bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of in vitro histone H3 glycosylation using H3 tail peptides
Authors: Merx Jona , Hintzen Jordi C. J. , Proietti Giordano , Elferink Hidde , Wang Yali , Porzberg Miriam R. B. , Sondag Daan , Bilgin Nurgül , Park Jin , Mecinović Jasmin , Boltje Thomas J. 
Published: November 2022

AbstractPosttranslational modifications (PTMs) on histone tails regulate eukaryotic gene expression by impacting the chromatin structure and by modulating interactions with other cellular proteins. One such PTM has been identified as serine and threonine glycosylation, the introduction of the ß-N-acetylglucosamine (GlcNAc) moiety on histone H3 tail at position Ser10 and Thr32. The addition of the ß-O-GlcNAc moiety on serine or threonine residues is facilitated by the O-GlcNAc transferase (OGT), and can be removed by the action of O-GlcNAcase (OGA). Conflicting reports on histone tail GlcNAc modification in vivo prompted us to investigate whether synthetic histone H3 tail peptides in conjunction with other PTMs are substrates for OGT and OGA in vitro. Our enzymatic assays with recombinantly expressed human OGT revealed that the unmodified and PTM-modified histone H3 tails are not substrates for OGT at both sites, Ser10 and Thr32. In addition, full length histone H3 was not a substrate for OGT. Conversely, our work demonstrates that synthetic peptides containing the GlcNAc functionality at Ser10 are substrates for recombinantly expressed human OGA, yielding deglycosylated histone H3 peptides. We also show that the catalytic domains of human histone lysine methyltransferases G9a, GLP and SETD7 and histone lysine acetyltransferases PCAF and GCN5 do somewhat tolerate glycosylated H3Ser10 close to lysine residues that undergo methylation and acetylation reactions, respectively. Overall, this work indicates that GlcNAcylation of histone H3 tail peptide in the presence of OGT does not occur in vitro.
Impact of molecular sequence data completeness on HIV cluster detection and a network science approach to enhance detection
Authors: Mazrouee Sepideh , Hallmark Camden J. , Mora Ricardo , Del Vecchio Natascha , Carrasco Hernandez Rocio , Carr Michelle , McNeese Marlene , Fujimoto Kayo , Wertheim Joel O. 
Published: November 2022

AbstractDetection of viral transmission clusters using molecular epidemiology is critical to the response pillar of the Ending the HIV Epidemic initiative. Here, we studied whether inference with an incomplete dataset would influence the accuracy of the reconstructed molecular transmission network. We analyzed viral sequence data available from ~ 13,000 individuals with diagnosed HIV (2012–2019) from Houston Health Department surveillance data with 53% completeness (n = 6852 individuals with sequences). We extracted random subsamples and compared the resulting reconstructed networks versus the full-size network. Increasing simulated completeness was associated with an increase in the number of detected clusters. We also subsampled based on the network node influence in the transmission of the virus where we measured Expected Force (ExF) for each node in the network. We simulated the removal of nodes with the highest and then lowest ExF from the full dataset and discovered that 4.7% and 60% of priority clusters were detected respectively. These results highlight the non-uniform impact of capturing high influence nodes in identifying transmission clusters. Although increasing sequence reporting completeness is the way to fully detect HIV transmission patterns, reaching high completeness has remained challenging in the real world. Hence, we suggest taking a network science approach to enhance performance of molecular cluster detection, augmented by node influence information.
Self-charging of sprays
Authors: Kooij Stefan , van Rijn Cees , Ribe Neil , Bonn Daniel 
Published: November 2022

AbstractThe charging of poorly conducting liquids due to flows is a well-known phenomenon, yet the precise charging mechanism is not fully understood. This is especially relevant for sprays, where the spray plume dynamics and maximum distance travelled of a spray dramatically changes for different levels of charging: charging of the droplets makes them repel, thereby preventing drop coalescence and altering the shape of the spray plume. As the charging depends on many factors including the flow and the interactions between the liquid and the nozzle, many models and scaling laws exist in the literature. In this work we focus on perhaps the simplest flow regime, laminar jets created by ultra short channels, and quantify the charging as a function of the different parameters. We present a simple model that collapses all the data for over 4 orders of magnitude difference in streaming currents for various nozzle sizes, flow velocities and surface treatments. We further show that the charging polarity can even be reversed by applying an oppositely charged coating to the nozzle, an important step for any application.
Deception about study purpose does not affect participant behavior
Authors: Rahwan Zoe , Fasolo Barbara , Hauser Oliver P. 
Published: November 2022

AbstractThe use of deception in research is divisive along disciplinary lines. Whereas psychologists argue that deception may be necessary to obtain unbiased measures, economists hold that deception can generate suspicion of researchers, invalidating measures and ‘poisoning’ the participant pool for others. However, experimental studies on the effects of deception, notably false-purpose deception—the most common form of experimental deception—are scarce. Challenges with participant attrition and avoiding confounds with a form of deception in which two related studies are presented as unrelated likely explain this scarcity. Here, we avoid these issues, testing within an experiment to what extent false-purpose deception affects honesty. We deploy two commonly used incentivized measures of honesty and unethical behavior: coin-flip and die-roll tasks. Across two pre-registered studies with over 2000 crowdsourced participants, we found that false-purpose deception did not affect honesty in either task, even when we deliberately provoked suspicion of deception. Past experience of deception also had no bearing on honesty. However, incentivized measures of norms indicated that many participants had reservations about researcher use of false-purpose deception in general—often considered the least concerning form of deception. Together, these findings suggest that while false-purpose deception is not fundamentally problematic in the context of measuring honesty, it should only be used as a method of last resort. Our results motivate further experimental research to study the causal effects of other forms of deception, and other potential spillovers.
Comparisons of healthy human brain temperature predicted from biophysical modeling and measured with whole brain MR thermometry
Authors: Sung Dongsuk , Risk Benjamin B. , Kottke Peter A. , Allen Jason W. , Nahab Fadi , Fedorov Andrei G. , Fleischer Candace C. 
Published: November 2022

AbstractBrain temperature is an understudied parameter relevant to brain injury and ischemia. To advance our understanding of thermal dynamics in the human brain, combined with the challenges of routine experimental measurements, a biophysical modeling framework was developed to facilitate individualized brain temperature predictions. Model-predicted brain temperatures using our fully conserved model were compared with whole brain chemical shift thermometry acquired in 30 healthy human subjects (15 male and 15 female, age range 18–36 years old). Magnetic resonance (MR) thermometry, as well as structural imaging, angiography, and venography, were acquired prospectively on a Siemens Prisma whole body 3 T MR scanner. Bland–Altman plots demonstrate agreement between model-predicted and MR-measured brain temperatures at the voxel-level. Regional variations were similar between predicted and measured temperatures (< 0.55 °C for all 10 cortical and 12 subcortical regions of interest), and subcortical white matter temperatures were higher than cortical regions. We anticipate the advancement of brain temperature as a marker of health and injury will be facilitated by a well-validated computational model which can enable predictions when experiments are not feasible.
Size dependence- and induced transformations- of fractional quantum Hall effects under tilted magnetic fields
Authors: Wijewardena U. Kushan , Nanayakkara Tharanga R. , Kriisa Annika , Reichl Christian , Wegscheider Werner , Mani Ramesh G. 
Published: November 2022

AbstractTwo-dimensional electron systems subjected to high transverse magnetic fields can exhibit Fractional Quantum Hall Effects (FQHE). In the GaAs/AlGaAs 2D electron system, a double degeneracy of Landau levels due to electron-spin, is removed by a small Zeeman spin splitting, $$g \mu _B B$$

g

μ
B

B

, comparable to the correlation energy. Then, a change of the Zeeman splitting relative to the correlation energy can lead to a re-ordering between spin polarized, partially polarized, and unpolarized many body ground states at a constant filling factor. We show here that tuning the spin energy can produce fractionally quantized Hall effect transitions that include both a change in $$\nu$$
ν
for the $$R_{xx}$$

R

xx

minimum, e.g., from $$\nu = 11/7$$

ν
=
11
/
7

to $$\nu = 8/5$$

ν
=
8
/
5

, and a corresponding change in the $$R_{xy}$$

R

xy

, e.g., from $$R_{xy}/R_{K} = (11/7)^{-1}$$

R

xy

/

R
K

=

(
11
/
7
)

-
1

to $$R_{xy}/R_{K} = (8/5)^{-1}$$

R

xy

/

R
K

=

(
8
/
5
)

-
1

, with increasing tilt angle. Further, we exhibit a striking size dependence in the tilt angle interval for the vanishing of the $$\nu = 4/3$$

ν
=
4
/
3

and $$\nu = 7/5$$

ν
=
7
/
5

resistance minima, including “avoided crossing” type lineshape characteristics, and observable shifts of $$R_{xy}$$

R

xy

at the $$R_{xx}$$

R

xx

minima- the latter occurring for $$\nu = 4/3, 7/5$$

ν
=
4
/
3
,
7
/
5

and the 10/7. The results demonstrate both size dependence and the possibility, not just of competition between different spin polarized states at the same $$\nu$$
ν
and $$R_{xy}$$

R

xy

, but also the tilt- or Zeeman-energy-dependent- crossover between distinct FQHE associated with different Hall resistances.
A retrospective analysis of the relationship between anti-cyclic citrullinated peptide antibody and interstitial lung disease in systemic sclerosis
Authors: Ha Jang Woo , Hong Yoo Jin , Cha Hyun Jin , Moon Jeonghun Daniel , Pyo Jung Yoon , Lee Sang-Won , Park Yong-Beom , Park Chul Hwan , Song Jason Jungsik 
Published: November 2022

AbstractAnti-cyclic citrullinated peptide antibody testing is used to diagnose rheumatoid arthritis and associated with interstitial lung disease in RA. Herein, we investigate the relationship between anti-CCP antibody and ILD in SSc. We performed a retrospective analysis at a tertiary medical center between 2005 and 2019. Patients with SSc, systemic lupus erythematosus, and polymyositis/dermatomyositis (PM/DM) were evaluated for anti-CCP antibody and ILD. Additionally, medical records of SSc patients with ILD were reviewed. SSc patients had the highest anti-CCP antibody positivity rate compared to those with SLE and PM/DM. The incidence of ILD was higher in SSc patients with anti-CCP antibody than in those without. The usual interstitial pneumonia (UIP) incidence was higher in the anti-CCP antibody-positive group than in the anti-CCP antibody-negative group. The DLCO was lower in the anti-CCP antibody-positive group than in the anti-CCP antibody-negative group. On multivariable analysis, factors associated with SSc-ILD were anti-CCP antibody or rheumatoid factor (β coefficient, 2.652 [95% CI 1.472 to 4.776]) and anti-Scl70 antibody (β coefficient, 4.011 [95% CI 2.142 to 7.508]). Anti-CCP antibody may be associated with a higher incidence of ILD in SSc. SSc patients with anti-CCP antibody may have more UIP pattern and lower DLCO.Trial Registration Retrospectively registered.
Ceragenin CSA-13 displays high antibacterial efficiency in a mouse model of urinary tract infection
Authors: Wnorowska Urszula , Piktel Ewelina , Deptuła Piotr , Wollny Tomasz , Król Grzegorz , Głuszek Katarzyna , Durnaś Bonita , Pogoda Katarzyna , Savage Paul B. , Bucki Robert 
Published: November 2022

AbstractCeragenins (CSAs) are synthetic, lipid-based molecules that display activities of natural antimicrobial peptides. Previous studies demonstrated their high in vitro activity against pathogens causing urinary tract infections (UTIs), but their efficiency in vivo was not explored to date. In this study, we aimed to investigate the bactericidal efficiency of ceragenins against E. coli (Xen14 and clinical UPEC strains) isolates both in vitro and in vivo, as well to explore CSA-13 biodistribution and ability to modulate nanomechanical alterations of infected tissues using animal model of UTI. CSA-44, CSA-131 and particularly CSA-13 displayed potent bactericidal effect against tested E. coli strains, and this effect was mediated by induction of oxidative stress. Biodistribution studies indicated that CSA-13 accumulates in kidneys and liver and is eliminated with urine and bile acid. We also observed that ceragenin CSA-13 reverses infection-induced alterations in mechanical properties of mouse bladders tissue, which confirms the preventive role of CSA-13 against bacteria-induced tissue damage and potentially promote the restoration of microenvironment with biophysical features unfavorable for bacterial growth and spreading. These data justify the further work on employment of CSA-13 in the treatment of urinary tract infections.
Functional and molecular dissection of HCMV long non-coding RNAs
Authors: Lee Sungwon , Kim Hyewon , Hong Ari , Song Jaewon , Lee Sungyul , Kim Myeonghwan , Hwang Sung-yeon , Jeong Dongjoon , Kim Jeesoo , Son Ahyeon , Lee Young-suk , Kim V. Narry , Kim Jong-seo , Chang Hyeshik , Ahn Kwangseog 
Published: November 2022

AbstractSmall, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus life cycle. Here, we dissected the functional and molecular landscape of HCMV lncRNAs. We found that HCMV lncRNAs occupy ~ 30% and 50–60% of total and poly(A)+viral transcriptome, respectively, throughout virus life cycle. RNA1.2, RNA2.7, and RNA4.9, the three abundantly expressed lncRNAs, appear to be essential in all infection states. Among these three lncRNAs, depletion of RNA2.7 and RNA4.9 results in the greatest defect in maintaining latent reservoir and promoting lytic replication, respectively. Moreover, we delineated the global post-transcriptional nature of HCMV lncRNAs by nanopore direct RNA sequencing and interactome analysis. We revealed that the lncRNAs are modified with N6-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth analysis demonstrated that m6A machineries stabilize HCMV lncRNAs, which could account for the overwhelming abundance of viral lncRNAs. Our study lays the groundwork for understanding the viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
The antipsychotic drug sulpiride in the ventral pallidum paradoxically impairs learning and induces place preference
Authors: Dusa Daniella , Ollmann Tamás , Kállai Veronika , Lénárd László , Kertes Erika , Berta Beáta , Szabó Ádám , László Kristóf , Gálosi Rita , Zagoracz Olga , Karádi Zoltán , Péczely László 
Published: November 2022

AbstractSulpiride, as a D2-like dopamine (DA) receptor (D2R) antagonist, is an important antipsychotic drug in the treatment of schizophrenia. Recently, we have shown that the activation of D2Rs in the ventral pallidum (VP) modulates the activity of the ventral tegmental area (VTA) DAergic neurons. According to our hypothesis, intra-VP sulpiride can influence the motivational and learning processes, pervasively modifying the behavior of examined animals. In the present study, sulpiride was microinjected into the VP of male Wistar rats in three different doses. Morris water maze (MWM) test was applied to investigate the effects of sulpiride on spatial learning, while conditioned place preference (CPP) test was used to examine the potential rewarding effect of the drug. In order to show, whether the animals can associate the rewarding effect with an area which can be recognized only on its spatial location, we introduced a modified version of the CPP paradigm, the spatial CPP test. Our results show that the intra-VP sulpiride dose-dependently impairs learning processes. However, the largest dose of sulpiride induces place preference. Results of the spatial CPP paradigm demonstrate that the animals cannot associate the rewarding effect of the drug with the conditioning area based on its spatial location. In the CPP paradigm, locomotor activity decrease could be observed in the sulpiride-treated rats, likely because of a faster habituation with the conditioning environment. In summary, we can conclude that intra-VP sulpiride has a dual effect: it diminishes the hippocampus-dependent spatial learning processes, in addition, it has a dose-dependent rewarding effect.
Encapsulated salts in velvet worm slime drive its hardening
Authors: Corrales-Ureña Yendry Regina , Schwab Fabienne , Ochoa-Martínez Efraín , Benavides-Acevedo Miguel , Vega-Baudrit José , Pereira Reinaldo , Rischka Klaus , Noeske Paul-Ludwig Michael , Gogos Alexander , Vanhecke Dimitri , Rothen-Rutishauser Barbara , Petri-Fink Alke 
Published: November 2022

AbstractSlime expelled by velvet worms entraps prey insects within seconds in a hardened biopolymer network that matches the mechanical strength of industrial polymers. While the mechanic stimuli-responsive nature and building blocks of the polymerization are known, it is still unclear how the velvet worms’ slime hardens so fast. Here, we investigated the slime for the first time, not only after, but also before expulsion. Further, we investigated the slime’s micro- and nanostructures in-depth. Besides the previously reported protein nanoglobules, carbohydrates, and lipids, we discovered abundant encapsulated phosphate and carbonate salts. We also detected CO2 bubbles during the hardening of the slime. These findings, along with further observations, suggest that the encapsulated salts in expelled slime rapidly dissolve and neutralize in a baking-powder-like reaction, which seems to accelerate the drying of the slime. The proteins’ conformation and aggregation are thus influenced by shear stress and the salts’ neutralization reaction, increasing the slime’s pH and ionic strength. These insights into the drying process of the velvet worm’s slime demonstrate how naturally evolved polymerizations can unwind in seconds, and could inspire new polymers that are stimuli-responsive or fast-drying under ambient conditions.
89Zr-panitumumab PET imaging for preoperative assessment of ameloblastoma in a PDX model
Authors: Stone Logan D. , Massicano Adriana V. F. , Stevens Todd M. , Warram Jason M. , Morlandt Anthony B. , Lapi Suzanne E. , Amm Hope M. 
Published: November 2022

AbstractAccurate assessment of tumor margins with specific, non-invasive imaging would result in the preservation of healthy tissue and improve long-term local tumor control, thereby reducing the risk of recurrence. Overexpression of epidermal growth factor receptor (EGFR) has been used in other cancers as an imaging biomarker to identify cancerous tissue. We hypothesize that expression of EGFR in ameloblastomas may be used to specifically visualize tumors. The aims of this study are to measure the specificity of radiolabeled 89Zr-panitumumab (an EGFR antibody) in vivo using patient-derived xenograft (PDX) models of ameloblastoma and positron emission tomography/computed tomography (PET/CT) scans. In PDX of ameloblastomas from four patients (AB-36, AB-37, AB-39 AB-53), the biodistribution of 89Zr-panitumumab was measured 120 h post-injection and was reported as the injected dose per gram of tissue (%ID/g; AB-36, 40%; AB-37, 62%; AB-39 18%; AB-53, 65%). The radiolabeled %ID/g was significantly greater in tumors of 89Zr-panitumumab-treated mice that did not receive unlabeled panitumumab as a blocking control for AB-36, AB-37, and AB-53. Radiolabeled anti-EGFR demonstrates specificity for ameloblastoma PDX tumor xenografts, we believe 89Zr-panitumumab is an attractive target for pre-surgical imaging of ameloblastomas. With this technology, we could more accurately assess tumor margins for the surgical removal of ameloblastomas.
Sugarcane cultivation practices modulate rhizosphere microbial community composition and structure
Authors: Moneda Ana Paula Corrêa , de Carvalho Lucas Amoroso Lopes , Teheran-Sierra Luis Guillermo , Funnicelli Michelli Inácio Gonçalves , Pinheiro Daniel Guariz 
Published: November 2022

AbstractSugarcane (Saccharum spp.) represents a crop of great economic importance, remarkably relevant in the food industry and energy supply chains from renewable sources. However, its conventional cultivation involves the intensive use of fertilizers, pesticides, and other agrochemical agents whose detrimental effects on the environment are notorious. Alternative systems, such as organic farming, have been presented as an environmentally friendly way of production. Still, the outcomes of different cropping systems on the microbiota associated with sugarcane—whose role in its health and growth is crucial—remain underexplored. Thus, we studied the rhizospheric microbiota of two adjacent sugarcane fields, which differ in terms of the type of farming system. For this, we used the sequencing of taxonomic markers of prokaryotes (gene 16S rRNA, subregions V3–V4) and fungi (Internal transcribed spacer 2) and evaluated the changes caused by the systems. Our results show a well-conserved microbiota composition among farming systems in the highest taxonomic ranks, such as phylum, class, and order. Also, both systems showed very similar alpha diversity indices and shared core taxa with growth-promoting capacities, such as bacteria from the Bacillus and Bradyrhizobium genera and the fungal genus Trichoderma. However, the composition at more specific levels denotes differences, such as the separation of the samples concerning beta diversity and the identification of 74 differentially abundant taxa between the systems. Of these, 60 were fungal taxa, indicating that this microbiota quota is more susceptible to changes caused by farming systems. The analysis of co-occurrence networks also showed the formation of peripheral sub-networks associated with the treatments—especially in fungi—and the presence of keystone taxa in terms of their ability to mediate relationships between other members of microbial communities. Considering that both crop fields used the same cultivar and had almost identical soil properties, we conclude that the observed findings are effects of the activities intrinsic to each system and can contribute to a better understanding of the effects of farming practices on the plant microbiome.
Resolving the bouba-kiki effect enigma by rooting iconic sound symbolism in physical properties of round and spiky objects
Authors: Fort Mathilde , Schwartz Jean-Luc 
Published: November 2022

AbstractThe “bouba-kiki effect”, where “bouba” is perceived round and “kiki” spiky, remains a puzzling enigma. We solve it by combining mathematical findings largely unknown in the field, with computational models and novel experimental evidence. We reveal that this effect relies on two acoustic cues: spectral balance and temporal continuity. We demonstrate that it is not speech-specific but rather rooted in physical properties of objects, creating audiovisual regularities in the environment. Round items are mathematically bound to produce, when hitting or rolling on a surface, lower-frequency spectra and more continuous sounds than same-size spiky objects. Finally, we show that adults are sensitive to such regularities. Hence, intuitive physics impacts language perception and possibly language acquisition and evolution too.