozzi Alessandro
Published: December 2022

The production of high-quality wines is strictly related to the correct management of the vineyard, which guarantees good yields and grapes with the right characteristics required for subsequent vinification. Winegrowers face a variety of challenges during the grapevine cultivation cycle: the most notorious are fungal and oomycete diseases such as downy mildew, powdery mildew, and gray mold. If not properly addressed, these diseases can irremediably compromise the harvest, with disastrous consequences for the production and wine economy. Conventional defense methods used in the past involved chemical pesticides. However, such approaches are in conflict with the growing attention to environmental sustainability and shifts from the uncontrolled use of chemicals to the use of integrated approaches for crop protection. Improvements in genetic knowledge and the availability of novel biotechnologies have created new scenarios for possibly producing grapes with a reduced, if not almost zero, impact. Here, the main approaches used to protect grapevines from fungal and oomycete diseases are reviewed, starting from conventional breeding, which allowed the establishment of new resistant varieties, followed by biotechnological methods, such as transgenesis, cisgenesis, intragenesis, and genome editing, and ending with more recent perspectives concerning the application of new products based on RNAi technology. Evidence of their effectiveness, as well as potential risks and limitations based on the current legislative situation, are critically discussed.
A Phylogenetic Framework to Simulate Synthetic Interspecies RNA-Seq Data
Authors: Bastide Paul , Soneson Charlotte , Stern David B , Lespinet Olivier , Gallopin Mélina
Published: December 2022

Interspecies RNA-Seq datasets are increasingly common, and have the potential to answer new questions about the evolution of gene expression. Single-species differential expression analysis is now a well-studied problem that benefits from sound statistical methods. Extensive reviews on biological or synthetic datasets have provided the community with a clear picture on the relative performances of the available methods in various settings. However, synthetic dataset simulation tools are still missing in the interspecies gene expression context. In this work, we develop and implement a new simulation framework. This tool builds on both the RNA-Seq and the phylogenetic comparative methods literatures to generate realistic count datasets, while taking into account the phylogenetic relationships between the samples. We illustrate the usefulness of this new framework through a targeted simulation study, that reproduces the features of a recently published dataset, containing gene expression data in adult eye tissue across blind and sighted freshwater crayfish species. Using our simulated datasets, we perform a fair comparison of several approaches used for differential expression analysis. This benchmark reveals some of the strengths and weaknesses of both the classical and phylogenetic approaches for interspecies differential expression analysis, and allows for a reanalysis of the crayfish dataset. The tool has been integrated in the R package compcodeR, freely available on Bioconductor.
Changing Incidence and Characteristics of Nontuberculous Mycobacterial Infections in Scotland and Comparison With Mycobacterium tuberculosis Complex Incidence (2011 to 2019)
Authors: Jarchow-MacDonald Anna , Smith Michael , Seagar Amie-Louise , Russell Clark D , Claxton Pauline , Laurenson Ian F , Moncayo-Nieto Olga-Lucia
Published: December 2022

Background

An increase in infections with nontuberculous mycobacteria (NTM) has been noted globally, and their incidence has overtaken that of Mycobacterium tuberculosis complex (MTBc) in many countries. Using data from a national reference laboratory, we aimed to determine if this trend could be observed in Scotland.

Methods

We undertook a retrospective review of all NTM isolates received by the Scottish Mycobacteria Reference Laboratory (SMRL) over 9 years from 2011 to 2019 inclusive. Clinical episodes were defined as per 2017 British Thoracic Society and 2020 American Thoracic Society/European Respiratory Society/European Society of Clinical Microbiology and Infectious Diseases/Infectious Diseases Society of America NTM guidelines. These rates were compared with Scottish tuberculosis rates over the same period.

Results

Of 8552 NTM isolates from 4586 patients in 2011 to 2019, 7739 (90.5%) were considered clinically relevant. These represented 2409 episodes of NTM infection, with M. avium, M. intracellulare, and M. abscessus complex being most common. A total of 1953 (81.1%) were pulmonary NTM infection episodes from 1470 patients and 456 extrapulmonary episodes from 370 patients. We estimated a rise in incidence from 3.4 to 6.5 per 100 000 person-years (2011–2019 inclusive), with an increase in NTM incidence over MTBc incidence in Scotland by 2017.

Conclusions

The incidence of NTM infection in Scotland has overtaken MTBc incidence. NTM infection leads to a costly health care burden, possibly as much as UK£1.47 million (US$ and €1.73 million) annually. We recommend standardization of isolate referral with clinical surveillance and implementation of agreed standards of care delivered through multidisciplinary teams. This would improve diagnosis and patient management as well as assessment of diagnostics and novel treatments through clinical trials.
APC/CCDC20 targets SCFFBL17 to activate replication stress responses in Arabidopsis
Authors: Pan Ting , Gao Shan , Cui Xiaoyu , Wang Lili , Yan Shunping
Published: December 2022

DNA replication stress threatens genome stability and affects plant growth and development. How plants resolve replication stress is poorly understood. The protein kinase WEE1-mediated cell cycle arrest is required for replication stress responses. The E3 ubiquitin ligases anaphase-promoting complex/cyclosome (APC/C) and Skp1/Cullin 1/F-box (SCF) are essential regulators of the cell cycle. Here, we show that APC/CCDC20 mediates the degradation of SCFFBL17 during replication stress responses in Arabidopsis thaliana. Biochemically, WEE1 interacts with and phosphorylates the APC/C co-activator APC10, which enhances the interaction between F-BOX-LIKE17 (FBL17) and CELL DIVISION CYCLE 20 (CDC20), an activator of APC/C. Both APC10 and CDC20 are required for the polyubiquitination and degradation of FBL17. Genetically, silencing CDC20 or APC10 confers plant hypersensitivity to replication stress, which is suppressed by loss of FBL17. Collectively, our study suggests that WEE1 activates APC/C to inhibit FBL17, providing insight into replication stress responses in plants.
The rise of antibiotic resistance in Campylobacter
Authors: Qin Xiaoxia , Wang Xin , Shen Zhangqi
Published: December 2022

Purpose of review

Campylobacter is a major foodborne pathogen that infects the human intestinal tract. This review discusses the current status of antibiotic resistance, transmission of antibiotic resistance genes, and strategies to combat the global Campylobacter epidemic.

Recent findings

Over the past 18 months, articles on Campylobacter antibiotic resistance have been published in ∼39 countries. Antibiotic-resistant Campylobacter have been detected in humans, livestock, poultry, wild animals, the environment, and food. Campylobacter spp. are resistant to a wide spectrum of antimicrobial agents, including the antibiotics quinolones, macrolides, tetracyclines, aminoglycosides, and chloramphenicols. Multidrug resistance is a globally emerging problem. Continuous antibiotic pressure promotes the spread of drug-resistant Campylobacter spp. Additionally, Campylobacter is well adapted to acquiring foreign drug resistance genes, including ermB, optrA, fexA, and cfrC, which are usually acquired from gram-positive bacteria.

The widespread use of antibiotics has caused a global epidemic of drug-resistant Campylobacter infections. Many countries are actively reducing the use of antibiotics and adopting alternatives in the livestock and poultry industries to control the spread of drug-resistant Campylobacter spp.
Villoglandular Pattern in HPV-associated Endocervical Adenocarcinoma is Associated With Excellent Prognosis: A Reappraisal of 31 Cases Using IECC and Silva Pattern Classification
Authors: Stolnicu Simona , Brito Maria J. , Karpathiou Georgia , Hoang Lynn , Felix Ana , Mateoiu Claudia , Fanni Daniela , Reques Armando , Garcia Angel , Hardisson David , Talu Canan K. , Furtado Antonia , Abu-Rustum Nadeem , Soslow Robert A. , Park Kay J.
Published: December 2022

Villoglandular adenocarcinoma of the cervix is a rare histologic entity that typically develops in young women, characterized by an association with oral contraceptives and excellent prognosis, though this point is controversial. These tumors have not been studied in the context of the International Endocervical Adenocarcinoma Criteria and Classification (IECC) or Silva Pattern Classification. We analyzed 31 cases that met strict diagnostic criteria, including being completely excised with negative margins. These were categorized according to IECC and Silva Pattern Classification and the association with various pathologic parameters analyzed. Most patients were young with a mean age of 41.1 (range 25–79). There were 14 (45.2%) pattern A, 11 (35.5%) pattern B, and 6 (19.3%) pattern C cases. Only 1 of 22 patients (4.5%) presented with lymph node metastasis at the time of diagnosis (pattern C, stage IB1) and 3 (9.7%) had lymphovascular invasion (2 pattern C, 1 pattern B). Overall survival was 100%, while recurrence-free survival was 96.2% for the entire cohort with only 1 case (3.2%) recurring 25 mo after surgery (IB2, pattern B). Kaplan Meier analysis (log rank test) revealed no significant correlation for recurrence-free survival at 5 and 10 yr associated with depth of invasion, tumor size, Silva pattern, FIGO stage, lymphovascular invasion, or lymph node metastasis. Cox univariate analysis demonstrated no independent prognostic factors predicting recurrence-free survival. These results indicate that completely excised villoglandular adenocarcinoma generally has an excellent prognosis and when Silva Pattern Classification is applied, those tumors that potentially have a higher chance for adverse outcomes can be identified.
Mammalian Target of Rapamycin Inhibitors and Kidney Function After Thoracic Transplantation: A Systematic Review and Recommendations for Management of Lung Transplant Recipients
Authors: Schmucki Katja , Hofmann Patrick , Fehr Thomas , Inci Ilhan , Kohler Malcolm , Schuurmans Macé M.
Published: December 2022

Background.

Chronic kidney disease (CKD) after lung transplantation is common and limits the survival of transplant recipients. The calcineurin inhibitors (CNI), cyclosporine A, and tacrolimus being the cornerstone of immunosuppression are key mediators of nephrotoxicity. The mammalian target of rapamycin (mTOR) inhibitors, sirolimus and everolimus, are increasingly used in combination with reduced CNI dosage after lung transplantation.

Methods.

This systematic review examined the efficacy and safety of mTOR inhibitors after lung transplantation and explored their effect on kidney function.

Results.

mTOR inhibitors are often introduced to preserve kidney function. Several clinical trials have demonstrated improved kidney function and efficacy of mTOR inhibitors. The potential for kidney function improvement and preservation increases with early initiation of mTOR inhibitors and low target levels for both mTOR inhibitors and CNI. No defined stage of CKD for mTOR inhibitor initiation exists, nor does severe CKD preclude the improvement of kidney function under mTOR inhibitors. Baseline proteinuria may negatively predict the preservation and improvement of kidney function. Discontinuation rates of mTOR inhibitors due to adverse effects increase with higher target levels.

Conclusions.

More evidence is needed to define the optimal immunosuppressive regimen incorporating mTOR inhibitors after lung transplantation. Not only the indication criteria for the introduction of mTOR inhibitors are needed, but also the best timing, target levels, and possibly discontinuation criteria must be defined more clearly. Current evidence supports the notion of nephroprotective potential under certain conditions.
A delay-specific neural indicator corresponds to delay-discounting behavior for both gain and loss
Authors: Kinjo Takuji , Yamagata Toyoki , Katayama Jun’ichi , Murata Asuka
Published: December 2022

Objectives

Delay-discounting, wherein the subjective value for delayed gain or loss decreases, has been attracting much attention from the social sciences as well as neuroscience and has been suggested asbeing related to reward processing in the brain. As reported, the feedback-related negativity (FRN), an electrophysiological measure of reward processing, increased by delayed-monetary gain and ΔFRN, which is the difference in FRNs for loss and gain at a certain time point, had no significant correlation with delay-discounting for gain. Thus, although a delay for gain could affect FRN, it is unclear whether FRN capturing such a delay effect has a direct relationship with delay-discounting in both gain and loss domains.

Methods

In this study, we introduced a delay-specific indicator, ΔFRN

delay
, that is, the difference between FRN with and without delays, and investigated its direct relationship during the doors task with the discounting rate measured by the delay-discounting task in both the gain and loss domains.

Results

We found that, for loss, the delay enhanced FRN, whereas no such effect was observed for gains, and that this indicator was significantly correlated with delay-discounting in both domains.

Conclusions

To our knowledge, this study is the first to suggest that FRN is sensitive to the effects of delay in losses on reward processing and that the new indicator directly corresponds to changes in subjective value as measured by delay-discounting.