bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biotransformation of protein-rich waste by
Yarrowia lipolytica
IPS21 to high-value products—amino acid supernatants
Authors: Wieczorek Dorota , Gendaszewska Dorota , Miśkiewicz Katarzyna , Słubik Anna , Ławińska Katarzyna 
Published: September 2023

ABSTRACT

The yeast strain
Yarrowia lipolytica
IPS 21 was tested for its ability to degrade potentially toxic chrome-tanned leather shavings (CTLS) in a liquid environment. Biological and chemical parameters were monitored during a 48-h period of biotransformation of the protein-rich waste. CTLS was added at a concentration of 0.1–4% (wt/wt) to a modified YPG medium (15 g L
−1
yeast extract and 5 g L
−1
NaCl). Biodegradation and bioconversion were performed in a one-step process. It was found that the higher degradation rate depended on the activity of the proteases and the pH of the medium, but not on the initial inoculum ratio and the activity of the dehydrogenase. The highest efficiency of the process was obtained for 4% (wt/wt) CTLS on day 2 (degradation rate 58–67%, biomass production 2.11–2.20 g L
−1
, protease activity 312 U mg
−1
protein, and pH 9.20). Our results showed that total chromium was probably not transported across the cytoplasmic membrane of
Y. lipolytica
IPS21 and that chromium (III) was not oxidized to chromium (VI). The phytotoxicity of selected amino acid supernatants [2.5% (vol/vol)] was tested after the bioconversion process. It was found that the supernatants had a stimulating effect on the plants tested. The root elongation was 29–28% higher than that of the reference samples. This result makes
Y. lipolytica
IPS21 a potential candidate for safely converting potentially toxic protein-rich wastes into valuable products without enzyme isolation, e.g., amino acid fertilizers.

IMPORTANCE

Enzyme technologies have the greatest practical relevance to environmental trends. Overcoming the barrier of the high cost of carbon substrates used for biotransformation is the main challenge of these methods. The huge potential of the use of extracellular proteases of
Yarrowia
species or amino acids in various industries indicates the need for the extension of basic research on waste as a carbon source for this yeast. The experiments demonstrated that it is possible to use
Y. lipolytica
IPS21 for bioconversion of chrome-tanned leather shavings (CTLS) in a single-step process and to produce high-value amino acid supernatant without having an isolated enzyme. In our study, we show the effect of 2.5% (vol/vol) CTLS supernatant obtained from
Y. lipolytica
IPS21 on the elongation of the root system of selected plants and provide information on the effect of environmental factors on the efficiency of the bioconversion and the migration of chromium.
ATG9A supports
Chlamydia trachomatis
infection via autophagy-independent mechanisms
Authors: Suzuki Michitaka , Funakoshi Tomoko , Kumagai Keigo , Komatsu Masaaki , Waguri Satoshi 
Published: September 2023

ABSTRACT

Chlamydia trachomatis
infection can be regulated by autophagy-related (
ATG
) genes. Here, we found that the depletion of
ATG9A
, one of the core
ATG
genes, in HeLa cells suppressed
C. trachomatis
growth in the inclusion. The growth was restored by re-expressing
ATG9A
or an
ATG9A
mutant impairing lipid scramblase activity in
ATG9A
-knockout (KO) cells. Moreover, the depletion of lipid transfer proteins ATG2A/B, responsible for isolation membrane expansion together with ATG9A, did not significantly alter the growth, suggesting that the non-autophagic function of ATG9A supports
C. trachomatis
infection.
ATG9A
-KO cells showed no infection-induced redistribution of the Golgi from the perinuclear region to inclusion, which was restored by re-expressing the mutant but not the
ATG9A
mutant lacking an N-terminal adapter protein-binding domain. Re-expression of the N-terminal deletion mutant in
ATG9A
-KO cells did not rescue
C. trachomatis
growth, suggesting the importance of this domain for its growth. Although
ATG9A
-KO cells showed enhanced TBK1 activation, interferon (IFN)-β was not significantly increased, excluding the possibility that upregulation of stimulator of IFN genes (STING) signaling suppressed bacterial growth. Taken together, these findings suggest that the proper trafficking, rather than the isolation membrane expansion function, of ATG9A assists
C. trachomatis
growth in the inclusion.

IMPORTANCE

ATG9A
is an autophagy-related gene that functions during the isolation membrane expansion process to form autophagosomes, but it also has other functions independent of autophagy. In this study, we employed
ATG9A
-deficient HeLa cells and found that the absence of
ATG9A
negatively impacted proliferation of
Chlamydia trachomatis
in inclusions. Furthermore, rescue experiments using
ATG9A
mutants revealed that this action was mediated not by its autophagic function but by its binding ability to clathrin adapter proteins. These findings suggest that the proper trafficking of ATG9A assists
C. trachomatis
growth in the inclusion.
CRISPR-based tools for targeted genetic manipulation in pathogenic
Sporothrix
species
Authors: Hatinguais Remi , Leaves Ian , Brown Gordon D. , Brown Alistair J. P. , Brock Matthias , Peres da Silva Roberta 
Published: September 2023

ABSTRACT

Sporothrix brasiliensis
is an emerging fungal pathogen frequently associated with zoonotic transmission of sporotrichosis by contaminated cats. Within 25 years, the disease has spread not only throughout Brazil but now to neighboring countries in Latin America. Thermo-dimorphism, melanin, glycans, adhesins, and secreted vesicles have been associated with the ability of
Sporothrix
species to cause disease in the mammalian host. Although certain virulence factors have been proposed as potential determinants for sporotrichosis, the scarcity of molecular tools for performing reverse genetics in
Sporothrix
has significantly impeded the dissection of mechanisms underlying the disease. Here, we demonstrate that PEG-mediated protoplast transformation is a powerful method for heterologous gene expression in
S. brasiliensis, S. schenckii,
and
S. chilensis
. Combined with CRISPR/Cas9 gene editing, this transformation protocol enabled the deletion of the putative DHN-melanin synthase gene
pks1
, which is a proposed virulence factor of
Sporothrix
species. To improve
in locus
integration of deletion constructs, we deleted the KU
80
homolog that is critical for non-homologous end-joining DNA repair. The use of Δ
ku80
strains from
S. brasiliensis
enhanced homologous-directed repair during transformation resulting in increased targeted gene deletion in combination with CRISPR/Cas9. In conclusion, our CRISPR/Cas9-based transformation protocol provides an efficient tool for targeted gene manipulation in
Sporothrix
species.

IMPORTANCE

Sporotrichosis caused by
Sporothrix brasiliensis
is a disease that requires long periods of treatment and is rapidly spreading across Latin America. The virulence of this fungus and the surge of atypical and more severe presentations of the disease raise the need for an understanding of the molecular mechanisms underlying sporotrichosis, as well as the development of better diagnostics and antifungal therapies. By developing molecular tools for accurate genetic manipulation in
Sporothrix,
this study addresses the paucity of reliable and reproducible tools for stable genetic engineering of
Sporothrix
species, which has represented a major obstacle for studying the virulence determinants and their roles in the establishment of sporotrichosis.
Neurodevelopmental outcomes at age 3 years after moderate preterm, late preterm and early term birth: the Japan Environment and Children’s Study
Authors: Hirata Katsuya , Ueda Kimiko , Wada Kazuko , Ikehara Satoyo , Tanigawa Kanami , Kimura Tadashi , Ozono Keiichi , Sobue Tomotaka , Iso Hiroyasu 
Published: September 2023

ObjectiveTo assess the association between gestational age classification at birth and the risk of neurodevelopmental impairments at age 3 years.DesignCohort study using the Japan Environment and Children’s Study database.PatientsA total of 86 138 singleton children born without physical abnormalities at 32–41 weeks of gestation enrolled between January 2011 and March 2014.Main outcome measuresNeurodevelopmental impairment, evaluated using the Ages and Stages Questionnaire (third edition).MethodsLogistic regression analysis was used to evaluate the risk of neurodevelopmental impairment in moderate preterm, late preterm and early term children compared with term children after adjusting for socioeconomic and perinatal factors.ResultsThe respective adjusted ORs (95% CIs) of incidence of scores below the cut-off value (<−2.0 SD) at age 3 years for moderate preterm, late preterm and early term births, compared with full-term births, were as follows: communication, 2.40 (1.54 to 3.73), 1.43 (1.19 to 1.72) and 1.11 (1.01 to 1.21); gross motor, 2.55 (1.69 to 3.85), 1.62 (1.36 to 1.93) and 1.20 (1.10 to 1.30); fine motor, 1.93 (1.34 to 2.78), 1.55 (1.35 to 1.77) and 1.08 (1.01 to 1.15); problem solving, 1.80 (1.22 to 2.68), 1.36 (1.19 to 1.56) and 1.07 (1.00 to 1.14) and personal-social, 2.09 (1.29 to 3.40), 1.32 (1.07 to 1.63) and 1.00 (0.91 to 1.11).ConclusionModerate preterm, late preterm and early term births were associated with developmental impairment at age 3 years compared with full-term births, with increasing prematurity. Careful follow-up of non-full-term children by paediatricians and other healthcare providers is necessary for early detection of neurodevelopmental impairment and implementation of available intervention.
Sensitivity, specificity, and diagnostic accuracy of WHO 2013 criteria for diagnosis of gestational diabetes mellitus in low risk early pregnancies: international, prospective, multicentre cohort study
Authors: Huhn Evelyn A , Göbl Christian S , Fischer Thorsten , Todesco Bernasconi Monya , Kreft Martina , Kunze Mirjam , Vogt Deborah R , Dölzlmüller Eva , Jaksch-Bogensperger Heidi , Heldstab Sandra , Eppel Wolfgang , Husslein Peter , Ochsenbein Kölble Nicole , Richter Anne , Bäz Elke , Winzeler Bettina , Hoesli Irene 
Published: September 2023

ObjectiveTo evaluate the predictability of gestational diabetes mellitus wth a 75 g oral glucose tolerance test (OGTT) in early pregnancy, based on the 2013 criteria of the World Health Organization, and to test newly proposed cut-off values.DesignInternational, prospective, multicentre cohort study.SettingSix university or cantonal departments in Austria, Germany, and Switzerland, from 1 May 2016 to 31 January 2019.ParticipantsLow risk cohort of 829 participants aged 18-45 years with singleton pregnancies attending first trimester screening and consenting to have an early 75 g OGTT at 12-15 weeks of gestation. Participants and healthcare providers were blinded to the results.Main outcome measuresFasting, one hour, and two hour plasma glucose concentrations after an early 75 g OGTT (12-15 weeks of gestation) and a late 75 g OGTT (24-28 weeks of gestation).ResultsOf 636 participants, 74 (12%) developed gestational diabetes mellitus, according to World Health Organization 2013 criteria, at 24-28 weeks of gestation. Applying WHO 2013 criteria to the early OGTT with at least one abnormal value gave a low sensitivity of 0.35 (95% confidence interval 0.24 to 0.47), high specificity of 0.96 (0.95 to 0.98), positive predictive value of 0.57 (0.41 to 0.71), negative predictive value of 0.92 (0.89 to 0.94), positive likelihood ratio of 10.46 (6.21 to 17.63), negative likelihood ratio of 0.65 (0.55 to 0.78), and diagnostic odds ratio of 15.98 (8.38 to 30.47). Lowering the postload glucose values (75 g OGTT cut-off values of 5.1, 8.9, and 7.8 mmol/L) improved the detection rate (53%, 95% confidence interval 41% to 64%) and negative predictive value (0.94, 0.91 to 0.95), but decreased the specificity (0.91, 0.88 to 0.93) and positive predictive value (0.42, 0.32 to 0.53) at a false positive rate of 9% (positive likelihood ratio 5.59, 4.0 to 7.81; negative likelihood ratio 0.64, 0.52 to 0.77; and diagnostic odds ratio 10.07, 6.26 to 18.31).ConclusionsThe results of this prospective low risk cohort study indicated that the 75 g OGTT as a screening tool in early pregnancy is not sensitive enough when applying WHO 2013 criteria. Postload glucose values were higher in early pregnancy complicated by diabetes in pregnancy. Lowering the postload cut-off values identified a high risk group for later development of gestational diabetes mellitus or those who might benefit from earlier treatment. Results from randomised controlled trials showing a beneficial effect of early intervention are unclear.Trial registrationClinicalTrials.govNCT02035059.
Recurrence and return to duty following patellar instability events in military personnel
Authors: Abraham Vivek M , Wieschhaus K , Goldman A H , Balazs G C 
Published: September 2023

IntroductionMilitary service members experience patellar dislocations at a rate 10 times that of civilians. The purpose of this study was to determine the return to duty rate of active duty military personnel following first-time or recurrent patellar dislocation. Secondary goals were to identify patient variables and radiographic parameters associated with recurrent instability and requiring medical separation from military service.MethodsThe Military Health System Data Repository was used to identify all active-duty military personnel who sustained a patellar dislocation between 2013 and 2018. Medical records were searched for patient variables including demographics, clinical findings, radiographic findings, treatment, adverse outcomes and military disposition. Patient variables associated with recurrent instability and undergoing medical separation were determined using univariate analysis and multivariate logistic regression. A total of 207 patients met inclusion and exclusion criteria.ResultsFollowing patellar instability event, 30% of the cohort underwent surgical treatment. Fourteen per cent (29 of 207) underwent medical separation from military service. Regardless of treatment, 9% (18 of 207) experienced recurrent dislocation and 3% (6 of 207) experienced recurrent instability without dislocation. On multivariate analysis, none of the studied patient variables were associated with recurrent instability or medical separation.ConclusionsAmong military personnel, return to duty rates are similar to return to sport rates in civilians. This study demonstrates no difference in risk of recurrent instability or medical separation based on anatomical factors, which is useful during shared decision-making regarding treatment options and goals.
Prognostic value of ultrasound tissue characterisation for a recurrence of mid-portion Achilles tendinopathy in military service members: a prospective cohort study
Authors: Paantjens M A , Helmhout P H , Backx F J G , Martens M T A W , Bakker E W P 
Published: September 2023

IntroductionTendon structure in mid-portion Achilles tendinopathy (mid-AT) appears poorly associated with symptoms. Yet, degenerative tendon changes on imaging have been associated with an increased risk of mid-AT. We aimed to investigate the prognostic value of ultrasound tissue characterisation (UTC) for a mid-AT recurrence in service members reporting to be recovered following standard care.MethodsMid-portion aligned fibrillar structure was quantified post-treatment in 37 participants. Recurrences were determined after 1 year of follow-up, based on self-perceived recurrence (yes/no) combined with a decrease in post-treatment Victorian Institute of Sports Assessment–Achilles score of at least the minimal important change of 7 points. Receiver operating characteristic curve analyses were used to determine a threshold for dichotomisation of outcomes for aligned fibrillar structure (normal representation/under-representation). Using multivariable logistic regression, the association between a mid-AT recurrence (yes/no) and the dichotomised aligned fibrillar structure was determined.ResultsEight participants (22%) experienced a recurrence. The threshold for aligned fibrillar structure was set at 73.2% (95% CI: 69.4% to 77.8%) according to Youden’s index. Values below this threshold were significantly associated with a mid-AT recurrence (odds ratio (OR) 9.7, 95% CI: 1.007 to 93.185). The OR for a mid-AT recurrence was 1.1 (95% CI: 1.002 to 1.150) for each additional month of symptom duration. The explained variance of our multivariable logistic regression model was 0.423; symptom duration appeared to be a better predictor than aligned fibrillar structure.ConclusionsThis study identified mid-portion aligned fibrillar structure and symptom duration as potential prognostic factors for a mid-AT recurrence in military service members. The threshold for aligned fibrillar structure of 73.2% can guide preventative interventions (eg, training load adjustments or additional tendon load programmes) aiming to improve tendon structure to minimise the future recurrence risk.Trial registration numberhttps://www.toetsingonline.nl/to/ccmo_search.nsf/Searchform?OpenForm, file number ToetsingOnline NL69527.028.19
Distinguishing between deterministic oscillations and noise
Authors: Rowland Adams Joe , Newman Julian , Stefanovska Aneta 
Published: September 2023

AbstractTime-dependent dynamics is ubiquitous in the natural world and beyond. Effectively analysing its presence in data is essential to our ability to understand the systems from which it is recorded. However, the traditional framework for dynamics analysis is in terms of time-independent dynamical systems and long-term statistics, as opposed to the explicit tracking over time of time-localised dynamical behaviour. We review commonly used analysis techniques based on this traditional statistical framework—such as the autocorrelation function, power-spectral density, and multiscale sample entropy—and contrast to an alternative framework in terms of finite-time dynamics of networks of time-dependent cyclic processes. In time-independent systems, the net effect of a large number of individually intractable contributions may be considered as noise; we show that time-dependent oscillator systems with only a small number of contributions may appear noise-like when analysed according to the traditional framework using power-spectral density estimation. However, methods characteristic of the time-dependent finite-time-dynamics framework, such as the wavelet transform and wavelet bispectrum, are able to identify the determinism and provide crucial information about the analysed system. Finally, we compare these two frameworks for three sets of experimental data. We demonstrate that while techniques based on the traditional framework are unable to reliably detect and understand underlying time-dependent dynamics, the alternative framework identifies deterministic oscillations and interactions.
Al and H incorporation and Al-diffusion in natural rutile and its high-pressure polymorph TiO
2
(II)
Authors: Joachim-Mrosko Bastian , Konzett Jürgen , Ludwig Thomas , Griffiths Thomas , Habler Gerlinde , Libowitzky Eugen , Stalder Roland 
Published: September 2023

Abstract

Rutile is an important accessory mineral in metamorphic rocks and is used as a geothermobarometer or geochronometer. This study aims to bridge the gap between diffusion studies in simplified and complex natural systems by investigating the incorporation and mobility of Al in natural rutile and its high-pressure polymorph TiO
2
(II).

Experiments were performed at 0.1 MPa to 7 GPa, 1223–1373 K, at buffered μ(Al
2
O
3
) and with
f
O
2
constrained to ≤CCO, which is the equilibrium between graphite and a CO-CO
2
gas phase. Based on electron probe microanalysis, secondary ion mass spectrometry and Fourier transform infrared analyses, we suggest a complex combination of mechanisms to explain the incorporation of Al and H in natural rutile and TiO
2
(II). This includes: (1) the incorporation of Al
3+
on octahedral Ti-sites charge balanced by the formation of oxygen vacancies; and (2) the incorporation of oxygen in interstitial positions charge balanced by hydrogen interstitials.

Determined Al-diffusivities in natural TiO
2
are approximately eight to nine orders of magnitude faster compared to previously published data. A possible explanation includes a significantly enhanced rate of ionic diffusion through the combined effect of hydrolytic weakening, enhanced Al-diffusion through extended defects and to a minor extent oxygen fugacity variations. Consequently, results of this study question that the inferred high closure temperatures for the Al-in-rutile geothermobarometer can be applied to all natural systems.
Antimicrobial Therapy as a Risk Factor of Multidrug-Resistant Acinetobacter Infection in COVID-19 Patients Admitted to the Intensive Care Unit
Authors: Mihalov P. , Hodosy J. , Koščálová A. , Čaprnda M. , Kachlíková M. , Jurenka J. , Bendžala M. , Sabaka P. 
Published: September 2023

Background. Multidrug-resistant Acinetobacter (MDR-Ab) is one of the most important pathogens causing superinfections in COVID-19 patients hospitalised in the intensive care unit (ICU). The occurrence of MDR-Ab superinfection significantly impairs the prognosis of patients in the ICU. Overuse of antibiotics in COVID-19 patients might contribute to the risk of developing MDR-Ab infection. Objective. The objective was to assess the role of prior antibiotic exposure as an independent predictor of MDR-Ab infection in COVID-19 patients admitted to the ICU. Methods. We conducted a retrospective cohort study in 90 patients admitted to the ICU of the Department of Infectology and Geographical Medicine, University Hospital in Bratislava, for respiratory failure due to COVID-19 between 1 September 2021 and 31 January 2022 (delta variant predominance). Patients underwent regular microbial screening. Superinfection was defined as infection occurring ≥48 h after admission. We assessed the role of prior antibiotic exposure and other factors as independent predictors of MDR-Ab isolation. Results. Fifty-eight male and 32 female patients were included in the analysis. Multidrug-resistant bacteria were cultured in 43 patients (47.8%), and MDR-Ab was isolated in 37 patients. Thirty-three (36.7%) patients had superinfection caused by MDR-Ab. Fifty-four (60%) patients were exposed to antibiotics prior to MDR-Ab isolation; of those, 35 (64.8%) patients received ceftriaxone. Prior exposure to ceftriaxone (odds ratio (OR) 4.1; 95% confidence interval (CI) 1.4–11.9;

P
<
0.05

), tocilizumab therapy (OR 4.7; 95% CI 1.3–15.0;

P
<

0.05

), and ICU length of stay exceeding 11 days (OR 3.7; 95% CI 1.3–10.3;

P
<

0.05

) were independent predictors of MDR-Ab infection. Conclusions. Prior exposure to ceftriaxone increases the risk of MDR-Ab infection in COVID-19 patients admitted to the ICU. Our findings suggest that antibiotic use in COVID-19 patients admitted to the ICU should be restricted to patients with documented bacterial superinfection.