bluuebunny/crossref_metadata_2025 huggingface dataset:
A high-throughput 384-well CometChip platform reveals a role for 3-methyladenine in the cellular response to etoposide-induced DNA damage
Authors: Li Jianfeng , Beiser Alison , Dey Nupur B , Takeda Shunichi , Saha Liton Kumar , Hirota Kouji , Parker L Lynette , Carter Mariah , Arrieta Martha I , Sobol Robert W
Published: September 2022

The Comet or single-cell gel electrophoresis assay is a highly sensitive method to measure cellular, nuclear genome damage. However, low throughput can limit its application for large-scale studies. To overcome these limitations, a 96-well CometChip platform was recently developed that increases throughput and reduces variation due to simultaneous processing and automated analysis of 96 samples. To advance throughput further, we developed a 384-well CometChip platform that allows analysis of ∼100 cells per well. The 384-well CometChip extends the capacity by 4-fold as compared to the 96-well system, enhancing application for larger DNA damage analysis studies. The overall sensitivity of the 384-well CometChip is consistent with that of the 96-well system, sensitive to genotoxin exposure and to loss of DNA repair capacity. We then applied the 384-well platform to screen a library of protein kinase inhibitors to probe each as enhancers of etoposide induced DNA damage. Here, we found that 3-methyladenine significantly increased levels of etoposide-induced DNA damage. Our results suggest that a 384-well CometChip is useful for large-scale DNA damage analyses, which may have increased potential in the evaluation of chemotherapy efficacy, compound library screens, population-based analyses of genome damage and evaluating the impact of environmental genotoxins on genome integrity.
Programmed death ligand 1 gene silencing in murine glioma models reveals cell line-specific modulation of tumor growth in vivo
Authors: Blomberg Evelina , Silginer Manuela , Roth Patrick , Weller Michael
Published: September 2022

Background

Glioblastoma is the most common brain tumor in adults and virtually incurable. Therefore, new therapeutic strategies are urgently needed. Immune checkpoint inhibition has not shown activity in various phase III trials and intra- as well as intertumoral expression of programmed death ligand 1 (PD-L1) varies in glioblastoma.

Methods

We abrogated constitutive PD-L1 gene expression by CRISPR/Cas9 in murine glioma models and characterized the consequences of gene deletion in vitro and in vivo.

Results

A heterogeneous expression of Pdl1 mRNA and PD-L1 protein was detected in the glioma cell panel in vitro and in vivo. PD-L1, but not PD-L2, was inducible by interferon β and γ. Co-culture with splenocytes induced PD-L1 expression in GL-261 and SMA-560, but not in CT-2A cells, in an interferon γ-dependent manner. Conversely, Pdl1 gene silencing conferred a survival benefit in CT-2A, but not in the other 2 models. Accordingly, PD-L1 antibody prolonged survival in CT-2A glioma-bearing mice. This activity required PD-L1 expression on tumor rather than host cells, and the survival gain mediated by PD-L1 loss was reproduced in immune-deficient RAG−/− mice.

Conclusions

PD-L1 is expressed and interferon-inducible in murine glioma cell lines. PD-L1 has model-specific roles for tumor growth. Future studies need to determine which subset of glioblastoma patients may benefit from PD-L1 antagonism as part of a multimodality therapeutic approach to glioblastoma.
Effects of nutrition on metabolic and endocrine outcomes in women with polycystic ovary syndrome: an umbrella review of meta-analyses of randomized controlled trials
Authors: Moslehi Nazanin , Zeraattalab-Motlagh Sheida , Rahimi Sakak Fatemeh , Shab-Bidar Sakineh , Tehrani Fahimeh Ramezani , Mirmiran Parvin
Published: September 2022

Context

Numerous meta-analyses have been conducted on the effects of nutritional interventions on various health outcomes in women with polycystic ovary syndrome (PCOS). However, the strength of the evidence and its clinical significance are unclear.

Objective

This umbrella review aimed to summarize the effects of nutritional interventions on women with PCOS and assess the strength of the evidence.

Data Sources

PubMed, Scopus, and Web of Science were searched from inception until March 17, 2021.

Data Extraction

Meta-analyses of randomized clinical trials (RCTs) that examined the impact of dietary modifications or supplementations on women with PCOS were selected. Data extraction, quality assessments of the meta-analyses, and evaluation of the strength of the evidence were conducted independently by 2 investigators and confirmed by a third.

Data Analysis

Twenty-eight RCT meta-analyses were included, reporting 40 different outcomes. Lower carbohydrate, Dietary Approaches to Stop Hypertension, or lower glycemic index/load diets in women with PCOS significantly improved some anthropometric and metabolic characteristics (with very low to low certainty). Probiotics/synbiotics reduced fasting plasma glucose, fasting insulin (FI), and homeostasis model assessment–estimated insulin resistance (HOMA-IR) (with moderate to high certainty). Curcumin supplementation decreased fasting plasma glucose, FI, and HOMA-IR (with moderate certainty). Fish oil supplementation decreased FI and HOMA-IR, and omega-3 reduced triglycerides (with moderate certainty). There were also improvements in FI after taking vitamin D or inositol supplements (with moderate certainty). Supplementation with fish oil increased adiponectin (with high certainty), and probiotics/synbiotics reduced total testosterone (with moderate certainty). In subfertile women with PCOS, inositol increased the ovulation rates (with moderate certainty).

Conclusion

There was no high-certainty evidence that diets alone in women with PCOS improved health or reproductive outcomes. Supplementation with vitamin D, probiotics/synbiotics, omega-3, inositol, and curcumin showed favorable effects on some metabolic outcomes. Probiotics/synbiotics possibly reduces total testosterone, and inositol stimulates ovulation in women with PCOS.

Registration

PROSPERO registration no. CRD42021251496.
Structural basis for proenzyme maturation, substrate recognition, and ligation by a hyperactive peptide asparaginyl ligase
Authors: Hu Side , El Sahili Abbas , Kishore Srujana , Wong Yee Hwa , Hemu Xinya , Goh Boon Chong , Zhipei Sang , Wang Zhen , Tam James P , Liu Chuan-Fa , Lescar Julien
Published: September 2022

Peptide ligases are versatile enzymes that can be utilized for precise protein conjugation for bioengineering applications. Hyperactive peptide asparaginyl ligases (PALs), such as butelase-1, belong to a small class of enzymes from cyclotide-producing plants that can perform site-specific, rapid ligation reactions after a target peptide asparagine/aspartic acid (Asx) residue binds to the active site of the ligase. How PALs specifically recognize their polypeptide substrates has remained elusive, especially at the prime binding side of the enzyme. Here we report crystal structures that capture VyPAL2, a catalytically efficient PAL from Viola yedoensis, in an activated state, with and without a bound substrate. The bound structure shows one ligase with the N-terminal polypeptide tail from another ligase molecule trapped at its active site, revealing how Asx inserts in the enzyme’s S1 pocket and why a hydrophobic residue is required at the P2′ position. Besides illustrating the anchoring role played by P1 and P2′ residues, these results uncover a role for the Gatekeeper residue at the surface of the S2 pocket in shifting the nonprime portion of the substrate and, as a result, the activity toward ligation or hydrolysis. These results suggest a picture for proenzyme maturation in the vacuole and will inform the rational design of peptide ligases with tailored specificities.
Stomatal conductance tracks soil-to-leaf hydraulic conductance in faba bean and maize during soil drying
Authors: Müllers Yannik , Postma Johannes A , Poorter Hendrik , van Dusschoten Dagmar
Published: September 2022

Although regulation of stomatal conductance is widely assumed to be the most important plant response to soil drying, the picture is incomplete when hydraulic conductance from soil to the leaf, upstream of the stomata, is not considered. Here, we investigated to what extent soil drying reduces the conductance between soil and leaf, whether this reduction differs between species, how it affects stomatal regulation, and where in the hydraulic pathway it occurs. To this end, we noninvasively and continuously measured the total root water uptake rate, soil water potential, leaf water potential, and stomatal conductance of 4-week-old, pot-grown maize (Zea mays) and faba bean (Vicia faba) plants during 4 days of water restriction. In both species, the soil–plant conductance, excluding stomatal conductance, declined exponentially with soil drying and was reduced to 50% above a soil water potential of −0.1 MPa, which is far from the permanent wilting point. This loss of conductance has immediate consequences for leaf water potential and the associated stomatal regulation. Both stomatal conductance and soil–plant conductance declined at a higher rate in faba bean than in maize. Estimations of the water potential at the root surface and an incomplete recovery 22 h after rewatering indicate that the loss of conductance, at least partly, occurred inside the plants, for example, through root suberization or altered aquaporin gene expression. Our findings suggest that differences in the stomatal sensitivity among plant species are partly explained by the sensitivity of root hydraulic conductance to soil drying.
The Current Status of Research Mentoring in Nursing Across 4 Countries
Authors: Im Eun-Ok , Wang Hsiu-Hung , Tsai Hsiu-Min , Sakashita Reiko , Oh Eui Geum , Kim Haewon , Chen Ching-Min
Published: September 2022

The purpose of this article is to discuss the current status of research mentoring in nursing across 4 countries (the United States, Taiwan, South Korea, and Japan) and to make suggestions for future research mentoring. Seven leaders reflected on the current status of research mentoring in nursing, provided exemplars/cases from their own experiences, and their reviews of the literature. Six themes were discussed: (a) “culturally defined”; (b) “professionally contextualized”; (c) “teaching research integrity and research practice”; (d) “with mutual respect and care”; (e) “based on effective communication”; and (f) “supported by institutional and governmental commitment and infrastructure.”
Post–Affordable Care Act Improvements in Cancer Stage Among Ohio Medicaid Beneficiaries Resulted From an Increase in Stable Coverage
Authors: Koroukian Siran M. , Dong Weichuan , Albert Jeffrey M. , Kim Uriel , Eom Kirsten y. , Rose Johnie , Owusu Cynthia , Zanotti Kristine M. , Cooper Gregory S. , Tsui Jennifer
Published: September 2022

Background:

The mechanisms underlying improvements in early-stage cancer at diagnosis following Medicaid expansion remain unknown. We hypothesized that Medicaid expansion allowed for low-income adults to enroll in Medicaid before cancer diagnosis, thus increasing the number of stably-enrolled relative to those who enroll in Medicaid only after diagnosis (emergently-enrolled).

Methods:

Using data from the 2011–2017 Ohio Cancer Incidence Surveillance System and Medicaid enrollment files, we identified individuals diagnosed with incident invasive breast (n=4850), cervical (n=1023), and colorectal (n=3363) cancer. We conducted causal mediation analysis to estimate the direct effect of pre- (vs. post-) expansion on being diagnosed with early-stage (-vs. regional-stage and distant-stage) disease, and indirect (mediation) effect through being in the stably- (vs. emergently-) enrolled group, controlling for individual-level and area-level characteristics.

Results:

The percentage of stably-enrolled patients increased from 63.3% to 73.9% post-expansion, while that of the emergently-enrolled decreased from 36.7% to 26.1%. The percentage of patients with early-stage diagnosis remained 1.3–2.9 times higher among the stably than the emergently-enrolled group, both pre-expansion and post-expansion. Results from the causal mediation analysis showed that there was an indirect effect of Medicaid expansion through being in the stably- (vs. emergently-) enrolled group [risk ratios with 95% confidence interval: 1.018 (1.010–1.027) for breast cancer, 1.115 (1.064–1.167) for cervical cancer, and 1.090 (1.062–1.118) for colorectal cancer.

Conclusion:

We provide the first evidence that post-expansion improvements in cancer stage were caused by an increased reliance on Medicaid as a source of stable insurance coverage.
Association Between Clinical Backgrounds and Malignant Progression of Suspected Intraductal Papillary Mucinous Neoplasm
Authors: Fukushima Genki , Abe Kodai , Kitago Minoru , Iwasaki Eisuke , Hirata Aya , Takemura Ryo , Ishii Ryota , Yagi Hiroshi , Abe Yuta , Hasegawa Yasushi , Fukuhara Seiichiro , Hori Shutaro , Tanaka Masayuki , Nakano Yutaka , Yokose Takahiro , Shimane Gaku , Kitagawa Yuko
Published: September 2022

Objectives

Some intraductal papillary mucinous neoplasms (IPMNs) have malignant potential and can become pancreatic cancer. The mechanism behind the malignant progression of IPMN remains unknown. We aimed to identify the risk factors and interactions between backgrounds for IPMN.

Methods

We retrospectively enrolled 980 patients of pancreatic cancer or suspected IPMN (sIPMN) who underwent endoscopic ultrasound or retrograde cholangiopancreatography. We classified them into pancreatic cancer, high-risk sIPMN, and low-risk sIPMN, and investigated the risk factors for high-risk sIPMN.

Results

Smoking habits (odds ratio [OR], 3.74; 95% confidence interval [CI], 2.04–6.85; P < 0.001), serum carbohydrate antigen 19–9 ≥37 U/mL (OR, 6.30; 95% CI, 2.88–13.80; P < 0.001), and family history of cancers (OR, 2.38; 95% CI, 1.30–4.37; P = 0.005) were independent risk factors for high-risk suspected IPMN. Odds ratios of diabetes and neutrophil-to-lymphocyte ratio of 2.45 or greater were significantly higher in patients with a family history of cancer than those without a family history of cancer (OR, 3.28; 95% CI, 0.52–20.80 vs 1.85; 95% CI, 0.78–4.41; OR, 2.44; 95% CI, 0.81–7.34 vs 1.24; 95% CI, 0.67–2.30, respectively).

Conclusions

Understanding the interactions between background factors can effectively prevent IPMNs' malignant transformation.
Pharmacological Ascorbate Enhances Chemotherapies in Pancreatic Ductal Adenocarcinoma
Authors: O'Leary Brianne R. , Ruppenkamp Elena K. , Steers Garett J. , Du Juan , Carroll Rory S. , Wagner Brett A. , Buettner Garry R. , Cullen Joseph J.
Published: September 2022

Objectives

Pharmacological ascorbate (P-AscH−, high-dose, intravenous vitamin C) has shown promise as an adjuvant therapy for pancreatic ductal adenocarcinoma (PDAC) treatment. The objective of this study was to determine the effects of P-AscH− when combined with PDAC chemotherapies.

Methods

Clonogenic survival, combination indices, and DNA damage were determined in human PDAC cell lines treated with P-AscH− in combination with 5-fluorouracil, paclitaxel, or FOLFIRINOX (combination of leucovorin, 5-fluorouracil, irinotecan, oxaliplatin). Tumor volume changes, overall survival, blood analysis, and plasma ascorbate concentration were determined in vivo in mice treated with P-AscH− with or without FOLFIRINOX.

Results

P-AscH− combined with 5-fluorouracil, paclitaxel, or FOLFIRINOX significantly reduced clonogenic survival in vitro. The DNA damage, measured by γH2AX protein expression, was increased after treatment with P-AscH−, FOLFIRINOX, and their combination. In vivo, tumor growth rate was significantly reduced by P-AscH−, FOLFIRINOX, and their combination. Overall survival was significantly increased by the combination of P-AscH− and FOLFIRINOX. Treatment with P-AscH− increased red blood cell and hemoglobin values but had no effect on white blood cell counts. Plasma ascorbate concentrations were significantly elevated in mice treated with P-AscH− with or without FOLFIRINOX.

Conclusions

The addition of P-AscH− to standard of care chemotherapy has the potential to be an effective adjuvant for PDAC treatment.
Prophylaxis of Post–Endoscopic Retrograde Cholangiopancreatography Pancreatitis Using Temporary Pancreatic Stents Versus Rectal Nonsteroidal Anti-inflammatory Drugs
Authors: Koshitani Tatsuya , Konaka Yoshitomo , Ohishi Takashi , Yasuda Tomoyo , Morinushi Tatsuo , Mita Masaki , Masuda Masataka , Nakano Keimei , Fuki Shuichi , Nakagawa Shuji
Published: September 2022

Objectives

Both pancreatic stenting and rectal nonsteroidal anti-inflammatory drugs (NSAIDs) prevent post–endoscopic retrograde cholangiopancreatography (ERCP) pancreatitis. The aim of the study was to compare post-ERCP pancreatitis (PEP) prophylaxis using pancreatic stents and/or rectal NSAIDs prospectively.

Methods

A total of 321 patients undergoing ERCP were studied. Each patient was randomly allocated to receive pancreatic stent placement (PS), 50 mg of rectal diclofenac (NSAID), or both (PS + NSAID) for PEP prophylaxis. The primary outcome was the occurrence rate of PEP, and secondary outcomes included the severity of PEP and serum pancreatic amylase and lipase levels on the day after ERCP.

Results

Five patients (PS: 2/101, NSAID: 1/106, PS + NSAID: 2/102) developed PEP, and the overall occurrence rate of PEP was 1.6% (5/309). The occurrence rates of PEP in the PS, NSAID, and PS + NSAID groups were statistically equivalent with an equivalent margin of 10%. The severity of PEP was mild in all 5 patients. Median serum pancreatic amylase and lipase levels in the NSAID group were significantly lower than those in the PS and PS + NSAID groups.

Conclusions

Rectal administration of 50 mg of diclofenac may become a first-line therapy for PEP prophylaxis in our country.
Effects of Aquatic Physical Therapy in Children With Congenital Femoral Deficiency Who Underwent Bone Lengthening Using an External Fixator: A Case Report
Authors: Castro Caio Roberto Aparecido de Paschoal , Kakihata Alessandra Mitie , Braga Douglas Martins
Published: September 2022

Introduction and Objective:

Congenital femoral deficiency (CFD) is a malformation that affects 0.2 persons per 10,000 live births. The orthopedic treatment proposed for this disease is bone lengthening using an external fixator (EF). During this treatment, reductions in the range of motion (ROM) of the knee, alterations in the gait speed (GS), and worse quality of life (QOL) commonly occur. Therefore, rehabilitation of patients with CFD receiving this treatment is essential. Aquatic physical therapy (APT) is an innovative approach for this population, however, there are no reports on the effects of APT in patients with CFD after bone lengthening. The objective of this study was to assess the influence of APT on the knee ROM, GS, and QOL of 2 children with CFD implanted with an EF.

Case Description:

Two children with right-sided CFD implanted with an EF were selected. They received an APT protocol focusing on balance, muscle activation, analgesia and mobility of the right knee, and gait. The right knee ROM, GS, and QOL were measured using right knee goniometry, a 10-m walk test before and after each session, and the Child Health Questionnaire–Parent Form 50 before and after the protocol.

Results:

An increase in the ROM of the right knee and an improvement in the QOL were observed after the protocol. Only one of the children had an increased GS.

Conclusion:

The APT protocol increased the knee ROM and improved QOL of the 2 children with CFD implanted with an EF.
High Unreported Mortality in Children and Youth (<25 Years) Living With HIV Who Were Lost to Care From Antiretroviral Therapy Programs in Southern Africa: Results From a Multicountry Tracing Study
Authors: Nyakato Patience , Christ Benedikt , Anderegg Nanina , Muhairwe Josephine , Jefferys Laura , van Dijk Janneke , Vinikoor Michael J. , van Lettow Monique , Chimbetete Cleophas , Phiri Sam J. , Egger Matthias , Ballif Marie , Yiannoutsos Constantin T. , Schomaker Michael , Kassanjee Reshma , Davies Mary-Ann , Cornell Morna ,   on behalf of International epidemiology Databases to Evaluate AIDS Southern Africa (IeDEA-SA)
Published: September 2022

Background:

Antiretroviral therapy program mortality maybe underestimated if deceased patients are misclassified as lost.

Methods:

We used two-stage inverse probability weighting to account for probability of being: sampled for tracing and found by the tracer.

Results:

Among 680 children and youth aged <25 years on antiretroviral therapy who were lost and traced in Southern Africa between October 2017 and November 2019, estimated mortality was high at 9.1% (62/680). After adjusting for measured covariates and within-site clustering, mortality remained lower for young adults aged 20–24 years compared with infants aged <2 years [adjusted hazard ratio: 0.40 (95% confidence interval: 0.31 to 0.51)].

Conclusions:

Our study confirms high unreported mortality in children and youth who are lost and the need for tracing to assess vital status among those who are lost to accurately report on program mortality.
Dengue vaccine development: challenges and prospects
Authors: Wilder-Smith Annelies
Published: September 2022

Purpose of review

Dengue vaccine development is a high public health priority. To date, no dengue vaccine is in widespread use. Here we review the challenges in dengue development and the latest results for the second-generation dengue vaccines.

Recent findings

The biggest hurdle is the immunological interaction between the four antigenically distinct dengue serotypes. The advantages of second-generation dengue vaccines are the inclusion of nonstructural proteins of the dengue backbone and a more convenient dosing with reduced numbers of doses needed.

Although dengue-primed individuals can already benefit from vaccination with the first licensed dengue vaccine CYD-TDV, the public health need for the dengue-naive population has not yet been met. The urgent need remains to identify correlates of both protection and enhancement; until such correlates have been identified, all second-generation dengue vaccines still need to go through full phase 3 trials. The 5-year efficacy and safety data for both second-generation dengue vaccines are imminent.
Variability in prey field structure drives inter-annual differences in prey encounter by a marine predator, the little penguin
Authors: Phillips Lachlan R. , Carroll Gemma , Jonsen Ian , Harcourt Robert , Brierley Andrew S. , Wilkins Adam , Cox Martin
Published: September 2022

Understanding how marine predators encounter prey across patchy landscapes remains challenging due to difficulties in measuring the three-dimensional structure of pelagic prey fields at scales relevant to animal movement. We measured at-sea behaviour of a central-place forager, the little penguin (
Eudyptula minor
), over 5 years (2015–2019) using GPS and dive loggers. We made contemporaneous measurements of the prey field within the penguins' foraging range via boat-based acoustic surveys. We developed a prey encounter index by comparing estimates of acoustic prey density encountered along actual penguin tracks to those encountered along simulated penguin tracks with the same characteristics as real tracks but that moved randomly through the prey field. In most years, penguin tracks encountered prey better than simulated random movements greater than 99% of the time, and penguin dive depths matched peaks in the vertical distribution of prey. However, when prey was unusually sparse and/or deep, penguins had worse than random prey encounter indices, exhibited dives that mismatched depth of maximum prey density, and females had abnormally low body mass (5.3% lower than average). Reductions in prey encounters owing to decreases in the density or accessibility of prey may ultimately lead to reduced fitness and population declines in central-place foraging marine predators.
Prosthetic valve endocarditis due to Candida parapsilosis- a rare case report
Authors: Sharma Shivang , Samantaray Subhashree , Kumar Deepak , Meena Durga Shankar , Chaudhary Rahul , Jain Vidhi , Bohra Gopal Krishana , Garg Mahendra Kumar
Published: September 2022

Fungal endocarditis is a rare and fatal condition ,  most frequently caused by   the  Candida  and  Aspergillus  species. Fever and changing heart murmur are the most common clinical manifestations. The diagnosis of fungal endocarditis is challenging, especially that of prosthetic valve endocarditis is extremely difficult. The optimal management of the condition still remains debatable.  We hereby present a case of prosthetic valve endocarditis caused by  Candida parapsilosis , managed empirically with liposomal amphotericin B and later on was shifted to combination therapy with high dose echinocandin and fluconazole, but had a fatal outcome because he could not undergo timely surgical intervention.  Treating  Candida parapsilosis  endocarditis cases are difficult because of their ability of biofilm production on native and prosthetic heart valves. A combined approach consisting of high index of clinical suspicion, early diagnosis by using serological markers followed by culture or PCR and prompt initiation of appropriate antifungals may aid in improving the outcome.
Genome analysis and phenotypic characterization of Halomonas hibernica isolated from a traditional food process with novel quorum quenching and catalase activities
Authors: Woods David F. , Kozak Iwona M. , O'Gara Fergal
Published: September 2022

Traditional food processes can utilize bacteria to promote positive organoleptic qualities and increase shelf life. Wiltshire curing has a vital bacterial component that has not been fully investigated from a microbial perspective. During the investigation of a Wiltshire brine, a culturable novel bacterium of the genusHalomonaswas identified by 16S rRNA gene (MN822133) sequencing and analysis. The isolate was confirmed as representing a novel species (Halomonas hibernicaB1.N12) using a housekeeping (HK) gene phylogenetic tree reconstruction with the selected genes 16S rRNA, 23S rRNA,atpA,gyrB,rpoDandsecA. The genome of the new isolate was sequenced and annotated and comparative genome analysis was conducted. Functional analysis revealed that the isolate has a unique phenotypic signature including high salt tolerance, a wide temperature growth range and substrate metabolism. Phenotypic and biochemical profiling demonstrated thatH. hibernicaB1.N12 possesses strong catalase activity which is an important feature for an industrial food processing bacterium, as it can promote an increased product shelf life and improve organoleptic qualities. Moreover,H. hibernicaexhibits biocontrol properties based on its quorum quenching capabilities. Our work on this novel isolate advances knowledge on potential mechanistic interplays operating in complex microbial communities that mediate traditional food processes.
Effect of storage temperature on the quality parameters of soft and
non-alcoholic malt drinks sold locally in Nigeria
Authors: Akpe Michael Akomaye , Ogbuji Michael Chukwudi , Agwupuye John Akwagiobe
Published: September 2022

To study the effect of storage temperature on the quality requirements of soft
and non-alcoholic malt drinks sold in a local market in Calabar, Nigeria, the
effect of temperature changes on quality parameters was determined at a
temperature range of 30-50°C. The mean values were compared with the
Nigerian Industrial Standards 217:2008 & 290:2013, National Science
Education Standards 2005, and FAO/INFOODS Databases in Nigeria 2018,
respectively. For the soft drink, they revealed that as the temperature
increased from 30 to 50°C, bitterness increased from 1.27 to 1.33 EBU, pH
decreased from 2.99 to 2.78, total acidity increased from 0.014 to 0.030 g/L,
original gravity decreased from 1,041 to 1,032 °Saccharin, ascorbic acid
content decreased from 116.52 to 6.74 mg/L and sugar content decreased from 10.9
to 9.9 mg/L, respectively. For the malt drink, the results revealed that
bitterness increased from 6.6 to 9.7 EBU, pH decreased from 5.0 to 4.52, total
acidity increased from 0.006 to 0.025 g/L, original gravity decreased from 1,055
to 1,045 °Saccharin, ascorbic acid decreased from 441.13 to 87.30 mg/L,
sugar content decreased from 14.0 to 13.4 mg/L, respectively. Alcoholic content
was not detected in both drinks. The results showed that increase in storage
temperature affects the quality parameters and nutritional values of these
drinks linearly with time.
Effect of nano-foamed structure film packaging on the quality of
young radish (Raphanus sativus L.) kimchi
during storage under supercooled and refrigerated conditions
Authors: Kang Miran , Park So Yoon , Shin Bo Sung , Hong Sung Moo , Choi Young Jin , Chun Ho Hyun
Published: September 2022

This study investigated changes in the quality and headspace
O2/CO2 concentrations of young radish
(Raphanus sativus L.) kimchi
(YR-kimchi) packaged using a multilayer (ML) film with or
without sachets containing a CO2 absorber and nano-foamed structure
(NFS) film, respectively, during storage at −2.2 or 4.0°C.
Compared to that in YR-kimchi samples stored at 4.0°C,
the total lactic acid bacteria count and titratable acidity of
YR-kimchi samples stored at −2.2°C increased
rapidly until 21 days of storage, irrespective of the packaging. After 32 days
of storage at 4.0°C, the reducing sugar content of young radish
kimchi packaged in ML film, ML film with a CO2
absorber sachet, and NFS film decreased by 54.9, 80.7, and 79.9%,
respectively, compared to before storage. However, the salinity of
YR-kimchi samples packaged with different film types showed
negligible differences during storage at −2.2 and 4.0°C. No
significant O2 reduction or CO2 accumulation was observed
in the headspace of NFS film-packaged young radish kimchi
stored at either temperature. Hence, these results indicated that NFS film
packaging combined with supercooled (−2.2°C) storage improved the
shelf life of YR-kimchi without packaging expansion during
storage.
Improving effect of domestic walnut (Juglans
regia) extract on high glucose- and oleic acid-induced
non-alcoholic fatty liver disease in HepG2 cells
Authors: Moon Jong Hyun , Joo Seung Gyum , Lee Uk , Kim Jong Min , Kang Jin Yong , Lee Hyo Lim , Kim Min Ji , Jeong Hye Rin , Go Min Ji , Kim Tae Yoon , Heo Ho Jin
Published: September 2022

This study was investigated to evaluate the in vitro
anti-diabetic activity and lipid accumulation inhibitory effect of the domestic
walnut (Junglans regia, Gimcheon 1ho cultivar) in high glucose-
and oleic acid-induced hepatic HepG2 cells. Eighty percent of ethanolic extract
from Gimcheon 1ho (GC) showed higher inhibitory effects against
α-amylase and α-glucosidase
activities when compared to other ethanolic extracts. GC significantly inhibited
the formation of advanced glycation end products (AGEs). The GC increased cell
viability against H2O2- and high glucose-induced cell
death determined by 3-(4,5-dimethyl-thiazol-2-yl)-2,5-diphenyl tetrazolium
bromide (MTT) assay. GC reduced the formation of reactive oxygen species (ROS)
in H2O2- and high glucose-induced HepG2 cells determined
by 2’,7’-dichlorofluorescein diacetate (DCF-DA) assay. GC
inhibited lipid accumulation in the oleic acid-induced HepG2 cells. The GC
increased AMP-activated protein kinase (AMPK) phosphorylation and decreased the
expression of lipid metabolism related proteins such as sterol regulatory
element-binding proteins 1 (SREBP-1), fatty acid synthase (FAS), sterol
regulatory element-binding protein 2 (SREBP-2) and
3-hydroxy-3-methyl-glutaryl-coenzyme A (HMGCR). The results suggest GC is a
potentially functional food material which can improve nonalcoholic fatty liver
disease by inhibiting lipid accumulation.
Mountains as refugia: evidence from bumble bee brain transcriptomes
Authors: Fisher Kaleigh , Duennes Michelle A. , Woodard S. Hollis
Published: September 2022

As anthropogenic change continues to impact global biodiversity, the importance of rapidly identifying biodiversity refugia cannot be overstated. In this study, we employed a molecular test of the hypothesis that mountains serve as refugia for bumble bees against anthropogenic stressors. To explore this hypothesis, we compared stress-related patterns of gene expression in the brains of wild, pollen-foraging bumble bees of two species, B. vosnesenskii and B. melanopygus, collected at different elevations throughout the Sierra Nevada Mountain range in California, USA. We found evidence that the expression of several immune and detoxification genes is associated with elevational differences. This suggests that bees are experiencing differential exposure to stressors along an elevational gradient, which is an important criterion for identifying refugia across dynamic and heterogenous environments. This study thus provides evidence that mountains may serve as refugia for bumble bees in response to anthropogenic stressors, as has been detected for many other organisms.
Modeling cell size regulation under complex and dynamic environments
Authors: Nieto César , Vargas-García César , Pedraza Juan Manuel , Singh Abhyudai
Published: September 2022

In nature, cells face changes in environmental conditions that can modify their growth rate. In these dynamic environments, recent experiments found changes in cell size regulation. Currently, there are few clues about the origin of these cell size changes. In this work, we model cell division as a stochastic process that occurs at a rate proportional to the size. We propose that this rate is zero if the cell is smaller than a minimum size. We show how this model predicts some of the properties found in cell size regulation. For example, among our predictions, we found that the mean cell size is an exponential function of the growth rate under steady conditions. We predict that cells become smaller and the way the division strategy changes during dynamic nutrient depletion. Finally, we use the model to predict cell regulation in an arbitrary complex dynamic environment.
A Programmable Model for Exploring the Functional Logic of the Drosophila Antennal Lobe
Authors: Lazar Aurel A. , Turkcan Mehmet Kerem , Zhou Yiyin
Published: September 2022

Recent progress on connectomics has resulted in huge datasets of brain structures in single-synapse scale. This calls for the modeling of executable circuits to discover the functional logic of these neural circuits in different scales. To provide an approach to standardize analyses of neuropils with multiple-input-multi-output channels, we put forward a programmable model focusing on the antennal lobe (AL), a circuit at the periphery of the olfactory system with nonlinear computation. We present an approach for constructing and analyzing antennal lobe circuits using models of glomeruli and local feedback loops. We establish the composability of the connectivity of glomeruli with local neuron feedback loops by combining pairs of glomeruli, and then by combining all glomeruli together to characterize the I/O of the entire AL. We thus provide a methodology for the quantitative characterization of the I/O of the AL as a function of feedback loop motifs.
Sequence-based Optimized Chaos Game Representation and Deep Learning for Peptide/Protein Classification
Authors: Huang Beibei , Zhang Eric , Chaudhari Rajan , Gimperlein Heiko
Published: September 2022

As an effective graphical representation method for 1D sequence (e.g., text), Chaos Game Representation (CGR) has been frequently combined with deep learning (DL) for biological analysis. In this study, we developed a unique approach to encode peptide/protein sequences into CGR images for classification. To this end, we designed a novel energy function and enhanced the encoder quality by constructing a Supervised Autoencoders (SAE) neural network. CGR was used to represent the amino acid sequences and such representation was optimized based on the latent variables with SAE. To assess the effectiveness of our new representation scheme, we further employed convolutional neural network (CNN) to build models to study hemolytic/non-hemolytic peptides and the susceptibility/resistance of HIV protease mutants to approved drugs. Comparisons were also conducted with other published methods, and our approach demonstrated superior performance.

Supplementary information

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In-situ quality monitoring during embedded bioprinting using integrated microscopy and classical computer vision
Authors: Sergis Vasileios , Kelly Daniel , Britchfield Graham , Pramanick Ankita , Mason Karl , Daly Andrew
Published: September 2022

Despite significant advances in bioprinting technology, current hardware platforms lack the capability for process monitoring and quality control. This limitation hampers the translation of the technology into industrial GMP-compliant manufacturing settings. To address this, we developed a novel bioprinting platform integrating a high-resolution camera for in-situ monitoring of extrusion outcomes during embedded bioprinting. Leveraging classical computer vision and image analysis techniques, we then created a custom software module for assessing print quality. This module enables quantitative comparison of printer outputs to input CAD models, measuring area and positional accuracy. To showcase the platform’s capabilities, we then investigated how the rheological properties of granular support hydrogels impact print quality during embedded bioprinting. Our results demonstrated that lower viscosity, faster thixotropy recovery, and smaller particle sizes significantly enhance print fidelity. This novel bioprinting platform, equipped with integrated process monitoring, holds great potential for establishing robust, reliable, and auditable biofabrication processes for industrial applications.
Regulation of oligodendrocyte lineage development by VAMP2/3 in the developing mouse spinal cord
Authors: Fekete Christopher D. , Horning Robert Z. , Doron Matan S. , Nishiyama Akiko
Published: September 2022

In the developing and adult CNS, new oligodendrocytes (OLs) are generated from a population of cells known as oligodendrocyte precursor cells (OPCs). As they begin to differentiate, OPCs undergo a series of highly regulated changes to morphology, gene expression, and membrane organization. This stage represents a critical bottleneck in oligodendrogenesis, and the regulatory program that guides it is still not fully understood. Here we show thatin vivotoxin-mediated cleavage of the vesicle associated SNARE proteins VAMP2/3 in the OL lineage of both male and female mice impairs the ability of early OLs to mature into functional, myelinating OLs. In the developing mouse spinal cord, many VAMP2/3-deficient OLs appeared to stall in the premyelinating, early OL stage, resulting in an overall loss of both myelin density and OL number. The Src kinase Fyn, a key regulator of oligodendrogenesis and myelination, is highly expressed among premyelinating OLs, but its expression decreases as OLs mature. We found that OLs lacking VAMP2/3 in the spinal cord white matter showed significantly higher expression of Fyn compared to neighboring control cells, potentially due to an extended premyelinating stage. Overall, our results show that functional VAMP2/3 in OL lineage cells is essential for proper myelin formation and plays a major role in controlling the maturation and terminal differentiation of premyelinating OLs.

Significance Statement

The production of mature oligodendrocytes (OLs) is essential for CNS myelination during development, myelin remodeling in adulthood, and remyelination following injury or in demyelinating disease. Prior to myelin sheath formation, newly formed OLs undergo a series of highly regulated changes during a stage of their development known as the premyelinating, or early OL stage. This stage acts as a critical checkpoint in OL development, and much is still unknown about the dynamic regulatory processes involved. In this study, we show that VAMP2/3, SNARE proteins involved in vesicular trafficking and secretion, play an essential role in regulating premyelinating OL development and are required for healthy myelination in the developing mouse spinal cord.
Bull Trout passage at beaver dams in two Montana streams
Authors: Wolf J. Marshall , Clancy Niall G. , Rosenthal Leo R.
Published: September 2022

Beaver (Castor canadensis) translocation and mimicry is an increasingly popular tool for process-based restoration of degraded streams. Processes influenced by beaver restoration include stream-floodplain connectivity, multi-threaded channel formation, enhanced riparian condition and fire resiliency, and streamflow attenuation. Beaver activity can also be a nuisance in agricultural settings, increase invasive species abundance, and create in-stream barriers to fish. Previous studies indicate that spring-spawning salmonid species can pass beaver dams in higher proportions than fall-spawning species. Thus, restoration or mimicry of beavers in streams containing fall-spawning, threatened Bull Trout (Salvelinus confluentus) is of concern to many biologists. We evaluated Bull Trout passage at beaver dams in two Montana streams: Meadow Creek (East Fork Bitterroot River drainage) in summer 2020 and Morrison Creek (Middle Fork Flathead River drainage) from 1997 to 2011. In Meadow Creek, 16% of PIT-tagged Bull Trout which entered a large beaver dam complex were detected upstream of some dams, but no fish moved through the entire 1 km complex. In Morrison Creek, redds were more likely than random to be located below dams, but two or more redds were found upstream of at least one dam in 6 of 9 years dams were present. These results suggest that beaver dams can affect the movement of Bull Trout, but that passage depends on the characteristics of individual dams and reach geomorphology. Our methods cannot distinguish between inhibition of fish movement and selection of beaver-created habitats by fish. Therefore, we suggest future research on beaver restoration in streams with Bull trout.
Drivers of interlineage variability in mitogenomic evolutionary rates in flatworms (Platyhelminthes) are multifactorial
Authors: Jakovlić Ivan , Zou Hong , Ye Tong , Wang Gui-Tang , Li Wen-Xiang , Zhang Dong
Published: September 2022

The forces driving interlineage variability in the evolutionary rates (both sequence and architecture) of mitochondrial genomes are often inconsistent and unpredictable. Herein we studied the impacts of multiple variables using 223 flatworm (Platyhelminthes) species and phylogenetic multilevel regression models. We found that: 1. Mitogenomic sequence evolution is faster in parasites associated with the thermally stable environment of endothermic hosts, but the overall impact of thermic habitat is small; 2. Mitogenome sizes are smaller in parasites of endothermic hosts, but the effects are small and inconsistent; 3. Mitogenomic gene order rearrangements (GORR) are positively correlated with mitogenomic size; 4. The expected positive correlation between GORR and sequence evolution is lineage-specific, and non-parasitic species exhibited a strong negative correlation; 5. Longevity has negligible impacts on mitogenomic evolution; 6. Parasitic (Neodermata) flatworm lineages exhibit higher evolutionary rates than non-parasitic lineages; 7. The effective population size has negligible impacts on mitogenomic evolution; 8. Comparatively, parasitism had by far the greatest impact on the mitogenomic evolution, but due to the monophyletic origin of this life-history strategy, alternative hypotheses cannot be rejected. A large number of factors impact the mitogenomic evolution in flatworms, with lineage-specific relative contributions, which sometimes produces incongruent lineage-specific mitogenomic evolution patterns.
Two-color live-cell STED nanoscopy by click labeling with cell-permeable fluorophores
Authors: Gregor Carola , Grimm Florian , Rehman Jasmin , Wurm Christian A. , Egner Alexander
Published: September 2022

STED nanoscopy allows for the direct observation of dynamic processes in living cells and tissues with diffraction-unlimited resolution. Although fluorescent proteins can be used for STED imaging, these labels are often outperformed in photostability by organic fluorescent dyes. This feature is especially crucial for time-lapse imaging. Unlike fluorescent proteins, organic fluorophores cannot be genetically fused to a target protein but require different labeling strategies. To achieve simultaneous imaging of more than one protein in the interior of the cell with organic fluorophores, bioorthogonal labeling techniques and cell-permeable dyes are required. In addition, the fluorophores should preferentially emit in the red spectral range to reduce potential phototoxic effects that can be induced by the STED light, which further restricts the choice of suitable markers. Here we demonstrate two-color STED imaging of living cells using various pairs of dyes that fulfill all of the above requirements. To this end, we combine click-chemistry-based protein labeling with other orthogonal and highly specific labeling methods, enabling long-term STED imaging of different target structures in living specimens.
Basolateral amygdala astrocytes are engaged by the acquisition and expression of a contextual fear memory
Authors: Suthard Rebecca L. , Senne Ryan A. , Buzharsky Michelle D. , Pyo Angela Y. , Dorst Kaitlyn E. , Diep Anh (Mia) H. , Cole Rebecca H. , Ramirez Steve
Published: September 2022

Astrocytes are key cellular regulators within the brain. The basolateral amygdala (BLA) is implicated in fear memory processing, yet most research has entirely focused on neuronal mechanisms, despite a significant body of work implicating astrocytes in learning and memory. In the present study, we usedin vivofiber photometry to record from amygdalar astrocytes across fear learning, recall, and three separate periods of extinction. We found that BLA astrocytes robustly responded to foot shock during acquisition, that their activity remained remarkably elevated across days in comparison to unshocked control animals, and that their increased activity persisted throughout extinction. Further, we found that astrocytes responded to the initiation and termination of freezing bouts during contextual fear conditioning and recall, and this behavior-locked pattern of activity did not persist throughout the extinction sessions. Importantly, astrocytes do not display these changes while exploring a novel context, suggesting that these observations are context or memory-dependent. Chemogenetic inhibition of fear ensembles in the BLA did not affect freezing behavior or astrocytic calcium dynamics. Overall, our work presents a real-time role for amygdalar astrocytes in fear processing and provides new insight into the emerging role of these cells in cognition and behavior.

Significance Statement

We show that basolateral amygdala astrocytes are robustly responsive to footshock, exhibit unique calcium event characteristics following contextual fear acquisition, and ramp up activity at the initiation and termination of freezing bouts during fear conditioning and recall. This astrocytic calcium response to freezing behavior is not observed during extinction sessions, despite unique calcium events continuing through three days of training compared to no-shock controls. We find that astrocytes display context specific changes in calcium signaling, but chemogenetic inhibition of BLA fear ensembles does not impact freezing behavior or calcium dynamics. These findings show that astrocytes play a key, real-time role in fear learning and memory.