bluuebunny/crossref_metadata_2025 huggingface dataset:
The Effects of Information Pollution on Poultry Companies: The Case of Turkey
Authors: KESKİN Berkay , GÜNEŞ Erdoğan
Published: May 2023

The poultry sector provides people and countries with many benefits in the social, economic and health domains. However, the poultry sector faces a number of important problems. One of these problems is information pollution. The rapid advances in information and communication technologies, in particular, made information pollution one of the most important problems of our contemporary age. Information pollution can have significant negative effects on companies and sectors, as well as threaten the reputation of the brand, the products and services offered by the businesses. The poultry industry is among the most affected by information pollution and Turkey represents an ideal case for studying the effects of information pollution on the poultry industry. The poultry sector has achieved significant growth in Turkey in recent years, but the problem of information pollution is an important factor that limits this growth. There are ongoing efforts by various organizations and agencies in Turkey to solve the problem. This study aims to examine the effects of information pollution on poultry producing companies in Turkey and identify the activities undertaken by producers to fight information pollution. Data were collected from companies that are members of BESD-BİR (Turkish Poultry Meat Producers and Breeders Association), which brings together the largest chicken producing companies in Turkey and account for 91% of all poultry production in Turkey. Basic statistical techniques and procedures such as frequency distributions, percentages, and arithmetic means were used to conduct descriptive statistical analysis. Likert-type questions were also included in the study for various purposes. Descriptive analysis method was used to analyze the suggestions made by the poultry producers to reduce information pollution in the sector. The results show that information pollution problem is an important problem for poultry producing companies in Turkey. Since a significant part of the companies are affected by the problem of information pollution, they have various activities aimed at solving this problem and informing consumers. The problem has slight to moderate effects on the sales, production decisions, marketing decisions, and investment decisions. It has been found that sales and production decisions are affected to a slightly larger extent compared to marketing and investment decisions. Poultry producing companies consider it important to carry out successful information campaigns and increase cooperation in the sector in order to solve information pollution problems.
Tekirdağ İli’nde Tingidae (Hemiptera) Türlerinin Doğal Düşmanları
Authors: AYSAL Tolga , KIVAN Müjgan
Published: May 2023

Bu çalışma Tekirdağ İli’nde Malkara, Saray, Süleymanpaşa ve Şarköy ilçelerinde Tingidae familyası türlerinin doğal düşmanları ve yayılışlarını saptamak amacıyla yürütülmüştür. Sörveyler 2011-2012 yıllarında odunsu bitkiler üzerinde yapılmıştır. Arazi çıkışları Nisan ayı başı-Ekim ayı sonu arasında, 10 gün aralıklarla gerçekleştirilmiştir. Örneklemelerde darbe ve gözle kontrol yöntemleri kullanılmıştır. Sörveyler sonucunda, Tingidae familyası türlerinin doğal düşmanı olarak; Coleoptera takımı Coccinellidae familyasından; Coccinella septempunctata (Linnaeus, 1758), Exochomus quadripustulatus (Linnaeus, 1758), Oenopia conglobata (Linnaeus, 1758), Stethorus gilvifrons (Mulsant, 1850), Hemiptera takımı Anthocoridae familyasından; Anthocoris nemoralis (Fabricius, 1794), Orius niger (Wolff, 1811), Orius vicinus (Ribaut, 1923), Miridae familyasından; Deraeocoris lutescens (Schilling, 1837), Stethoconus pyri (Mella, 1869) ve Neuroptera takımı Chrysopidae familyasından; Chrysoperla carnea (Stephens, 1836) olmak üzere toplam 10 predatör tür saptanmıştır. Hymenoptera takımı Mymaridae familyasından ise Erythmelus panis (Enock, 1909) türü yumurta parazitoiti olarak tespit edilmiştir. Tekirdağ genelinde en çok bulunan tür S. pyri olmuştur. Bu türü C. septempuctata takip etmiştir. İlde en az bulunan türlerin ise sırasıyla A. nemoralis ve S. gilvifrons olduğu saptanmıştır. Doğal düşmanların yayılışlarının da bulunma oranlarıyla hemen hemen benzer olduğu belirlenmiştir. İlde bulunan tüm doğal düşmanların Stephanitis pyri (Fabricius, 1775) (Armut kaplanı) ile beslendiği tespit edilmiştir. O. conglobata’nın Armut kaplanı dışında Monosteira unicostata (Mulsant ve Rey, 1852) ile; A. nemoralis, O. niger ve O. vicinus’un da Corythuca ciliata (Say, 1832) ile beslendiği kaydedilmiştir. Tespit edilen doğal düşmanların birçoğu Tekirdağ faunası için ilk kayıttır. Bu türler içerisinde, yapılan gözlemler ve el edilen bulgulara göre; Armut kaplanı ile beslenen S. pyri ve C. ciliata ile beslenen Orius türlerinin diğer doğal düşmanlara göre daha önemli olduğu düşünülmektedir. Bu nedenle ileriye yönelik çalışmalarda, öncelikle bahsi geçen bu türlerin laboratuvar ve/veya arazi koşullarında biyolojileri ve etkinliklerinin araştırılması daha uygun olacaktır.
Sentiment Analysis of Sentence-Level using Dependency Embedding and Pre-trained BERT Model
Authors: Ruskanda Fariska Zakhralativa , Setiawan Stefanus Stanley Yoga , Aditama Nadya , Khodra Masayu Leylia
Published: May 2023

Sentiment analysis is a valuable field of research in NLP with many applications. Dependency tree is one of the language features that can be utilized in this field. Dependency embedding, as one of the semantic representations of a sentence, has shown to provide more significant results compared to other embeddings, which makes it a potential way to improve the performance of sentiment analysis tasks. This study aimed to investigate the effect of dependency embedding on sentence-level sentiment analysis through experimental research. The study replaced the Vocabulary Graph embedding in the VGCN-BERT sentiment classification system architecture with several dependency embedding representations, including word vector, context vector, average of word and context vectors, weighting on word and context vectors, and merging of word and context vectors. The experiments were conducted on two datasets, SST-2 and CoLA, with more than 19 thousand labeled sentiment sentences. The results indicated that dependency embedding can enhance the performance of sentiment analysis at the sentence level.
Kitap İncelemesi (Metodolojik Bireyciliğin Eleştirisi)
Authors: İNCE Abdulkadir
Published: May 2023

Bu çalışmada Prof. Dr. Vefa Saygın Öğütle’nin ilk basımı 2013 yılında Ayrıntı Yayınları tarafından yapılan Metodolojik Bireyciliğin Eleştirisi adlı kitabının tanıtımı hedeflenmektedir.
Distance Education and Professional Perspectives of Nursing Students with the COVID-19 Pandemic
Authors: ŞARA Yasemin , BEKMEZCİ Ebru
Published: May 2023

Aim: The implementation of nursing education with a distance education model and the aggravation of the working conditions in the clinic may affect the professional point of view of student nurses during COVID-19 pandemic. Thus, this study was conducted with a qualitative research design to investigate the reflections of COVID-19 on the distance education and professional perspective of undergraduate senior nursing students.

Material and Methods: This research was conducted with a qualitative research design based on the phenomenological approach. The sample size was determined according to data saturation, and data were collected from 20 nursing senior-level undergraduate students. The research data were collected using the Semi-Structured Qualitative Data Form prepared by the researchers. Researchers used the Colaizzi method in data analysis. The data regarding the interviews were transcribed by both researchers separately MAXQDA 11.0 qualitative data analysis software was used, and the codes, themes, and categories were determined.

Results: The themes determined from the reflections of the senior level undergraduate nursing students on distance education and professional perspectives are [1] emotional states, [2] educational life, [3] occupational readiness, and [4] opinions about the nursing profession.

Conclusion: Our study provides a deep insight into the professional perceptions, feelings, opinions, distance education experiences, and professional perspectives of distance education nursing students who will graduate during the COVID-19 pandemic. The data obtained in the present study will help nursing students identify the areas of need related to professional readiness and the difficulties in their education.
Estimation of Birth Weight from HbA1c and Glucose Levels in Diabetic Pregnancies
Authors: SUMAN Kamuran , GÖK Ebru , BÜTÜN Zafer , BÜTÜN Pınar , BÜYÜK Musa , SUMAN Murat
Published: May 2023

Aim: The aim of this study was to investigate the sensitivity of baby birth weight estimation in relation to HbA1c levels of pregnant women diagnosed with pre-gestational diabetes mellitus (PGDM) and gestational diabetes mellitus (GDM).

Material and Methods: 105 patients who met the criteria agreed to participate in our study, of whom 7 were type 1 DM and 32 were type 2 DM. The pregnancy history of the patients who agreed to participate was obtained with a lot of demographic information as well as weight gains during pregnancy, HbA1c and fasting blood glucose levels.

Results: Fasting glucose values were measured at 28 and 32 weeks of gestation. The blood glucose values that we measured one hour after satiation and HbA1c were higher in the PDGM group than in the GDM group. There was no significant difference between weight gain and BMI values. We used ROC curve analysis to test the predictive power of fasting and postprandial blood glucose levels or weight gain during pregnancy in our patients with GDM for LGA babies(LGA) (AUC: 0.663, %95 CI [0.526, 0.800], AUC: 0.678, %95 CI [0.540, 0.816], AUC: 0.677, %95 CI [0.548, 0.805], respectively).In addition, ROC analysis was used in evaluating fasting blood glucose measurements, 1-hour postprandial blood glucose measurements, and HbA1c levels to predict LGA.(AUC: 0.889, %95 CI [0.782, 0.996], AUC: 0.893, %95 CI [0.737, 1.000], AUC:0.931, %95 CI [0.807, 1.000], respectively).

Conclusion: In both healthy people and pregnant women, it is important to keep blood glucose levels within normal limits. In pregnant women diagnosed with PDGM or GDM, this is even more important as the welfare of the baby is considered. LGA deliveries can be avoided in pregnant women with PDGM by close monitoring of postprandial blood glucose and HbA1c levels. Close monitoring of GWG is also beneficial in the follow-up of pregnant women diagnosed with GDM.
Evaluation of Cerebrospinal Fluid Results in Patients Presenting with a Prediagnosis of Meningitis
Authors: AKYÜZ ÖZKAN Esra , TANRIVERDİ ÇAYCI Yeliz
Published: May 2023

Aim: It was aimed to determine the microorganisms and antibiotic susceptibilities obtained from cerebrospinal fluid samples (CSF).

Material and Methods: CSF samples of 138 patients who admitted with a prediagnosis of meningitis to Ondokuz Mayıs University Pediatric Emergency Department between 01/01/2021-01/01/2022 was included. CSF cultures, identification of bacteria and their antibiotic susceptibilities were evaluated by VITEK 2 (bioMeriux, France) automated identification system. If the growth was detected by blood culture system, the specimen was cultivated onto the 5% blood agar, Eosin Methylene Blue agar and chocolate agar. Also, CSF samples were studied for both viral and bacterial agents with the Smart Cycler (Cepheid, USA) device working with Real-Time PCR method. In this system, Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae, Cytomegalovirus, Herpes simplex type-1, Herpes simplex type-2, Human herpes virus type-6 (HHV-6), Varicella zoster virus and Epstein Barr virus agents were detected.

Results: Of the 138 CSF samples, 50,88% were male and 49,12% were female. The mean age of the patients was 36 ± 55 months. Bacterial agents were detected in 18 (13,8%) of the CSF samples and viral agents in 12 (9,2%) samples. Staphylococcus epidermidis (64.6%), Staphylococcus aureus (7.7%) and Streptococcus pneumonia (6.9%) took the first three places in bacterial agents. Among the viral agents, HHV-6 was the most common followed by Enteroviruses.

Conclusion: It has been observed that the profiles and resistance status of microorganisms frequently seen in CSF have changed over the years.
Wiskott Aldrich Sendromu: Kısa Derleme
Authors: DİKİCİ Ümmügülsüm , ÖZDEMİR Öner
Published: May 2023

Wiskott Aldrich Sendromu (WAS) X’e bağlı resesif kalıtılan, nadir görülen genetik bir hastalıktır. WAS proteini (WASp) genindeki mutasyondan kaynaklanmaktadır. WAS proteini aktin hücre iskeleti organizasyonu ve sinyalizasyonunda rol oynar, bunun yanında bağışıklık sistemi hücrelerinin işlevlerinde kritik bir rol sahibidir. Hastalığın karakteristik klinik triadı mikrotrombositopeni, egzama ve immun yetmezliktir. Hastaların kliniği WASP mutasyonunun tipine göre şiddetli fenotipten (klasik WAS) daha hafif olanlara (X'e bağlı trombositopeni (XLT) ve X'e bağlı nötropeni) kadar değişiklik göstermektedir. WAS hastalarında bakteriyal, fungal ve viral enfeksiyonlara yatkınlıkla beraber, otoimmun hastalık (otoimmun hemolitik anemi, vaskülit, inflamatuar barsak hastalığı) ve malignite (özellikle lenfoma) riski artmıştır. WAS hastalarında tedavi yönetimi, klinik fenotipe göre bireyselleştirilmelidir. Enfeksiyonlara yönelik profilaktik antibiyoterapi ve intravenöz immünoglobulin replasman tedavisi uygulanmaktadır. Allojenik hematopoietik kök hücre nakli ise WAS'lı hastalar için altta yatan immün yetmezlik ve trombositopeninin düzeltilmesini sağlayan altın standart tedavidir. Son zamanlarda hematopoietik kök hücre gen tedavisi de potansiyel terapötik strateji olarak gündeme gelmiştir. Otolog gen tedavisi, allojenik kök hücre nakli için donörü olmayan hastalara umut verici bir alternatif olarak görünmektedir.
Dossiês temáticos publicados em periódicos acadêmicos brasileiros da área de Música (2016-2020)
Authors: Pereira Torres Borges Renato
Published: May 2023

Este artigo apresenta uma compilação dos 87 dossiês temáticos publicados entre 2016 e 2020 em 27 revistas acadêmicas de Música do Brasil e considerações a respeito desta produção e de suas condições de visibilidade. Foram analisadas as capas, editoriais, sites, itens e sumários de 187 edições para identificar os dossiês. Como principais resultados, destacam-se uma organização esquemática dos 87 dossiês em 7 categorias, a grande variedade temática dos dossiês, o papel de periódicos de Programas de Pós-Graduação nas discussões sobre questões estruturais da área e a necessidade de compatibilização de inconsistências nas publicações. Estima-se que estas observações ofereçam subsídios para editores em suas decisões e que a compilação apresentada seja ferramenta básica de pesquisa para qualquer pesquisador da área de Música.
Microneedle patches containing mesoporous polydopamine nanoparticles loaded with triamcinolone acetonide for the treatment of oral mucositis
Authors: Qu Xiaoying , Guo Xiaoli , Zhu Tingting , Zhang Zhe , Wang Wanchun , Hao Yuanping
Published: May 2023

Oral mucositis (OM) is the most common disease of the oral mucosa, which affects people’s daily production and life. Triamcinolone ointment is the common clinical drug for OM treatment. However, the hydrophobic properties of triamcinolone acetonide (TA) and the complex microenvironment of the oral cavity led to its low bioavailability and unstable therapeutic effects on ulcer wounds. Herein, dissolving microneedle patches (MNs) composed of mesoporous polydopamine nanoparticles (MPDA) loaded with TA (TA@MPDA), sodium hyaluronic acid (HA), and Bletilla striata polysaccharide (BSP) are prepared as the transmucosal delivery system. The prepared TA@MPDA-HA/BSP MNs exhibit well-arranged microarrays, high mechanical strength and fast solubility (<3 min) properties. In addition, the hybrid structure improves the biocompatibility of TA@MPDA and expedites oral ulcer healing in the SD rat model through the synergistic anti-inflammatory and pro-healing effects of microneedle ingredients (hormones, MPDA and Chinese herbs extracts), with 90% less amount of TA compared with Ning Zhi Zhu®. TA@MPDA-HA/BSP MNs are shown to be their great potential as novel ulcer dressings for OM management.
Fused multi-modal similarity network as prior in guiding brain imaging genetic association
Authors: He Bing , Xie Linhui , Varathan Pradeep , Nho Kwangsik , Risacher Shannon L. , Saykin Andrew J. , Yan Jingwen ,   The Alzheimer's Disease Neuroimaging Initiative
Published: May 2023

Introduction

Brain imaging genetics aims to explore the genetic architecture underlying brain structure and functions. Recent studies showed that the incorporation of prior knowledge, such as subject diagnosis information and brain regional correlation, can help identify significantly stronger imaging genetic associations. However, sometimes such information may be incomplete or even unavailable.

Methods

In this study, we explore a new data-driven prior knowledge that captures the subject-level similarity by fusing multi-modal similarity networks. It was incorporated into the sparse canonical correlation analysis (SCCA) model, which is aimed to identify a small set of brain imaging and genetic markers that explain the similarity matrix supported by both modalities. It was applied to amyloid and tau imaging data of the ADNI cohort, respectively.

Results

Fused similarity matrix across imaging and genetic data was found to improve the association performance better or similarly well as diagnosis information, and therefore would be a potential substitute prior when the diagnosis information is not available (i.e., studies focused on healthy controls).

Discussion

Our result confirmed the value of all types of prior knowledge in improving association identification. In addition, the fused network representing the subject relationship supported by multi-modal data showed consistently the best or equally best performance compared to the diagnosis network and the co-expression network.
Remnant cholesterol, stronger than triglycerides, is associated with incident non-alcoholic fatty liver disease
Authors: Cheng Yiping , Zhang Qiang , Li Haizhen , Zhou Guangshuai , Shi Ping , Zhang Xu , Guan Liying , Yan Fang , Xu Chao
Published: May 2023

Introduction

Non-alcoholic fatty liver disease (NAFLD) is characterized by excess accumulation of triglycerides within the liver. However, whether the circulating levels of triglycerides and cholesterol transported in triglyceride-rich lipoproteins (remnant cholesterol, remnant-C) are related to the occurrence of NAFLD has not yet been studied. This study aims to assess the association of triglycerides and remnant-C with NAFLD in a Chinese cohort of middle aged and elderly individuals.

Methods

All subjects in the current study are from the 13,876 individuals who recruited in the Shandong cohort of the REACTION study. We included 6,634 participants who had more than one visit during the study period with an average follow-up time of 43.34 months. The association between lipid concentrations and incident NAFLD were evaluated by unadjusted and adjusted Cox proportional hazard models. The potential confounders were adjusted in the models including age, sex, hip circumference (HC), body mass index (BMI), systolic blood pressure, diastolic blood pressure, fasting plasma glucose (FPG), diabetes status and cardiovascular disease (CVD) status.

Results

In multivariable-adjusted Cox proportional hazard model analyses, triglycerides (hazard ratio[HR], 95% confidence interval [CI]:1.080,1.047-1.113;p<0.001), high-density lipoprotein cholesterol (HDL-C) (HR, 95% CI: 0.571,0.487-0.670; p<0.001), and remnant-C (HR, 95% CI: 1.143,1.052-1.242; p=0.002), but not total cholesterol (TC) or low-density lipoprotein cholesterol (LDL-C), were associated with incident NAFLD. Atherogenic dyslipidemia (triglycerides>1.69 mmol/L, HDL-C<1.03 mmol/L in men or<1.29 mmol/L in women) was also associated with NAFLD (HR, 95% CI: 1.343,1.177-1.533; p<0.001). Remnant-C levels were higher in females than in males and increased with increasing BMI and in participants with diabetes and CVD compared with those without diabetes or CVD. After adjusting for other factors in the Cox regression models, we found that serum levels of TG and remnant-C, but not TC or LDL-C, were associated with NAFLD outcomes in women group, non-cardiovascular disease status, non-diabetes status and middle BMI categories (24 to 28 kg/m2).

Discussion

In the middle aged and elderly subset of the Chinese population, especially those who were women, non-CVD status, non-diabetes status and middle BMI status (24 to 28 kg/m2), levels of triglycerides and remnant-C, but not TC or LDL-C, were associated with NAFLD outcomes independent of other risk factors.
Baseline level and change trajectory of the triglyceride-glucose index in relation to the development of NAFLD: a large population-based cohort study
Authors: Wang Yaqin , Wang Jiangang , Liu Lei , Yang Pingting , Deng Shuwen , Liu Xuelian , Zhao Linlin , Wang Changfa , Li Ying
Published: May 2023

Background

Insulin resistance (IR) and nonalcoholic fatty liver disease (NAFLD) are closely related. The triglyceride-glucose index (TyG index) has been proposed as a new indicator of IR. It remains unclear whether the triglyceride-glucose (TyG) index is prospectively associated with incident nonalcoholic fatty liver disease (NAFLD).

Methods

This large-scale study comprised 1 prospective cohort totaling 22,758 subjects without NAFLD at baseline who underwent repeated health examinations and 1 subcohort totaling 7,722 subjects with more than three visits. The TyG index was ascertained mathematically by ln (fasting triglycerides [mg/dL] × fasting glucose [mg/dL]/2). NAFLD was diagnosed by ultrasound without other concomitant liver diseases. A combinatorial Cox proportional hazard model and latent class growth mixture modeling method were used to identify the association of the TyG index and its transition trajectories with NAFLD risk.

Results

During 53,481 person-years of follow-up, there were 5319 incident cases with NAFLD. Compared with those in the lowest quartile of the baseline TyG index, participants in the highest quartile had 2.52-fold (95% confidence interval, 2.21–2.86) higher odds of incident NAFLD. Similarly, restricted cubic spline analysis showed a dose–response relationship (p nonlinearity<0.001). Subgroup analyses showed a more significant association in the female and normal body size populations (p for interaction<0.001). Three distinct trajectories of changes in the TyG index were identified. Compared with the continued low group, the moderately increasing and highly increasing groups conferred 1.91-fold (1.65–2.21) and 2.19-fold (1.73–2.77) higher NAFLD risk, respectively.

Conclusions

Participants with a higher baseline TyG index or a higher excessive TyG exposure were associated with an increased NAFLD risk. The findings imply that lifestyle interventions and modulation of IR might be considered to both reduce TyG index levels and prevent NAFLD development.
Recurrence and mortality rate in an Italian multi-center case series of parathyroid atypical adenomas and carcinomas
Authors: Barale Marco , Nervo Alice , Craparo Andrea , Pusterla Alessia , Retta Francesca , Maiorino Federica , Castellano Elena , Piovesan Alessandro , Gianotti Laura , Borretta Giorgio , Procopio Massimo , Arvat Emanuela
Published: May 2023

Introduction

There are few data regarding the clinical outcome of patients with parathyroid carcinoma (PC) and atypical adenoma (AA) after surgery. Aim of our study was to investigate disease recurrence and mortality rate as well as their predictors in a series of patients with PC or AA.

Methods

Clinical and biochemical parameters, histological features, incidence of disease recurrence and mortality rate were retrospectively assessed in 39 patients (51% males, mean age 56.2 ± 17.2 years) diagnosed with PC (n=24) or AA (n=15) and followed up for 6.8 ± 5.0 years after surgery.

Results

No differences in baseline characteristics were registered between the two groups, except for higher KI67 values in PC than AA (6.9 ± 3.9% vs 3.4 ± 2.1%, p<0.01). Eight patients (21%) experienced recurrence after a mean follow-up of 5.1 ± 2.7 years, with higher relapse rate in PC than AA (25% vs 13%), though this difference did not reach statistical significance. Mortality rate was 10% in the whole sample, without significant differences between PC and AA. Relapsing cases had been undergone the most extensive surgery more frequently and they had a higher mortality rate in comparison to non relapsing patients (38% vs 6% and 38% vs 3%, respectively, p<0.03 for both). In comparison to survivors, deceased patients were submitted to the most extensive surgery more frequently (50% vs 9%), they were older (74.8 ± 4.6 vs 53.2 ± 16.3 years), and they had higher KI67 values (11.7 ± 4.9 vs 4.8 ± 2.8, p<0.03 for all comparisons).

Conclusions

During seven-year follow-up after surgery, no significant differences in recurrence and mortality rate were observed between PC and AA patients. Death was associated with disease relapse, older age and higher KI67 values. These findings suggest a similar and careful long-term follow-up in both parathyroid tumors, especially in older patients, and emphasize the need of further studies in large cohorts to throw light on this crucial clinical issue.
Effects of urbanization, biotic and abiotic factors on aquatic insect diversity in urban ponds
Authors: Keinath Silvia , Onandia Gabriela , Griesbaum Frederic , Rödel Mark-Oliver
Published: May 2023

Urbanization leads to drastic modifications of the terrestrial and aquatic environment. However, urban ponds may provide valuable habitats for different taxa, including aquatic insects and amphibians. We aim to understand how a set of biotic and abiotic factors influence aquatic insect diversity in 18 urban ponds in the German metropolis Berlin, one of the greenest whilst most densely populated European cities. Greenspace is important for the terrestrial stages of some aquatic insects and amphibians, providing crucial resources. Thus, greenspace was assumed to have positive effects on aquatic insect diversity, whereas built-up area was assumed to affect diversity negatively. Because some aquatic insects prey on tadpoles, their abundance and diversity were assumed to depend on tadpole abundance, which in turn, depends on other food (i.e., phytoplankton) availability in ponds. We visited the ponds twice a year, in spring and summer, and collected data on aquatic insects that are known to prey on tadpoles, tadpole abundance, phytoplankton biomass, the presence or absence of large insect predators, as well as physical–chemical parameters. We assumed higher total aquatic insect abundance, genera richness, alpha-diversity, and evenness, as well as abundance and genera richness of different aquatic insect taxonomic groups to be associated with high tadpole abundance in ponds surrounded by high amount of greenspace and low levels of built-up area. Accordingly, we expected aquatic insects to be modulated by phytoplankton biomass, the presence of newts and fish, and to be affected by ponds’ abiotic conditions. Our results showed that biological interactions and abiotic water conditions override urban effects in ponds’ terrestrial surroundings on aquatic insect diversity levels, whereas aquatic insects’ taxonomic groups responded differently on different land-use types around ponds. We explain our findings due to different dependences and demands towards terrestrial and/or aquatic habitats by different taxonomic groups of aquatic insects, and differences in their colonization behavior.
Impact of landscape configuration and composition on pollinator communities across different European biogeographic regions
Authors: Bottero Irene , Dominik Christophe , Schweiger Olivier , Albrecht Matthias , Attridge Eleanor , Brown Mark J. F. , Cini Elena , Costa Cecilia , De la Rúa Pilar , de Miranda Joachim R. , Di Prisco Gennaro , Dzul Uuh Daniel , Hodge Simon , Ivarsson Kjell , Knauer Anina C. , Klein Alexandra-Maria , Mänd Marika , Martínez-López Vicente , Medrzycki Piotr , Pereira-Peixoto Helena , Potts Simon , Raimets Risto , Rundlöf Maj , Schwarz Janine M. , Senapathi Deepa , Tamburini Giovanni , Talaván Estefanía Tobajas , Stout Jane C.
Published: May 2023

Introduction

Heterogeneity in composition and spatial configuration of landscape elements support diversity and abundance of flower-visiting insects, but this is likely dependent on taxonomic group, spatial scale, weather and climatic conditions, and is particularly impacted by agricultural intensification. Here, we analyzed the impacts of both aspects of landscape heterogeneity and the role of climatic and weather conditions on pollinating insect communities in two economically important mass-flowering crops across Europe.

Methods

Using a standardized approach, we collected data on the abundance of five insect groups (honey bees, bumble bees, other bees, hover flies and butterflies) in eight oilseed rape and eight apple orchard sites (in crops and adjacent crop margins), across eight European countries (128 sites in total) encompassing four biogeographic regions, and quantified habitat heterogeneity by calculating relevant landscape metrics for composition (proportion and diversity of land-use types) and configuration (the aggregation and isolation of land-use patches).

Results

We found that flower-visiting insects responded to landscape and climate parameters in taxon- and crop-specific ways. For example, landscape diversity was positively correlated with honey bee and solitary bee abundance in oilseed rape fields, and hover fly abundance in apple orchards. In apple sites, the total abundance of all pollinators, and particularly bumble bees and solitary bees, decreased with an increasing proportion of orchards in the surrounding landscape. In oilseed rape sites, less-intensively managed habitats (i.e., woodland, grassland, meadows, and hedgerows) positively influenced all pollinators, particularly bumble bees and butterflies. Additionally, our data showed that daily and annual temperature, as well as annual precipitation and precipitation seasonality, affects the abundance of flower-visiting insects, although, again, these impacts appeared to be taxon- or crop-specific.

Discussion

Thus, in the context of global change, our findings emphasize the importance of understanding the role of taxon-specific responses to both changes in land use and climate, to ensure continued delivery of pollination services to pollinator-dependent crops.
Identification of optimal codons and analysis of phylogenetic relationship in Osteochilus salsburyi (Teleostei: Cypriniformes) based on complete mitogenome
Authors: Zhang Cheng , Zhang Shun , Tian Zhe , Wang Danli , Xu Shanliang
Published: May 2023

Introduction

Mitogenomes are frequently used in the study of fish phylogenetic and evolutionary studies. However, there is currently no information available regarding the evolution history ofOsteochilus salsburyi. To address this gap, an experiment was designed to gain a deeper understanding of this species.

Methods

Here, we analyzed the mitochondrial structure, phylogenetic relationship, and optimal codon usage ofO. salsburyibased on complete mitochondrial genome.

Results

The complete mitogenome ofO. salsburyiwas 16,598 bp (GenBank Accession No:MW114837), including 22 tRNAs, 13 PCGs, two rRNAs, and two non-coding regions. The typical clover-leaf secondary structures of all 22 tRNA genes were detected. Moreover, the palindromic motifs TACAT and ATGTA of theD-looptended to form hairpin loop structures, while the second-longest OLregion contained a conserved motif 5’-GCCGG-3’. The relationships amongOsteochilusspecies recovered from same mitochondrial characters were in agreement. The phylogeny based on nucleotide sequences supported the monophyly of the genusOsteochilus. Using the ΔRSCU (Relative Synonymous Codon Usage) method, six optimal codons (ACC, UAC, AAC, UGU, AGC, and GGC) were determined. Furthermore, we estimated the divergence time ofO. salsburyito be 154.06 Mya, during late Jurassic. Based on the maximum likelihood and Bayesian inference methods were used for phylogenetic analyses, and identical topologies were obtained.

Discussion

Ultimately, our results supported that the classification ofO. salsburyias a species of the genusOsteochilus. In this study, the phylogenetic relationships among availableOsteochilusmitogenomes were reported for the first time. This study should help us better understand the evolutionary status and species protection ofO. salsburyi.
Automated clustering reveals CD4+ T cell subset imbalances in rheumatoid arthritis
Authors: Mulhearn Ben , Marshall Lysette , Sutcliffe Megan , Hannes Susan K. , Fonseka Chamith , Hussell Tracy , Raychaudhuri Soumya , Barton Anne , Viatte Sebastien
Published: May 2023

Background

Despite the report of an imbalance between CD4+ T helper (Th) cell subsets in rheumatoid arthritis (RA), patient stratification for precision medicine has been hindered by the discovery of ever more Th cell subsets, as well as contradictory association results.

Objectives

To capture previously reported Th imbalance in RA with deep immunophenotyping techniques; to compare hypothesis-free unsupervised automated clustering with hypothesis-driven conventional biaxial gating and explore if Th cell heterogeneity accounts for conflicting association results.

Methods

Unstimulated and stimulated peripheral blood mononuclear cells from 10 patients with RA and 10 controls were immunophenotyped with a 37-marker panel by mass cytometry (chemokine receptors, intra-cellular cytokines, intra-nuclear transcription factors). First, conventional biaxial gating and standard definitions of Th cell subsets were applied to compare subset frequencies between cases and controls. Second, unsupervised clustering was performed with FlowSOM and analysed using mixed-effects modelling of Associations of Single Cells (MASC).

Results

Conventional analytical techniques fail to identify classical Th subset imbalance, while unsupervised automated clustering, by allowing for unusual marker combinations, identified an imbalance between pro- and anti-inflammatory subsets. For example, a pro-inflammatory Th1-like (IL-2+ T-bet+) subset and an unconventional but pro-inflammatory IL-17+ T-bet+ subset were significantly enriched in RA (odds ratio=5.7, p=2.2 x 10-3; odds ratio=9.7, p=1.5x10-3, respectively). In contrast, a FoxP3+ IL-2+ HLA-DR+ Treg-like subset was reduced in RA (odds ratio=0.1, p=7.7x10-7).

Conclusion

Taking an unbiased approach to large dataset analysis using automated clustering algorithms captures non-canonical CD4+ T cell subset imbalances in RA blood.
Mechanisms of action of monoclonal antibodies in oncology integrated in IMGT/mAb-DB
Authors: Manso Taciana , Kushwaha Anjana , Abdollahi Nika , Duroux Patrice , Giudicelli Véronique , Kossida Sofia
Published: May 2023

Background

Cancer cells activate different immune checkpoint (IC) pathways in order to evade immunosurveillance. Immunotherapies involving ICs either block or stimulate these pathways and enhance the efficiency of the immune system to recognize and attack cancer cells. In this way, the development of monoclonal antibodies (mAbs) targeting ICs has significant success in cancer treatment. Recently, a systematic description of the mechanisms of action (MOA) of the mAbs has been introduced in IMGT/mAb-DB, the IMGT® database dedicated to mAbs for therapeutic applications. The characterization of these antibodies provides a comprehensive understanding of how mAbs work in cancer.

Methods

In depth biocuration taking advantage of the abundant literature data as well as amino acid sequence analyses from mAbs managed in IMGT/2Dstructure-DB, the IMGT® protein database, allowed to define a standardized and consistent description of the MOA of mAbs targeting immune checkpoints in cancer therapy.

Results

A fine description and a standardized graphical representation of the MOA of selected mAbs are integrated within IMGT/mAb-DB highlighting two main mechanisms in cancer immunotherapy, either Blocking or Agonist. In both cases, the mAbs enhance cytotoxic T lymphocyte (CTL)-mediated anti-tumor immune response (Immunostimulant effect) against tumor cells. On the one hand, mAbs targeting co-inhibitory receptors may have a functional Fc region to increase anti-tumor activity by effector properties that deplete Treg cells (Fc-effector function effect) or may have limited FcγR binding to prevent Teff cells depletion and reduce adverse events. On the other hand, agonist mAbs targeting co-stimulatory receptors may bind to FcγRs, resulting in antibody crosslinking (FcγR crosslinking effect) and substantial agonism.

Conclusion

In IMGT/mAb-DB, mAbs for cancer therapy are characterized by their chains, domains and sequence and by several therapeutic metadata, including their MOA. MOAs were recently included as a search criterion to query the database. IMGT® is continuing standardized work to describe the MOA of mAbs targeting additional immune checkpoints and novel molecules in cancer therapy, as well as expanding this study to other clinical domains.
Chromosomal microarray analysis supplements exome sequencing to diagnose children with suspected inborn errors of immunity
Authors: Beers Breanna J. , Similuk Morgan N. , Ghosh Rajarshi , Seifert Bryce A. , Jamal Leila , Kamen Michael , Setzer Michael R. , Jodarski Colleen , Duncan Rylee , Hunt Devin , Mixer Madison , Cao Wenjia , Bi Weimin , Veltri Daniel , Karlins Eric , Zhang Lingwen , Li Zhiwen , Oler Andrew J. , Jevtich Kathleen , Yu Yunting , Hullfish Haley , Bielekova Bibiana , Frischmeyer-Guerrerio Pamela , Dang Do An , Huryn Laryssa A. , Olivier Kenneth N. , Su Helen C. , Lyons Jonathan J. , Zerbe Christa S. , Rao V. Koneti , Keller Michael D. , Freeman Alexandra F. , Holland Steven M. , Franco Luis M. , Walkiewicz Magdalena A. , Yan Jia
Published: May 2023

Purpose

Though copy number variants (CNVs) have been suggested to play a significant role in inborn errors of immunity (IEI), the precise nature of this role remains largely unexplored. We sought to determine the diagnostic contribution of CNVs using genome-wide chromosomal microarray analysis (CMA) in children with IEI.

Methods

We performed exome sequencing (ES) and CMA for 332 unrelated pediatric probands referred for evaluation of IEI. The analysis included primary, secondary, and incidental findings.

Results

Of the 332 probands, 134 (40.4%) received molecular diagnoses. Of these, 116/134 (86.6%) were diagnosed by ES alone. An additional 15/134 (11.2%) were diagnosed by CMA alone, including two likely de novo changes. Three (2.2%) participants had diagnostic molecular findings from both ES and CMA, including two compound heterozygotes and one participant with two distinct diagnoses. Half of the participants with CMA contribution to diagnosis had CNVs in at least one non-immune gene, highlighting the clinical complexity of these cases. Overall, CMA contributed to 18/134 diagnoses (13.4%), increasing the overall diagnostic yield by 15.5% beyond ES alone.

Conclusion

Pairing ES and CMA can provide a comprehensive evaluation to clarify the complex factors that contribute to both immune and non-immune phenotypes. Such a combined approach to genetic testing helps untangle complex phenotypes, not only by clarifying the differential diagnosis, but in some cases by identifying multiple diagnoses contributing to the overall clinical presentation.
The role of E3 ubiquitin ligases and deubiquitinases in bladder cancer development and immunotherapy
Authors: Wang Xuemei , Zhang Ying , Wu Yao , Cheng Hongjing , Wang Xueju
Published: May 2023

Bladder cancer is one of the common malignant urothelial tumors. Post-translational modification (PTMs), including ubiquitination, acetylation, methylation, and phosphorylation, have been revealed to participate in bladder cancer initiation and progression. Ubiquitination is the common PTM, which is conducted by E1 ubiquitin-activating enzyme, E2 ubiquitin-conjugating enzyme and E3 ubiquitin-protein ligase. E3 ubiquitin ligases play a key role in bladder oncogenesis and progression and drug resistance in bladder cancer. Therefore, in this review, we summarize current knowledge regarding the functions of E3 ubiquitin ligases in bladder cancer development. Moreover, we provide the evidence of E3 ubiquitin ligases in regulation of immunotherapy in bladder cancer. Furthermore, we mention the multiple compounds that target E3 ubiquitin ligases to improve the therapy efficacy of bladder cancer. We hope our review can stimulate researchers and clinicians to investigate whether and how targeting E3 ubiquitin ligases acts a novel strategy for bladder cancer therapy.
The microbiome of the ice-capped Cayambe Volcanic Complex in Ecuador
Authors: Díaz Magdalena , Monfort-Lanzas Pablo , Quiroz-Moreno Cristian , Rivadeneira Erika , Castillejo Pablo , Arnau Vicente , Díaz Wladimiro , Agathos Spiros N. , Sangari Félix J. , Jarrín-V Pablo , Molina C. Alfonso
Published: May 2023

A major challenge in microbial ecology is to understand the principles and processes by which microbes associate and interact in community assemblages. Microbial communities in mountain glaciers are unique as first colonizers and nutrient enrichment drivers for downstream ecosystems. However, mountain glaciers have been distinctively sensitive to climate perturbations and have suffered a severe retreat over the past 40  years, compelling us to understand glacier ecosystems before their disappearance. This is the first study in an Andean glacier in Ecuador offering insights into the relationship of physicochemical variables and altitude on the diversity and structure of bacterial communities. Our study covered extreme Andean altitudes at the Cayambe Volcanic Complex, from 4,783 to 5,583 masl. Glacier soil and ice samples were used as the source for 16S rRNA gene amplicon libraries. We found (1) effects of altitude on diversity and community structure, (2) the presence of few significantly correlated nutrients to community structure, (3) sharp differences between glacier soil and glacier ice in diversity and community structure, where, as quantified by the Shannon γ-diversity distribution, the meta-community in glacier soil showed more diversity than in glacier ice; this pattern was related to the higher variability of the physicochemical distribution of variables in the former substrate, and (4) significantly abundant genera associated with either high or low altitudes that could serve as biomarkers for studies on climate change. Our results provide the first assessment of these unexplored communities, before their potential disappearance due to glacier retreat and climate change.
Recruitment of the rhizo-microbiome army: assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential
Authors: Park Inmyoung , Seo Young-Su , Mannaa Mohamed
Published: May 2023

The viable community of microorganisms in the rhizosphere significantly impacts the physiological development and vitality of plants. The assembly and functional capacity of the rhizosphere microbiome are greatly influenced by various factors within the rhizosphere. The primary factors are the host plant genotype, developmental stage and status, soil properties, and resident microbiota. These factors drive the composition, dynamics, and activity of the rhizosphere microbiome. This review addresses the intricate interplay between these factors and how it facilitates the recruitment of specific microbes by the host plant to support plant growth and resilience under stress. This review also explores current methods for engineering and manipulating the rhizosphere microbiome, including host plant-mediated manipulation, soil-related methods, and microbe-mediated methods. Advanced techniques to harness the plant's ability to recruit useful microbes and the promising use of rhizo-microbiome transplantation are highlighted. The goal of this review is to provide valuable insights into the current knowledge, which will facilitate the development of cutting-edge strategies for manipulating the rhizosphere microbiome for enhanced plant growth and stress tolerance. The article also indicates promising avenues for future research in this field.
Computational identification of promoters in Klebsiella aerogenes by using support vector machine
Authors: Lin Yan , Sun Meili , Zhang Junjie , Li Mingyan , Yang Keli , Wu Chengyan , Zulfiqar Hasan , Lai Hongyan
Published: May 2023

Promoters are the basic functional cis-elements to which RNA polymerase binds to initiate the process of gene transcription. Comprehensive understanding gene expression and regulation depends on the precise identification of promoters, as they are the most important component of gene expression. This study aimed to develop a machine learning-based model to predict promoters in Klebsiella aerogenes (K. aerogenes). In the prediction model, the promoter sequences in K. aerogenes genome were encoded by pseudo k-tuple nucleotide composition (PseKNC) and position-correlation scoring function (PCSF). Numerical features were obtained and then optimized using mRMR by combining with support vector machine (SVM) and 5-fold cross-validation (CV). Subsequently, these optimized features were inputted into SVM-based classifier to discriminate promoter sequences from non-promoter sequences in K. aerogenes. Results of 10-fold CV showed that the model could yield the overall accuracy of 96.0% and the area under the ROC curve (AUC) of 0.990. We hope that this model will provide help for the study of promoter and gene regulation in K. aerogenes.
Preserved blood-brain barrier and neurovascular coupling in female 5xFAD model of Alzheimer’s disease
Authors: Zhukov Oleg , He Chen , Soylu-Kucharz Rana , Cai Changsi , Lauritzen Andreas D. , Aldana Blanca Irene , Björkqvist Maria , Lauritzen Martin , Kucharz Krzysztof
Published: May 2023

Introduction

Dysfunction of the cerebral vasculature is considered one of the key components of Alzheimer’s disease (AD), but the mechanisms affecting individual brain vessels are poorly understood.

Methods

Here, using in vivo two-photon microscopy in superficial cortical layers and ex vivo imaging across brain regions, we characterized blood–brain barrier (BBB) function and neurovascular coupling (NVC) at the level of individual brain vessels in adult female 5xFAD mice, an aggressive amyloid-β (Aβ) model of AD.

Results

We report a lack of abnormal increase in adsorptive-mediated transcytosis of albumin and preserved paracellular barrier for fibrinogen and small molecules despite an extensive load of Aβ. Likewise, the NVC responses to somatosensory stimulation were preserved at all regulatory segments of the microvasculature: penetrating arterioles, precapillary sphincters, and capillaries. Lastly, the Aβ plaques did not affect the density of capillary pericytes.

Conclusion

Our findings provide direct evidence of preserved microvascular function in the 5xFAD mice and highlight the critical dependence of the experimental outcomes on the choice of preclinical models of AD. We propose that the presence of parenchymal Aβ does not warrant BBB and NVC dysfunction and that the generalized view that microvascular impairment is inherent to Aβ aggregation may need to be revised.