bluuebunny/crossref_metadata_2025_split huggingface dataset:
A case of cryptic diversity in the bat Hsunycteris thomasi (Lonchophyllinae, Chiroptera): New insights into unrecognized species
Authors: Benathar Thayse Cristine Melo , Trevelin Leonardo Carreira , Carneiro Jeferson Costa , Rodrigues Luis Reginaldo Ribeiro , Sampaio Iracilda , O'Brien Patricia Caroline , Ferguson‐Smith Malcolm Andrew , Yangg Fengtang , Nagamachi Cleusa Yoshiko , Pieczarka Julio César 
Published: July 2024

AbstractIntegrating different lines of evidence is currently recognized as the most robust approach to investigating taxonomic questions, particularly those concerning cryptic diversity. In recent years, different sources of evidence have pointed to new cryptic taxa for bats, with the genus Hsunycteris being an excellent study group because of its large karyotypic variability and high genetic divergence revealed by the latest taxonomic and systematic reviews. This study tests the cryptic diversity hypothesis for the Hsunycteris thomasi complex through an integrative approach using species delimitation, phylogenetic analysis, chromosome painting, and linear morphometry. Our results suggest the existence of three lineages for H. thomasi that are morphologically indistinguishable, confirming the two previously described lineages in the literature and adding a third. We argue that the paraphyly in H. thomasi, as reported by previous studies, should be treated as independent species since they have unique evolutionary histories. Finally, we demonstrate that chromosomal and molecular methods are indispensable for recognizing and confirming groups that include cryptic species or species with confusing and controversial taxonomy.
Feeling the Distance: Exploring Novice Student Designers' Perceptions of the Psychological Distance and Empathic Response Toward Variations of a Sustainable Design Problem
Authors: Prabhu Rohan , Herzog Jenna , Fodale Rebekah , Alsager Alzayed Mohammad , Starkey Elizabeth M. 
Published: July 2024

Abstract
Prior research suggests novice designers find it challenging to integrate social context into the engineering design process. This challenge could be particularly pronounced in sustainable design tasks because the effects of climate change are perceived to be psychologically distant, and this distance inhibits active engagement in sustainable behavior. However, most of this work assesses psychological distance as an aggregate of its various subcomponents (e.g., temporal, social, spatial, and hypothetical). Limited research has explored how these individual components vary based on the socio-spatial context of the design problem. Additionally, empathy development could be an effective mechanism to bridge psychological distance. However, little is known about the impact of empathy-focused problem formulation on students' perceptions of these problems. To explore these gaps, we studied students' perceptions of problem formulations in a 2 × 2 factorial between-subjects experiment. The problem formulations varied in (1) their socio-spatial context (i.e., positioned in the United States versus India) and (2) their empathy focus (i.e., with and without a persona). We measured the students' perceptions of the problem formulations using two metrics: (1) perceived psychological distance (i.e., socio-spatial, temporal, and hypothetical) and (2) perceived empathic response. We find that participants reported the problem contextualized in India to be a more immediate threat compared to the same problem set in the United States. Moreover, we find no significant differences in the other components of psychological distance or empathic response between the problem variants. This novel finding suggests that the studied sample perceives certain environmental issues as currently affecting people in other parts of the world, and not themselves, but only from a temporal lens. These findings call for educators to carefully consider temporal framing when using socio-spatially far sustainable design problems as a lack of consideration could create faulty perceptions of environmental issues.
Investigation of Three-Dimensional Wake Width for Offshore Wind Turbines Under Complex Environmental Conditions by Large Eddy Simulation
Authors: Liu Haixiao , Liu Mingqiu , Liang Zhichang 
Published: July 2024

Abstract
The wake of wind turbines is a main concern for offshore wind farms, in which the wake width is a key index and needs to be accurately predicted. However, the existing wake width models have shortcomings in predicting the wake of wind turbines in different offshore environments. In view of this, large eddy simulation (LES) is adopted to simulate offshore wind turbines under various environmental conditions. The analyses show that there are evident differences in wake widths between horizontal and vertical directions. The variations in turbulence intensity and wind speed in the environment have significant effects on the wake width. By fitting the simulation results, a three-dimensional (3D) wake width model is proposed to predict the wake widths in horizontal and vertical directions, which considers the effects of lateral and vertical turbulence intensities on the wake width in different directions, and uses the thrust coefficient to reflect the effect of wind speed. The proposed 3D model is then compared with existing models through test cases, indicating that it is more accurate in predicting wake widths in horizontal and vertical directions under different environmental conditions, meanwhile showing good applicability in complex offshore environments.
Effect of Variable Load on Centralized Dimple in an Opposite Sliding Condition
Authors: Du Hengrui , Wang Jing , Wang Xinqing 
Published: July 2024

Abstract
In ball bearings without a cage, adjacent balls exhibit a zero-entrainment velocity (ZEV) contact condition, which is worse than typical pure rolling or rolling–sliding contact, and the contact between adjacent balls under periodic loading is notably more complicated. In this work, thermal elastohydrodynamic lubrication (EHL) numerical calculation is carried out under the condition of periodic impact and opposite sliding line contact over a wide range of surface speeds. The pressure is solved by a multigrid method, the elastic deformation is evaluated using a multigrid integration method, and the temperature field is calculated by a column-by-column scanning technique. The results show that the loading–unloading process exerts significant influence on the variation of the centralized dimple, pressure, and temperature rises as well as the oil characteristics. With the increase of surface speed, the effect of load fluctuations diminishes, and the central dimple exhibits the following evolutionary trend under ZEV conditions: no dimple at very low velocity—small central dimple—large typical dimple—no dimple at high velocity. The result indicates that under the ZEV condition of EHL stage, elevated velocities decrease the coefficient of friction and augment the film thickness.
Effect of Thermal Conductivity on Maximum Film Pressure in Point Elastohydrodynamic Lubrication Contact of Ceramics With Transverse Surface Roughness
Authors: Kaneta Motohiro 
Published: July 2024

Abstract
Based on a fully flooded transient non-Newtonian thermoelastic fluid lubrication analysis of representative engineering ceramics and steels with different thermal conductivities and surface roughness, it is found that the material combination that causes the reduction of the maximum film pressure is closely related to the thermal conductivity of the contact materials and the surface temperature of the smooth-surfaced materials, and the maximum pressure reduction method is proposed. The results make a significant contribution to the design of mechanical elements involving contact between materials with different thermal conductivities and surface roughness.
Do Motor–Cognitive and Motor–Motor Dual-Task Training Differently Affect Dual-Task Interference in Individuals With Intellectual Disability?
Authors: Borji Rihab , Baccouch Rym , Laatar Rabeb , Falhi Sirine , Sahli Sonia , Rebai Haithem 
Published: July 2024

This study explored the effect of different dual-task (DT) training programs on DT interference in adults with intellectual disability. Center-of-pressure (CoP) mean velocity in single-task (ST) and cognitive-DT conditions and the Timed Up-and-Go Test (TUGT) during ST, cognitive-DT, and motor-DT conditions were assessed before and after intervention in a cognitive–motor training group, a motor–motor training group, and a control group. Before training, CoP mean velocity and TUGT time increased (p < .001) in DT compared with the ST condition. After training, the CoP mean velocity values remained unchanged (p = .07) in DT compared with the ST condition among the cognitive–motor training group. Furthermore, compared with the ST condition, no increase (p = 1) was reported in the TUGT time during the cognitive-DT condition for the cognitive–motor training group and during the motor-DT for the motor–motor training group (p = .12). The effect of DT training on DT interference depends on the training modality.
Self-Reported Performance and Hormonal-Cycle-Related Symptoms in Competitive Female Athletes
Authors: Ihalainen Johanna K. , Takalo Sinikka , Mjøsund Katja , Solli Guro Strøm , Valtonen Maarit , Kokkonen Marja , Hackney Anthony C. , Mikkonen Ritva S. 
Published: July 2024

Introduction: The present scientific consensus is that the menstrual cycle (MC) and hormonal contraceptive (HC) cycle only influence performance trivially. Nevertheless, athletes perceive changes in performance that they associate with different phases of their hormonal cycle. Methods: A total of 959 female athletes completed a questionnaire, of which 750 were included in the present analysis. The questionnaire included questions about demographics and experiences of the MC and HC (symptoms, perceived impact on performance characteristics). Results: In total, 55% of athletes reported a natural MC while 45% reported HC use. Meanwhile, 56% of all athletes reported a decline in perceived performance during the bleeding or inactive phase, whereas 26% of all athletes reported no changes in performance over their hormonal cycle. All athletes reported an average of 10 ± 7 symptoms during hormonal cycles. The naturally menstruating (NM) group reported more symptoms than the HC group (p < .05). The most frequent symptoms reported were abdominal pain, bloating, and mood swings. Only 7% of all athletes (4.1% in NM and 11.3% in HC) reported an absence of any symptoms. Quantity of total symptoms was associated with a perceived decrease in performance (R2 = .138, p < .05). Hormonal cycles had the greatest negative effect on mental performance with 37% reporting a large to very large effect. Conclusions: Perceived negative effects on performance were similar in both NM and HC groups while perceived mental performance (e.g., mood and attention) appeared to be most affected by both MC and HC.
A TrmBL2-like transcription factor mediates the growth phase-dependent expression of halolysin SptA in a concentration-dependent manner in
Natrinema gari
J7-2
Authors: Yin Jing , Liu Yang , He Dan , Li Ping , Qiao Mengting , Luo Hongyi , Qu Xiaoyi , Mei Sha , Wu Yi , Sun Yiqi , Gan Fei , Tang Bing , Tang Xiao-Feng 
Published: July 2024

ABSTRACT

To cope with a high-salinity environment, haloarchaea generally employ the twin-arginine translocation (Tat) pathway to transport secretory proteins across the cytoplasm membrane in a folded state, including Tat-dependent extracellular subtilases (halolysins) capable of autocatalytic activation. Some halolysins, such as SptA of
Natrinema gari
J7-2, are produced at late-log phase to prevent premature enzyme activation and proteolytic damage of cellular proteins in haloarchaea; however, the regulation mechanism for growth phase-dependent expression of halolysins remains largely unknown. In this study, a DNA-protein pull-down assay was performed to identify the proteins binding to the 5′-flanking sequence of
sptA
encoding halolysin SptA in strain J7-2, revealing a TrmBL2-like transcription factor (NgTrmBL2). The Δ
trmBL2
mutant of strain J7-2 showed a sharp decrease in the production of SptA, suggesting that NgTrmBL2 positively regulates
sptA
expression. The purified recombinant NgTrmBL2 mainly existed as a dimer although monomeric and higher-order oligomeric forms were detected by native-PAGE analysis. The results of electrophoretic mobility shift assays (EMSAs) showed that NgTrmBL2 binds to the 5′-flanking sequence of
sptA
in a non-specific and concentration-dependent manner and exhibits an increased DNA-binding affinity with the increase in KCl concentration. Moreover, we found that a distal
cis
-regulatory element embedded in the neighboring upstream gene negatively regulates
trmBL2
expression and thus participates in the growth phase-dependent biosynthesis of halolysin SptA.

IMPORTANCE

Extracellular proteases play important roles in nutrient metabolism, processing of functional proteins, and antagonism of haloarchaea, but no transcription factor involved in regulating the expression of haloaechaeal extracellular protease has been reported yet. Here we report that a TrmBL2-like transcription factor (NgTrmBL2) mediates the growth phase-dependent expression of an extracellular protease, halolysin SptA, of haloarchaeon
Natrinema gari
J7-2. In contrast to its hyperthermophilic archaeal homologs, which are generally considered to be global transcription repressors, NgTrmBL2 functions as a positive regulator for sptA expression. This study provides new clues about the transcriptional regulation mechanism of extracellular protease in haloarchaea and the functional diversity of archaeal TrmBL2.
ROK family regulator NagC promotes prodigiosin biosynthesis independent of
N
-acetylglucosamine in
Serratia
sp. ATCC 39006
Authors: Liu Weijie , Shi Rui , Zhang Ying , Li Chenchen , Zhou Xuge , Jensen Marcus Sepo , Yang Jing , Zhao Siyi , Liu Jiawen , Zhu Jingrong , Liu Cong , Sun Di 
Published: July 2024

ABSTRACT

Serratia
sp. ATCC 39006 is an important model strain for the study of prodigiosin production, whose prodigiosin biosynthesis genes (
pigA-O
) are arranged in an operon. Several transcription factors have been shown to control the transcription of the
pig
operon. However, since the regulation of prodigiosin biosynthesis is complex, the regulatory mechanism for this process has not been well established. In most γ-proteobacteria, the ROK family regulator NagC acts as a global transcription factor in response to
N
-acetylglucosamine (GlcNAc). In
Serratia
sp. ATCC 39006, NagC represses the transcription of two divergent operons,
nagE
and
nagBAC
, which encode proteins involved in the transport and metabolism of GlcNAc. Moreover, NagC directly binds to a 21-nt region that partially overlaps the −10 and −35 regions of the
pig
promoter and promotes the transcription of prodigiosin biosynthesis genes, thereby increasing prodigiosin production. Although NagC still acts as both repressor and activator in
Serratia
sp. ATCC 39006, its transcriptional regulatory activity is independent of GlcNAc. NagC was first found to regulate antibiotic biosynthesis in Gram-negative bacteria, and NagC-mediated regulation is not responsive to GlcNAc, which contributes to future studies on the regulation of secondary metabolism by NagC in other bacteria.

IMPORTANCE
The ROK family transcription factor NagC is an important global regulator in the γ-proteobacteria. A large number of genes involved in the transport and metabolism of sugars, as well as those associated with biofilm formation and pathogenicity, are regulated by NagC. In all of these regulations, the transcriptional regulatory activity of NagC responds to the supply of GlcNAc in the environment. Here, we found for the first time that NagC can regulate antibiotic biosynthesis, whose transcriptional regulatory activity is independent of GlcNAc. This suggests that NagC may respond to more signals and regulate more physiological processes in Gram-negative bacteria.
Expansion of Auxiliary Activity Family 5 sequence space via biochemical characterization of six new copper radical oxidases
Authors: Fong Jessica K. , Mathieu Yann , Vo Minh Tri , Bellemare Annie , Tsang Adrian , Brumer Harry 
Published: July 2024

ABSTRACT

Bacterial and fungal copper radical oxidases (CROs) from Auxiliary Activity Family 5 (AA5) are implicated in morphogenesis and pathogenesis. The unique catalytic properties of CROs also make these enzymes attractive biocatalysts for the transformation of small molecules and biopolymers. Despite a recent increase in the number of characterized AA5 members, especially from subfamily 2 (AA5_2), the catalytic diversity of the family as a whole remains underexplored. In the present study, phylogenetic analysis guided the selection of six AA5_2 members from diverse fungi for recombinant expression in
Komagataella pfaffii
(syn.
Pichia pastoris
) and biochemical characterization
in vitro
. Five of the targets displayed predominant galactose 6-oxidase activity (EC 1.1.3.9), and one was a broad-specificity aryl alcohol oxidase (EC 1.1.3.7) with maximum activity on the platform chemical 5-hydroxymethyl furfural (EC 1.1.3.47). Sequence alignment comparing previously characterized AA5_2 members to those from this study indicated various amino acid substitutions at active site positions implicated in the modulation of specificity.

IMPORTANCE
Enzyme discovery and characterization underpin advances in microbial biology and the application of biocatalysts in industrial processes. On one hand, oxidative processes are central to fungal saprotrophy and pathogenesis. On the other hand, controlled oxidation of small molecules and (bio)polymers valorizes these compounds and introduces versatile functional groups for further modification. The biochemical characterization of six new copper radical oxidases further illuminates the catalytic diversity of these enzymes, which will inform future biological studies and biotechnological applications.
Clostridioides difficile
superoxide reductase mitigates oxygen sensitivity
Authors: Kochanowsky Rebecca , Carothers Katelyn , Roxas Bryan Angelo P. , Anwar Farhan , Viswanathan V. K. , Vedantam Gayatri 
Published: July 2024

ABSTRACT

Clostridioides difficile
causes a serious diarrheal disease and is a common healthcare-associated bacterial pathogen. Although it has a major impact on human health, the mechanistic details of
C. difficile
intestinal colonization remain undefined.
C. difficile
is highly sensitive to oxygen and requires anaerobic conditions for
in vitro
growth. However, the mammalian gut is not devoid of oxygen, and
C. difficile
tolerates moderate oxidative stress
in vivo
. The
C. difficile
genome encodes several antioxidant proteins, including a predicted superoxide reductase (SOR) that is upregulated upon exposure to antimicrobial peptides. The goal of this study was to establish SOR enzymatic activity and assess its role in protecting
C. difficile
against oxygen exposure. Insertional inactivation of
sor
rendered
C. difficile
more sensitive to superoxide, indicating that SOR contributes to antioxidant defense. Heterologous
C. difficile sor
expression in
Escherichia coli
conferred protection against superoxide-dependent growth inhibition, and the corresponding cell lysates showed superoxide scavenging activity. Finally, a
C. difficile
SOR mutant exhibited global proteome changes under oxygen stress when compared to the parent strain. Collectively, our data establish the enzymatic activity of
C. difficile
SOR, confirm its role in protection against oxidative stress, and demonstrate SOR’s broader impacts on the
C. difficile
vegetative cell proteome.

IMPORTANCE

Clostridioides difficile
is an important pathogen strongly associated with healthcare settings and capable of causing severe diarrheal disease. While considered a strict anaerobe
in vitro
,
C. difficile
has been shown to tolerate low levels of oxygen in the mammalian host. Among other well-characterized antioxidant proteins, the
C. difficile
genome encodes a predicted superoxide reductase (SOR), an understudied component of antioxidant defense in pathogens. The significance of the research reported herein is the characterization of SOR’s enzymatic activity, including confirmation of its role in protecting
C. difficile
against oxidative stress. This furthers our understanding of
C. difficile
pathogenesis and presents a potential new avenue for targeted therapies.
Lipidomics of homeoviscous adaptation to low temperatures in
Staphylococcus aureus
utilizing exogenous straight-chain unsaturated fatty acids
Authors: Barbarek Shannon C. , Shah Ritika , Paul Sharanya , Alvarado Gloria , Appala Keerthi , Phillips Caiden , Henderson Emma C. , Strandquist Evan T. , Pokorny Antje , Singh Vineet K. , Gatto Craig , Dahl Jan-Ulrik , Hines Kelly M. , Wilkinson Brian J. 
Published: July 2024

ABSTRACT

It is well established that
Staphylococcus aureus
can incorporate exogenous straight-chain unsaturated fatty acids (SCUFAs) into membrane phospho- and glyco-lipids from various sources in supplemented culture media and when growing
in vivo
during infection. Given the enhancement of membrane fluidity when oleic acid (C18:1Δ9) is incorporated into lipids, we were prompted to examine the effect of medium supplementation with C18:1Δ9 on growth at low temperatures. C18:1Δ9 supported the growth of a cold-sensitive, branched-chain fatty acid (BCFA)-deficient mutant at 12°C. Interestingly, we found similar results in the BCFA-sufficient parental strain, supported by the fact that the incorporation of C18:1Δ9 into the membrane increased membrane fluidity in both strains. We show that the incorporation of C18:1Δ9 and its elongation product C20:1Δ11 into membrane lipids was required for growth stimulation and relied on a functional FakAB incorporation system. Lipidomics analysis of the phosphatidylglycerol and diglycosyldiacylglycerol lipid classes revealed major impacts of C18:1Δ9 and temperature on lipid species. Growth at 12°C in the presence of C18:1Δ9 also led to increased production of the carotenoid pigment staphyloxanthin. The enhancement of growth by C18:1Δ9 is an example of homeoviscous adaptation to low temperatures utilizing an exogenous fatty acid. This may be significant in the growth of
S. aureus
at low temperatures in foods that commonly contain C18:1Δ9 and other SCUFAs in various forms.

IMPORTANCE

We show that
Staphylococcus aureus
can use its known ability to incorporate exogenous fatty acids to enhance its growth at low temperatures. Individual species of phosphatidylglycerols and diglycosyldiacylglycerols bearing one or two degrees of unsaturation derived from the incorporation of C18:1Δ9 at 12°C are described for the first time. In addition, enhanced production of the carotenoid staphyloxanthin occurs at low temperatures. The studies describe a biochemical reality underlying membrane biophysics. This is an example of homeoviscous adaptation to low temperatures utilizing exogenous fatty acids over the regulation of the biosynthesis of endogenous fatty acids. The studies have likely relevance to food safety in that unsaturated fatty acids may enhance the growth of
S. aureus
in the food environment.