Miracle-dz/UniFAR-FTUs huggingface dataset:
Unraveling the Structural Transformation of Wood Lignin During Deep Eutectic Solvent Treatment

Deep eutectic solvents (DESs) can efficiently promote the efficiency of cellulose enzymatic hydrolysis through the removal of lignin component in lignocellulosic biomass pretreatment. Unraveling the fundamental structural variant of lignin during DES treatment would facilitate to understand the DES-based biomass pretreatment in a clear perspective. Herein, an enzymatic mild acidolysis lignin (EMAL) and a series of β-O-4 lignin model compounds were employed to be treated with choline chloride (ChCl)/lactic acid (LA) (1:2) DES, from which the structural variant of all lignin fractions can be realized in a detailed version. The β-O-4 linkages, existing in either realistic lignin or model compounds, could be cleaved by ChCl/LA, thus leading to the decrease of molecular weight and the rise of hydroxyl groups. The influence of reaction temperature and time was also examined in view of some key structural parameters. Experimental evidences from model compounds confirmed that the repolymerization occurs with the depolymerization of lignin, which may account for the low production of monomeric products during DES treatment.
Transcutaneous Vagus Nerve Stimulation Does Not Affect Verbal Memory Performance in Healthy Volunteers

Introduction Invasive vagus nerve stimulation (VNS) improves word recognition memory in patients with epilepsy. Recent studies with transcutaneous VNS (tVNS) have also shown positive effects on various subdomains of cognitive functioning in healthy volunteers. In this randomized, controlled, crossover study, we investigated the effect of tVNS on a word recognition memory paradigm in healthy volunteers to further investigate the potential of tVNS in the treatment of cognitive disorders. Methods We included 41 healthy participants aged between 18 and 30 years (young age group) and 24 healthy participants aged between 45 and 80 years (older age group). Each participant completed a word recognition memory paradigm during three different conditions: true tVNS, sham, and control. During true tVNS, stimulation was delivered at the cymba conchae. Sham stimulation was delivered by stimulating the earlobe. In the control condition, no stimulation was given. In each condition, participants were asked to remember highlighted words from three test paragraphs. Accuracy scores were calculated for immediate recall after each test paragraph and for delayed recognition at the end of the paradigm. We hypothesized that highlighted words from paragraphs in the true tVNS condition would be more accurately recalled and/or recognized compared to highlighted words from paragraphs in the sham or control condition. Results In this randomized study, tVNS did not affect the accuracy scores for immediate recall or delayed recognition in both age groups. The younger group showed significantly higher accuracy scores than the older group. The accuracy scores improved over time, and the most recently learned words were better recognized. Participants rated true tVNS as significantly more painful; however, pain was not found to affect accuracy scores. Conclusion In this study, tVNS did not affect verbal memory performance in healthy volunteers. Our results could not replicate the positive effects of invasive VNS on word recognition memory in epilepsy patients. Future research with the aim of improving cognitive function should focus on the rational identification of optimized and individualized stimulation settings primarily in patients with cognitive deficits.
Integrated Non-targeted and Targeted Metabolomics Uncovers Amino Acid Markers of Oral Squamous Cell Carcinoma

Purpose: It is very important to develop potential molecular associated with oral squamous cell carcinoma (OSCC) malignant transformation and progression. Thus, the aim of our study was to determine the amino acid metabolic characteristics of OSCC patients and test their diagnostic value. Experimental Design: Eight pairs of matched tumor and normal samples were collected for gas chromatography–mass spectrometry (GC-MS) high-throughput untargeted analysis. Another 20 cases (each case including tumor and normal tissues) were also enrolled for ultrahigh-performance liquid chromatography–tandem mass spectrometer (UHPLC-MS/MS) amino acid quantitative analysis. T-test and receiver operating characteristic (ROC) curve analysis were used to determine candidate markers. Principal component analysis, partial least squares discriminant analysis, and heat map analysis were used to verify the ability of candidate markers to distinguish tumors from normal tissues. Results: A total of 10 amino acids biomarker were selected as OSCC candidate diagnostic biomarkers by GC-MS high-throughput untargeted metabolomics analyses [area under the curve (AUC) >0.80]. We further measured the specific concentration of these candidate amino acids biomarkers in another batch of 20 cases by UHPLC-MS/MS quantitative analysis. The result validated that nine amino acids had been detected, which had statistically significant difference (t-test, p < 0.05). Moreover, three of nine amino acid markers (glutamate, aspartic acid, and proline) displayed high sensitivity and specificity (AUC >0.90) by ROC curve analysis and obtained optimal sensitivity and specificity by binary logistic regression in the Glmnet package (AUC = 0.942). Conclusions: In conclusion, a panel including three amino acids (glutamate, aspartic acid, and proline) was identified as potential diagnostic biomarkers of OSCC by a combination of non-targeted and targeted metabolomics methods.
Rhodopsin: A Potential Biomarker for Neurodegenerative Diseases

Retinal alterations have recently been associated with numerous neurodegenerative diseases. Rhodopsin is a G-protein coupled receptor found in the rod cells of the retina. As a biomarker associated with retinal thinning and degeneration, it bears potential in the early detection and monitoring of several neurodegenerative diseases. In this review article, we summarize the findings of correlations between rhodopsin and several neurodegenerative disorders as well as the potential of a novel technique, cSLO, in the quantification of rhodopsin.
Localization of Breast Lesion Using Mammographic-Basic Views

The incidence of breast cancer is more in developed countries (>1000 per million) than in developing countries (<200 per million) but the rate of cancer mortality is higher in developing countries than in developed countries [1]. Cancerous breast lesions accounts for 6% of all cancers in Nepal. This disease is mostly detected in advanced or very late stage due to female illiteracy and lack of awareness in Nepal. Human Female breast is composed of mainly glandular and adipose tissue and has 4 quadrants i.e. upper outer, upper inner, lower outer, lower inner and sub-areolar region. This study was done for two years on females of eastern region of Nepal who visited BPKIHS for mammography examination and at the end of the study it was concluded that Upper outer quadrant of the breast is most susceptible to breast lesion with highest number of pathologies occurring in that area and also mammography was found to be an idealistic imaging modality for both screening and diagnostic purposes of breast
Elasmosaurid Phylogeny and Paleobiogeography, with a Reappraisal of Aphrosaurus furlongi from the Maastrichtian of the Moreno Formation

ABSTRACT The holotype of the elasmosaurid Aphrosaurus furlongi from the Maastrichtian levels of the Moreno Formation is redescribed and considered a valid species based on one autapomorphy, a deep trough in the ventral surface of vertebral centra of the posterior cervicals, and the following combination of features: wide and short clavicle-interclavicle complex with concave anterior border and without posterior medial process or medial ventral keel, humerus with anterior depression, and posterior limb with accessory element on the posterior margin. The phylogenetic analysis recovered A. furlongi as an elasmosaurid within Weddellonectia. The phylogenetic analysis generated a new topology of Elasmosauridae. A new clade, Euelasmosaurida, is recovered, including all post-Cenomanian elasmosaurids other than Zarafasaura oceanis. Euelasmosaurida is composed of two main clades: Elasmosaurinae and Weddellonectia. The latter includes mostly Weddellian elasmosaurids, including Aristonectinae. Based on the new phylogenetic results, the evolution of key cranial and postcranial characters is discussed. Two key intervals of elasmosaurid evolutionary history are recognized: the Cenomanian, with the appearance of Euelasmosaurida, and the Santonian, with the differentiation of Weddellonectia and Elasmosaurinae.
Patterns in Microbial Assemblages Exported From the Meltwater of Arctic and Sub-Arctic Glaciers

Meltwater streams connect the glacial cryosphere with downstream ecosystems. Dissolved and particulate matter exported from glacial ecosystems originates from contrasting supraglacial and subglacial environments, and exported microbial cells have the potential to serve as ecological and hydrological indicators for glacial ecosystem processes. Here, we compare exported microbial assemblages from the meltwater of 24 glaciers from six (sub)Arctic regions – the southwestern Greenland Ice Sheet, Qeqertarsuaq (Disko Island) in west Greenland, Iceland, Svalbard, western Norway, and southeast Alaska – differing in their lithology, catchment size, and climatic characteristics, to investigate spatial and environmental factors structuring exported meltwater assemblages. We found that 16S rRNA gene sequences of all samples were dominated by the phyla Proteobacteria, Bacteroidetes, and Actinobacteria, with Verrucomicrobia also common in Greenland localities. Clustered OTUs were largely composed of aerobic and anaerobic heterotrophs capable of degrading a wide variety of carbon substrates. A small number of OTUs dominated all assemblages, with the most abundant being from the genera Polaromonas, Methylophilus, and Nitrotoga. However, 16–32% of a region’s OTUs were unique to that region, and rare taxa revealed unique metabolic potentials and reflected differences between regions, such as the elevated relative abundances of sulfur oxidizers Sulfuricurvum sp. and Thiobacillus sp. at Svalbard sites. Meltwater alpha diversity showed a pronounced decrease with increasing latitude, and multivariate analyses of assemblages revealed significant regional clusters. Distance-based redundancy and correlation analyses further resolved associations between whole assemblages and individual OTUs with variables primarily corresponding with the sampled regions. Interestingly, some OTUs indicating specific metabolic processes were not strongly associated with corresponding meltwater characteristics (e.g., nitrification and inorganic nitrogen concentrations). Thus, while exported assemblage structure appears regionally specific, and probably reflects differences in dominant hydrological flowpaths, OTUs can also serve as indicators for more localized microbially mediated processes not captured by the traditional characterization of bulk meltwater hydrochemistry. These results collectively promote a better understanding of microbial distributions across the Arctic, as well as linkages between the terrestrial cryosphere habitats and downstream ecosystems.
Too Much of a Good Thing: How Ectopic DNA Replication Affects Bacterial Replication Dynamics

Each cell division requires the complete and accurate duplication of the entire genome. In bacteria, the duplication process of the often-circular chromosomes is initiated at a single origin per chromosome, resulting in two replication forks that traverse the chromosome in opposite directions. DNA synthesis is completed once the two forks fuse in a region diametrically opposite the origin. In some bacteria, such as Escherichia coli, the region where forks fuse forms a specialized termination area. Polar replication fork pause sites flanking this area can pause the progression of replication forks, thereby allowing forks to enter but not to leave. Transcription of all required genes has to take place simultaneously with genome duplication. As both of these genome trafficking processes share the same template, conflicts are unavoidable. In this review, we focus on recent attempts to add additional origins into various ectopic chromosomal locations of the E. coli chromosome. As ectopic origins disturb the native replichore arrangements, the problems resulting from such perturbations can give important insights into how genome trafficking processes are coordinated and the problems that arise if this coordination is disturbed. The data from these studies highlight that head-on replication–transcription conflicts are indeed highly problematic and multiple repair pathways are required to restart replication forks arrested at obstacles. In addition, the existing data also demonstrate that the replication fork trap in E. coli imposes significant constraints to genome duplication if ectopic origins are active. We describe the current models of how replication fork fusion events can cause serious problems for genome duplication, as well as models of how such problems might be alleviated both by a number of repair pathways as well as the replication fork trap system. Considering the problems associated both with head-on replication-transcription conflicts as well as head-on replication fork fusion events might provide clues of how these genome trafficking issues have contributed to shape the distinct architecture of bacterial chromosomes.
Complex Spatial Genetic Connectivity of Mussels Mytilus chilensis Along the Southeastern Pacific Coast and Its Importance for Resource Management

ABSTRACT To ensure the maintenance of natural mussel beds along the southeastern Pacific coast of Chile, it is important to understand their population dynamics. This means evaluating their genetic population structure and gene flow, and the degree of connectivity among natural beds. To do this, the spatial genetic population structure of seven natural Mytilus chilensis beds within the mussels' present distribution range along the Chilean coast was evaluated. Genetic differences were established between populations with cytochrome oxidase I (COI) gene sequences (Fst = 0.099) and microsatellites (Fst = 0.048), showing that locations that consistently presented greater differentiation were those at the extremes of the geographical distribution. An “isolation by distance” pattern was not observed in the COI and microsatellite data. We suggest that because of the high resolution of these markers, the differences between locations may be explained by high reproductive variance, which determines local changes in each reproductive cycle of the species. These changes would account for the differences between the natural beds. Furthermore, differentiated genetic types were observed in some locations, demonstrating the presence of local processes in some cases, perhaps caused by gene flow restrictions resulting from the local geomorphological and oceanographic conditions. The gene structure and connectivity of natural beds in sessile species with larval dispersion are strongly determined by local retention characteristics. For this reason, the data generated in this study can be used to improve population management. These data can also be used to support and motivate the creation of a marine protected area containing natural beds of this species with sufficient levels of genetic diversity.
Biophysical Habitat Features Explain Colonization and Size Distribution of Introduced Trochus (Gastropoda)

The tegulid gastropod, Rochia nilotica is harvested in small-scale fisheries throughout Southeast Asia and the Pacific Islands, many of which were created from inter-country translocations. This species is found on structurally complex shallow reefs, but its specific habitat requirements have not yet been quantified in order to maximize the success of future translocations and help future-proof the fishery in changing ocean conditions. At 28 sites around Samoa, where the species was introduced in the early 2000s, we measured a suite of habitat variables along transects in which R. nilotica were counted and the shell sizes measured in a parallel study. Boosted regression tree analyses revealed that R. nilotica were most abundant at reef locations that were shallow, with fairly consistent depth, had high coverage of branching coral, low cover of erect macroalgae, low wave exposure and high surface complexity. Smaller individuals were associated with wide reef flats and high cover of branching coral, whereas larger animals occurred in deeper water with high surface complexity. Multivariate analyses showed this species to be a habitat generalist, sharing much of its niche with an endemic herbivorous gastropod, Tectus pyramis. Future stocking programs should focus on sites with habitats optimal for both adults and juveniles. R. nilotica populations are likely to be especially affected by broadscale stressors that result in declines in live coral cover and substratum complexity and increasing coverage of macroalgae on coral reefs.
Factors Related to the Post-operative Recurrence of Atypical Meningiomas

Aim: This study aimed to investigate the relationship between clinicopathological characteristics of atypical meningiomas (AM) and its post-operative recurrence. Materials and Methods: The clinicopathological characteristics and findings from follow up were retrospectively reviewed and compared between AM and benign meningioma (BM) patients. Univariate and multivariate analyses were employed to identify the factors related to the post-operative recurrence of AM. Results: More BM patients were females and received complete resection; the recurrence rate was significantly lower in BM patients as compared to AM patients. The progesterone receptor (PR), E-cadherin protein (E-Ca) and β-catenin positive rates and Ki67 labeling index were significantly different between two groups. Univariate analysis showed the age, tumor size, tumor invasiveness, E-Ca expression, and extent of resection were related to the post-operative recurrence of AM. However, multivariate analysis showed only the extent of resection and tumor invasiveness were the independent factors associated with the post-operative recurrence of AM. Conclusions: The extent of resection and tumor invasiveness are related to the post-operative recurrence of AM. To improve the surgical procedures to maximize the tumor resection is important to improve the prognosis of AM patients.
Life Finds a Way: Young Adults With Lesbian Mothers Reflect on Their Childhood Prior to Legal Recognition of Same-Sex Parents in Sweden

The strapline “life finds a way,” from the classic movie Jurassic Park, referred to how the all-female dinosaurs in a theme park had been able to reproduce, despite the laws of nature. Similarly, the participants in the present study described how their lesbian mothers had shown that “life finds a way,” when having children and forming a family, prior to the legal recognition of same-sex parents in Sweden. The study draws on interviews with eight young Swedish adults, aged 17–30 (average age 25). They had been raised by lesbian couples but were born prior to the legal recognition of same-sex parenthood. Prior to a legal change in 2003, a same-sex couple could not share legal parenthood. Further, female couples were excluded from Swedish assisted reproduction programs until 2005. The interviews have been analyzed thematically, and the article presents the results in four themes. The first theme, circumvent, oppose, or adapt to legal obstacles, shows the participants’ reflections on how their parents navigated legal obstacles in order to have children and to live together as a family. The second theme, legal obstacles do not affect everyday life, depicts a common experience of how a lack of legal recognition seldom mattered to the participants during their childhood. Rather, they explained how their parents had been able to form parenthood and close relations without legal recognition. In contrast, the third theme describes occasions when legal parenthood matters. This theme highlights occasions when the lack of legal parenthood was problematic or devastating for the participants, such as when parents divorced, or one parent died. The final theme, the meaning of legal parents in adulthood, explores the participants’ reflections on the meaning and impact of legal ties (or lack of legal ties) between themselves as young adults and their parents. The findings are discussed in relation to previous research on children and young adults with same-sex parents.
Investigating the Hand Ownership Illusion With Two Views Merged in

Researchers investigating virtual/augmented reality have shown humans' marked adaptability, especially regarding our sense of body ownership; their cumulative findings have expanded the concept of what it means to have a body. Herein, we report the hand ownership illusion during “two views merged in. ” In our experiment, participants were presented two first-person perspective views of their arm overlapped, one was the live feed from a camera and the other was a playback video of the same situation, slightly shifted toward one side. The relative visibility of these two views and synchrony of tactile stimulation were manipulated. Participants' level of embodiment was evaluated using a questionnaire and proprioceptive drift. The results show that the likelihood of embodying the virtual hand is affected by the relative visibility of the two views and synchrony of the tactile events. We observed especially strong hand ownership of the virtual hand in the context of high virtual hand visibility with synchronous tactile stimulation.
Vibrio and Bacterial Communities Across a Pollution Gradient in the Bay of Bengal: Unraveling Their Biogeochemical Drivers

The highly populated coasts of the Bay of Bengal are particularly vulnerable to water-borne diseases, pollution and climatic extremes. The environmental factors behind bacterial community composition and Vibrio distribution were investigated in an estuarine system of a cholera-endemic region in the coastline of Bangladesh. Higher temperatures and sewage pollution were important drivers of the abundance of toxigenic Vibrio cholerae. A closer relation between non-culturable Vibrio and particulate organic matter (POM) was inferred during the post-monsoon. The distribution of operational taxonomic units (OTUs) of Vibrio genus was likely driven by salinity and temperature. The resuspension of sediments increased Vibrio abundance and organic nutrient concentrations. The δ13C dynamic in POM followed an increasing gradient from freshwater to marine stations; nevertheless, it was not a marker of sewage pollution. Bacteroidales and culturable coliforms were reliable indicators of untreated wastewater during pre and post-monsoon seasons. The presumptive incorporation of depleted-ammonium derived from ammonification processes under the hypoxic conditions, by some microorganisms such as Cloacibacterium and particularly by Arcobacter nearby the sewage discharge, contributed to the drastic 15N depletion in the POM. The likely capacity of extracellular polymeric substances production of these taxa may facilitate the colonization of POM from anthropogenic origin and may signify important properties for wastewater bioremediation. Genera of potential pathogens other than Vibrio associated with sewage pollution were Acinetobacter, Aeromonas, Arcobacter, and Bergeyella. The changing environmental conditions of the estuary favored the abundance of early colonizers and the island biogeography theory explained the distribution of some bacterial groups. This multidisciplinary study evidenced clearly the eutrophic conditions of the Karnaphuli estuary and assessed comprehensively its current bacterial baseline and potential risks. The prevailing conditions together with human overpopulation and frequent natural disasters, transform the region in one of the most vulnerable to climate change. Adaptive management strategies are urgently needed to enhance ecosystem health.