bluuebunny/crossref_metadata_2025_split huggingface dataset:
The earliest Baltic amber in Western Europe
Authors: Murillo-Barroso M. , Cólliga A. Martín , Martinón-Torres M. 
Published: August 2023

AbstractThe occurrence of Baltic amber through Europe has traditionally been associated to the spread of the Bell Beaker culture during the 3rd millennium BC. In Iberia, this phenomenon is particularly noticeable in the southern half. Here we present an amber bead recovered in a Late Neolithic funerary cave (3634–3363 cal BC) from northeastern Iberia where more than 12 individuals had been buried. Fourier transform infrared spectroscopy results of four samples revealed their complete resemblance with Baltic succinite reference spectra. Despite being a single bead, this finding provides the earliest evidence for the arrival of Baltic amber to the Mediterranean and Western Europe, before the Bell Beaker phenomenon and more than a millennium earlier than traditionally thought. This finding has implications for our understanding of early exchange networks of exotic materials, and their associated social structures.
Biochemical analysis of Komagataella phaffii oxidative folding proposes novel regulatory mechanisms of disulfide bond formation in yeast
Authors: Palma Arianna , Rettenbacher Lukas A. , Moilanen Antti , Saaranen Mirva , Pacheco-Martinez Christian , Gasser Brigitte , Ruddock Lloyd 
Published: August 2023

AbstractOxidative protein folding in the endoplasmic reticulum (ER) is driven mainly by protein disulfide isomerase PDI and oxidoreductin Ero1. Their activity is tightly regulated and interconnected with the unfolded protein response (UPR). The mechanisms of disulfide bond formation have mainly been studied in human or in the yeast Saccharomyces cerevisiae. Here we analyze the kinetics of disulfide bond formation in the non-conventional yeast Komagataella phaffii, a common host for the production of recombinant secretory proteins. Surprisingly, we found significant differences with both the human and S. cerevisiae systems. Specifically, we report an inactive disulfide linked complex formed by K. phaffii Ero1 and Pdi1, similarly to the human orthologs, but not described in yeast before. Furthermore, we show how the interaction between K. phaffii Pdi1 and Ero1 is unaffected by the introduction of unfolded substrate into the system. This is drastically opposed to the previously observed behavior of the human pathway, suggesting a different regulation of the UPR and/or possibly different interaction mechanics between K. phaffii Pdi1 and Ero1.
Evolution of termination codons of proteins and the TAG-TGA paradox
Authors: Trexler Mária , Bányai László , Kerekes Krisztina , Patthy László 
Published: August 2023

AbstractIn most eukaryotes and prokaryotes TGA is used at a significantly higher frequency than TAG as termination codon of protein-coding genes. Although this phenomenon has been recognized several years ago, there is no generally accepted explanation for the TAG-TGA paradox.Our analyses of human mutation data revealed that out of the eighteen sense codons that can give rise to a nonsense codon by single base substitution, the CGA codon is exceptional: it gives rise to the TGA stop codon at an order of magnitude higher rate than the other codons. Here we propose that the TAG-TGA paradox is due to methylation and hypermutabilty of CpG dinucleotides. In harmony with this explanation, we show that the coding genomes of organisms with strong CpG methylation have a significant bias for TGA whereas those from organisms that lack CpG methylation use TGA and TAG termination codons with similar probability.
Effect of exercise on the hypothalamic–pituitary–gonadal axis in a rat model of Alzheimer’s disease
Authors: khairy Eman Y. , Salama Ola A. 
Published: August 2023

AbstractHypothalamic–pituitary–gonadal (HPG) axis dysregulation was suggested to play a crucial role in Alzheimer’s disease (AD). This study investigated the effects of exercise on HPG hormones in an AD rat model, as a possible mechanism underlying the favorable effect of exercise on AD. Forty male Wistar albino rats 2–3 months old were subdivided randomly into two groups (n = 20 each): AD group (injected intraperitoneally with aluminum chloride (70 mg/kg/day) for 6 weeks) and Control group. Each group was subdivided into exercised or non-exercised group (n = 10 each). Exercised groups were subjected to a swimming protocol (60 min/day, 5 days/week, 4 weeks). Serum HPG hormones, hippocampal β-amyloid levels and Morris water-maze cognition were assessed. Results demonstrated higher levels of β-amyloid, gonadotropin releasing hormone (GnRH), luteinizing hormone (LH) and follicle stimulating hormone (FSH) together with lower testosterone levels and cognitive impairment in the AD rats compared to controls. Β-amyloid levels negatively correlated with testosterone levels and positively correlated with GnRH, LH and FSH among the AD rats. Higher testosterone and lower GnRH, LH, FSH and β-amyloid levels, as well as cognitive improvement, were observed in the exercised compared to non-exercised AD rats, suggesting a modulatory role of exercise training on AD-associated HPG axis dysregulation.
Catalyst- and metal-free C(sp2)–H bond selenylation of (N-hetero)-arenes using diselenides and trichloroisocyanuric acid at room temperature
Authors: Neto José S. S. , Granja Isis J. A. , Scheide Marcos R. , Franco Marcelo S. , Moraes Cassio A. O. , Beatriz Adilson , de Lima Dênis P. , Botteselle Giancarlo V. , Frizon Tiago E. A. , Saba Sumbal , Rafique Jamal , Braga Antonio L. 
Published: August 2023

AbstractIn this paper, we report an eco-friendly approach for the C(sp2)–H bond selenylation of imidazopyridines and other N-heteroarenes as well as simple arenes at ambient temperature. This new protocol consists of the reaction between (N-hetero)-arenes and the diorganyl-diselenides and trichloroisocyanuric acid (TCCA)-ethanol reagent system. In a short reaction time, the desired selenylated products were obtained regioselectively in good yields, with tolerance for a wide range of functional groups.
Development of carboxymethyl cellulose-graphene oxide biobased composite for the removal of methylene blue cationic dye model contaminate from wastewater
Authors: Mohamed Eman N. , Abd-Elhamid Ahmed I. , El-Bardan Ali A. , Soliman Hesham M. A. , Mohy-Eldin Mohamed S. 
Published: August 2023

AbstractUtilizing Glutaraldehyde crosslinked sodium carboxymethyl cellulose (CMC-GA) hydrogel and its nanographene oxide composite (CMC-GA-GOx), an effective carboxymethyl cellulose-graphene oxide biobased composites adsorbent was developed for the adsorption removal of methylene blue (MB) cationic dye contaminate from industrial wastewater. The CMC-GA-GOx composites developed were characterized using FTIR, RAMAN, TGA, SEM, and EDX analysis instruments. Through batch experiments, several variables affecting the removal of MB dye, including the biocomposites GO:CMC composition, adsorption time, pH and temperature, initial MB concentration, adsorbent dosage, and NaCl concentration, were investigated under different conditions. The maximum dye removal percentages ranged between 93 and 98%. They were obtained using biocomposites CMC-GA-GO102 with 20% GO weight percent, adsorption time 25 min, adsorption temperature 25 °C, MB concentrations 10–30 ppm, adsorption pH 7.0, and 0.2 g adsorbent dose. The experimental data of the adsorption process suit the Langmuir isotherm more closely with a maximal monolayer adsorption capacity of 76.92 mg/g. The adsorption process followed the kinetic model of pseudo-second order. The removal of MB was exothermic and spontaneous from a thermodynamic standpoint. In addition, thermodynamic results demonstrated that adsorption operates most effectively at low temperatures. Finally, the reusability of the developed CMC-GA-GO102 has been proved through 10 successive cycles where only 14% of the MB dye removal percentage was lost. These results suggest that the developed CMC-GA-GO102 composite may be an inexpensive and reusable adsorbent for removing organic cationic dyes from industrial wastewater.
Cervicovaginal Gardnerella sialidase-encoding gene in persistent human papillomavirus infection
Authors: Novak Juliano , Belleti Rafael , da Silva Pinto Gabriel Vitor , do Nascimento Bolpetti Aline , da Silva Márcia Guimarães , Marconi Camila 
Published: August 2023

AbstractDisturbed vaginal microbiota have a role in the persistence of high-oncogenic-risk human papillomavirus (hrHPV) and Gardnerella spp. is closely related with this condition. Such bacteria are the major source of cervicovaginal sialidases, important for microbiota alterations. The sialidase-encoding gene nanH3 is account for their sialidase activity. Thus, a subset of 212 women positive for hrHPV at the first visit were included in the analysis of the current study aiming to compare the loads of nanH3 in cervicovaginal fluid (CFV) of women with persistent hrHPV infection and with those cleared the infection after a year. Participants were assigned to two study groups named “persistence” (n = 124, 53.22%) or “clearance” (n = 88, 37.77%), according to the HPV status upon enrollment and follow-up. Absolute quantification of nanH3 gene was performed using quantitative real-time PCR (qPCR). Persistence and clearance group did not show statistical difference in the load of nanH3 gene (p = 0.19). When considering the subset of women with HPV16, differences in number of copies of nanh3 gene was observed between the persistent (7.39E+08 copies/μL) and clearance group (2.85E+07 copies/μL) (p = 0.007). Therefore, baseline loads of nanH3 gene is increased in women that persist with cervical HPV16 infection after 12 months.
Interlukin-4 weakens resistance to stress injury and megakaryocytic differentiation of hematopoietic stem cells by inhibiting Psmd13 expression
Authors: Gao Ai , Xu Shuhui , Li Qing , Zhu Caiying , Wang Fengjiao , Wang Yajie , Hao Sha , Dong Fang , Cheng Hui , Cheng Tao , Gong Yuemin 
Published: August 2023

AbstractThrombocytopenia is a major and fatal complication in patients with acute myeloid leukemia (AML), which results from disrupted megakaryopoiesis by leukemic niche and blasts. Our previous research revealed that elevated interleukin-4 (IL-4) in AML bone marrow had adverse impact on multiple stages throughout megakaryopoiesis including hematopoietic stem cells (HSCs), but the specific mechanism remains unknown. In the present study, we performed single-cell transcriptome analysis and discovered activated oxidative stress pathway and apoptosis pathway in IL-4Rαhigh versus IL-4Rαlow HSCs. IL-4 stimulation in vitro led to apoptosis of HSCs and down-regulation of megakaryocyte-associated transcription factors. Functional assays displayed higher susceptibility of IL-4Rαhigh HSCs to tunicamycin and irradiation-induced apoptosis, demonstrating their vulnerability to endoplasmic reticulum (ER) stress injury. To clarify the downstream signaling of IL-4, we analyzed the transcriptomes of HSCs from AML bone marrow and found a remarkable down-regulation of the proteasome component Psmd13, whose expression was required for megakaryocytic-erythroid development but could be inhibited by IL-4 in vitro. We knocked down Psmd13 by shRNA in HSCs, and found their repopulating capacity and megakaryocytic differentiation were severely compromised, with increased apoptosis in vivo. In summary, our study uncovered a previous unrecognized regulatory role of IL-4-Psmd13 signaling in anti-stress and megakaryocytic differentiation capability of HSCs.
Stimulating growth, root quality, and yield of carrots cultivated under full and limited irrigation levels by humic and potassium applications
Authors: Elshamly Ayman M. S. , Nassar Saad M. A. 
Published: August 2023

AbstractWater stress poses a significant challenge for carrot cultivation, leading to decreased yield and inefficient water use efficiency. Therefore, it is crucial to provide plants with suitable supplements that enhance their stress resistance. In this study, we investigated the effectiveness of humic and potassium applications on carrot growth, yield characteristics, root quality, and water use efficiency under varying irrigation levels. A split-split plot experiment was conducted, with two levels of gross water requirements (GWR) (100% and 80%) assigned to the main plots. The subplots were treated with humic acid through foliar application (Hsp) or soil drenching (Hgd). The sub-subplots were further divided to assess the impact of foliar potassium sources (potassium humate, Kh) and mineral applications (potassium sulfate, K2SO4). The results revealed a substantial reduction in carrot yield under limited irrigation, reaching about 32.2% lower than under GWR100%. Therefore, under limited irrigation conditions, the combined application of Hgd and K2SO4 resulted in a significant yield increase of 78.9% compared to the control under GWR80%. Conversely, under GWR100%, the highest average yield was achieved by applying either Hsp and Kh or Hsp and K2SO4, resulting in yields of 35,833 kg ha−1 and 40,183 kg ha−1, respectively. However, the combination of Hgd and Kh negatively affected the yield under both GWR100% and GWR80%. Nonetheless, applying Kh in combination with Hgd under GWR80% led to improved nitrogen, phosphorus, potassium, potassium/sodium ratio, and total sugar concentrations, while reducing sodium content in carrot roots. Based on this study, it is recommended to adopt GWR80% and treat plants with a combination of Hgd and foliar K2SO4. This approach can help plants overcome the negative effects of water stress, improve yield and root quality, and achieve optimal water use efficiency.
Spin-lattice-dynamics analysis of magnetic properties of iron under compression
Authors: dos Santos Gonzalo , Meyer Robert , Tramontina Diego , Bringa Eduardo M. , Urbassek Herbert M. 
Published: August 2023

AbstractCompression of a magnetic material leads to a change in its magnetic properties. We examine this effect using spin-lattice dynamics for the special case of bcc-Fe, using both single- and poly-crystalline Fe and a bicontinuous nanofoam structure. We find that during the elastic phase of compression, the magnetization increases due to a higher population of the nearest-neighbor shell of atoms and the resulting higher exchange interaction of neighboring spins. In contrast, in the plastic phase of compression, the magnetization sinks, as defects are created, increasing the disorder and typically decreasing the average atom coordination number. The effects are more pronounced in single crystals than in polycrystals, since the presence of defects in the form of grain boundaries counteracts the increase in magnetization during the elastic phase of compression. Also, the effects are more pronounced at temperatures close to the Curie temperature than at room temperature. In nanofoams, the effect of compression is minor since compression proceeds more by void reduction and filament bending—with negligible effect on magnetization—than by strain within the ligaments. These findings will prove useful for tailoring magnetization under strain by introducing plasticity.
A principled link between object naming and representation is available to infants by seven months of age
Authors: LaTourrette Alexander , Chan Dana Michelle , Waxman Sandra R. 
Published: August 2023

AbstractBy their first birthdays, infants represent objects flexibly as a function of not only whether but how the objects are named. Applying the same name to a set of different objects from the same category supports object categorization, with infants encoding commonalities among objects at the expense of individuating details. In contrast, applying a distinct name to each object supports individuation, with infants encoding distinct features at the expense of categorical information. Here, we consider the development of this nuanced link between naming and representation in infants’ first year. Infants at 12 months (Study 1; N = 55) and 7 months (Study 2; N = 96) participated in an online recognition memory task. All infants saw the same objects, but their recognition of these objects at test varied as a function of how they had been named. At both ages, infants successfully recognized objects that had been named with distinct labels but failed to recognize these objects when they had all been named with the same, consistent label. This new evidence demonstrates that a principled link between object naming and representation is available by 7 months, early enough to support infants as they begin mapping words to meaning.
Evaluation of influences of forest cover change on landslides by comparing rainfall-induced landslides in Japanese artificial forests with different ages
Authors: Sato Tadamichi , Katsuki Yoh , Shuin Yasuhiro 
Published: August 2023

AbstractIn this study, we evaluated the influence of forest cover changes on rainfall-induced shallow landslides by comparing two shallow landslides and debris flows that occurred on plantation forests of different ages in Japan: the Kake disaster in 1988 and the Asakura disaster in 2017. At Kake, the trees ranged in age from 10 to 30 years, whereas at Asakura the trees were over 40 years old. The rainfall characteristics that triggered each landslide were estimated using a three-layer tank model, and the results, as well as the volume of driftwood produced by the landslides, were then compared. Both landslides occurred when the first tank storage layer value, corresponding to the temporal variation in groundwater level in the shallow soil layer, exceeded its previous maximum. The return period of this value at the time of the landslides was 3.0-fold higher in the more mature forests of Asakura than in the young forests of Kake. The upper limit of driftwood volume was 30-fold higher in Asakura than in Kake. Our findings indicated that shallow landslides and debris flows become increasingly rare as forests mature; however, the large volume of driftwood produced by landslides in mature forests may cause substantial damage when extreme rainfall events exceed the landslide resistance of those forests. These insights may be applied to effective landslide risk management.
Determination of exciton binding energy using photocurrent spectroscopy of Ge quantum-dot single-hole transistors under CW pumping
Authors: Hong Po-Yu , Lai Chi-Cheng , Tsai Ting , Lin Horng-Chih , George Thomas , Kuo David M. T. , Li Pei-Wen 
Published: August 2023

AbstractWe reported exciton binding-energy determination using tunneling-current spectroscopy of Germanium (Ge) quantum dot (QD) single-hole transistors (SHTs) operating in the few-hole regime, under 405–1550 nm wavelength (λ) illumination. When the photon energy is smaller than the bandgap energy (1.46 eV) of a 20 nm Ge QD (for instance, λ = 1310 nm and 1550 nm illuminations), there is no change in the peak voltages of tunneling current spectroscopy even when the irradiation power density reaches as high as 10 µW/µm2. In contrast, a considerable shift in the first hole-tunneling current peak towards positive VG is induced (ΔVG ≈ 0.08 V at 0.33 nW/µm2 and 0.15 V at 1.4 nW/µm2) and even additional photocurrent peaks are created at higher positive VG values (ΔVG ≈ 0.2 V at 10 nW/µm2 irradiation) by illumination at λ = 850 nm (where the photon energy matches the bandgap energy of the 20 nm Ge QD). These experimental observations were further strengthened when Ge-QD SHTs were illuminated by λ = 405 nm lasers at much lower optical-power conditions. The newly-photogenerated current peaks are attributed to the contribution of exciton, biexciton, and positive trion complexes. Furthermore, the exciton binding energy can be determined by analyzing the tunneling current spectra.
Functional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes
Authors: Otero-Ruiz Alejandro , Rodriguez-Anaya Libia Zulema , Lares-Villa Fernando , Lozano Aguirre Beltrán Luis Fernando , Lares-Jiménez Luis Fernando , Gonzalez-Galaviz Jose Reyes , Cruz-Mendívil Abraham 
Published: August 2023

AbstractBalamuthia mandrillarisis a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome ofB. mandrillarisisolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence ofAcanthamoebaspp. andTrypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches forB. mandrillarisinfections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.
Microbiomes and metabolomes of dominant coral reef primary producers illustrate a potential role for immunolipids in marine symbioses
Authors: Mannochio-Russo Helena , Swift Sean O. I. , Nakayama Kirsten K. , Wall Christopher B. , Gentry Emily C. , Panitchpakdi Morgan , Caraballo-Rodriguez Andrés M. , Aron Allegra T. , Petras Daniel , Dorrestein Kathleen , Dorrestein Tatiana K. , Williams Taylor M. , Nalley Eileen M. , Altman-Kurosaki Noam T. , Martinelli Mike , Kuwabara Jeff Y. , Darcy John L. , Bolzani Vanderlan S. , Wegley Kelly Linda , Mora Camilo , Yew Joanne Y. , Amend Anthony S. , McFall-Ngai Margaret , Hynson Nicole A. , Dorrestein Pieter C. , Nelson Craig E. 
Published: August 2023

AbstractThe dominant benthic primary producers in coral reef ecosystems are complex holobionts with diverse microbiomes and metabolomes. In this study, we characterize the tissue metabolomes and microbiomes of corals, macroalgae, and crustose coralline algae via an intensive, replicated synoptic survey of a single coral reef system (Waimea Bay, Oʻahu, Hawaii) and use these results to define associations between microbial taxa and metabolites specific to different hosts. Our results quantify and constrain the degree of host specificity of tissue metabolomes and microbiomes at both phylum and genus level. Both microbiome and metabolomes were distinct between calcifiers (corals and CCA) and erect macroalgae. Moreover, our multi-omics investigations highlight common lipid-based immune response pathways across host organisms. In addition, we observed strong covariation among several specific microbial taxa and metabolite classes, suggesting new metabolic roles of symbiosis to further explore.