bluuebunny/crossref_metadata_2025_split huggingface dataset:
UniProtExtractR: an app and R package for easily extracting protein-specific UniProtKB information and fine-tuning organelle resolution
Authors: Panov Alexandra , Harper J Wade 
Published: November 2023

Abstract

Summary
UniProtKB is a publicly accessible database of annotated protein features for numerous organisms; however, globally extracting protein entry information for data visualization and categorization can be challenging. While the UniProtKB entry syntax maintains database consistency, it simultaneously obscures key terms within long character strings. To increase accessibility, UniProtExtractR is both an app and R package that extracts desired information across nine UniProtKB categories: DNA binding, Pathway, Transmembrane, Signal peptide, Protein families, Domain [FT], Motif, Involvement in disease, and Subcellular location [CC]. The app features interactive frequency tables that globally summarize both the original UniProtKB input query as well as the extracted/changed entry values. Moreover, UniProtExtractR includes a tractable mapping algorithm to define custom organelle-level resolution. UniProtExtractR exists as a freely accessible Shiny app that requires no coding experience as well as R package, the code of which is entirely open source.

Availability and implementation
UniProtExtractR source code and user manual, including example files and troubleshooting, is available at https://github.com/alex-bio/UniProtExtractR. The Shiny app is hosted at https://harperlab.connect.hms.harvard.edu/uniprotextractR.
Compositional analysis of microbiome data using the linear decomposition model (LDM)
Authors: Hu Yi-Juan , Satten Glen A 
Published: November 2023

Abstract

Summary
There are compelling reasons to test compositional hypotheses about microbiome data. We present here linear decomposition model-centered log ratio (LDM-clr), an extension of our LDM approach to allow fitting linear models to centered-log-ratio-transformed taxa count data. As LDM-clr is implemented within the existing LDM program, this extension enjoys all the features supported by LDM, including a compositional analysis of differential abundance at both the taxon and community levels, while allowing for a wide range of covariates and study designs for either association or mediation analysis.

Availability and implementation
LDM-clr has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM.
Spatiotemporal patterns of historical connections between Amazonian and Atlantic forests
Authors: Fabrício Machado Arielli , Nakamura Gabriel , Duarte Ritter Camila , Duarte Leandro 
Published: November 2023

Abstract
Despite the disjunct distribution of the Amazonian and the Atlantic forests, three historical connections between those biomes have been hypothesized: through Northeast Brazil, the Brazilian Cerrado, and the Southeast–Northwest. Temporal variation has been suggested to occur in these connections, with recent connections for the Northeast and older connections for the Southeast–Northwest. We tested for the hypothesis of temporal variation in these connections using Neotropical mammals as a study group. Phylogenetic and spatial data of sister groups from each forest were combined to access the spatiotemporal patterns of these connections. The relationship between distance route and divergence times was tested using linear regression. The results revealed that the previously suggested spatiotemporal pattern was corroborated only for Rodentia but not for Didelphimorphia and Chiroptera, showing both old and recent connections for all routes. In addition, each family revealed specific connections at different times. We refute the previously proposed absence of old connections through the Northeast route. Rather, temporal variation in the Northeast differs among the mammalian groups according to their evolutionary histories. Owing to the biogeographical history of each group, different connections were found at different times. Therefore, connections between these forests cannot be explained by a single spatiotemporal pattern.
Serum metallomics reveals insights into the associations of elements with the progression of preleukemic diseases toward acute leukemia
Authors: Siddiqui Amna Jabbar , Khan Noman , Fatima Kauser , Farooq Sabiha , Ramzan Muhammad , El-Seedi Hesham R , Uddin Jalal , Muhsinah Abdullatif Bin , Musharraf Syed Ghulam 
Published: November 2023

Abstract
Acute leukemia (AL) is a critical neoplasm of white blood cells with two main subtypes: acute lymphoblastic leukemia (ALL) and acute myeloid leukemia (AML). This study is focused on understanding the association of the preleukemic disease aplastic anemia (APA) with ALL and AML at metallomic level, using healthy subjects as a control. In this study, a validated and efficient inductively coupled plasma-mass spectrometry/MS-based workflow was employed to profile a total of 13 metallomic features. The study encompassed 41 patients with AML, 62 patients with ALL, 46 patients with APA, and 55 age-matched healthy controls. The metallomic features consisted of eight essential elements (Ca, Co, Cu, Fe, Mg, Mn, Se, and Zn) and five non-essential/toxic elements (Ag, Cd, Cr, Ni, and Pb). Six out of the 13 elements were found to be substantially different (P &lt; .05) using absolute concentrations between serum samples of AL (ALL and AML) and preleukemia (APA) patients in comparison with healthy subjects. Elements including magnesium, calcium, iron, copper, and zinc were upregulated and only one element (chromium) was downregulated in serum samples of disease when compared with healthy subjects. Through the utilization of both univariate tests and multivariate classification modeling, it was determined that chromium exhibited a progressive behavior among the studied elements. Specifically, chromium displayed a sequential upregulation from healthy individuals to preleukemic disease (APA), and ultimately in patients diagnosed with ALL. Overall, metallomic-based biomarkers may have the utility to predict the association of APA with ALL.
Composite quality measures of abdominal surgery at a population level: systematic review
Authors: Rajesh Joel , Sorensen Jan , McNamara Deborah A 
Published: November 2023

Abstract

Background
Measurement of surgical quality at a population level is challenging. Composite quality measures derived from administrative and clinical information systems could support system-wide surgical quality improvement by providing a simple metric that can be evaluated over time. The aim of this systematic review was to identify published studies of composite measures used to assess the overall quality of abdominal surgical services at a hospital or population level.

Methods
A search was conducted in PubMed and MEDLINE for references describing measurement instruments evaluating the overall quality of abdominal surgery. Instruments combining multiple process and quality indicators into a single composite quality score were included. The identified instruments were described in terms of transparency, justification, handling of missing data, case-mix adjustment, scale branding and choice of weight and uncertainty to assess their relative strengths and weaknesses (PROSPERO registration: CRD42022345074).

Results
Of 5234 manuscripts screened, 13 were included. Ten unique composite quality measures were identified, mostly developed within the past decade. Outcome measures such as mortality rate (40 per cent), length of stay (40 per cent), complication rate (60 per cent) and morbidity rate (70 per cent) were consistently included. A major challenge for all instruments is the reliance of valid administrative data and the challenges of assigning appropriate weights to the underlying instrument components. A conceptual framework for composite measures of surgical quality was developed.

Conclusion
None of the composite quality measures identified demonstrated marked superiority over others. The degree to which administrative and clinical data influences each composite measure differs in important ways. There is a need for further testing and development of these measures.
Total neoadjuvant therapy followed by a watch-and-wait strategy for patients with rectal cancer (TOWARd): protocol for single-arm phase II/III confirmatory trial (JCOG2010)
Authors: Hashimoto Tadayoshi , Tsukamoto Shunsuke , Murofushi Keiko , Ito Yoshinori , Hirano Hidekazu , Tsukada Yuichiro , Sasaki Keita , Mizusawa Junki , Fukuda Haruhiko , Takashima Atsuo , Kanemitsu Yukihide 
Published: November 2023

Abstract

Background
Radical surgery is the standard treatment for rectal cancer, but can impact quality of life. Recently, the concept of total neoadjuvant therapy with a watch-and-wait strategy has been proposed in which patients with a cCR after total neoadjuvant therapy do not proceed to surgery. However, most investigations of a watch-and-wait strategy have reported cases where cCR was achieved coincidentally via total neoadjuvant therapy. The aim is to assess whether total neoadjuvant therapy is effective in early-stage rectal cancer in patients that achieve cCR and are offered a watch-and-wait strategy.

Methods
JCOG2010 (TOWARd) is a multi-institutional, single-arm phase II/III confirmatory investigation of the safety and efficacy of total neoadjuvant therapy followed by a watch-and-wait strategy for rectal cancer. Key eligibility criteria include cT2–3 N0 M0 rectal adenocarcinoma, tumour diameter less than or equal to 5 cm, age 18–75 years, performance status 0–1, and no history of pelvic irradiation or rectal surgery. Total neoadjuvant therapy involves neoadjuvant chemoradiotherapy (capecitabine and radiotherapy: 45 Gy/25 fractions to the whole pelvis plus boost of 5.4 Gy/3 fractions to the primary tumour) followed by consolidation chemotherapy (four cycles of capecitabine/oxaliplatin). Patients will be re-staged every 8 weeks after total neoadjuvant therapy, and those who achieve cCR will undergo a watch-and-wait strategy, those with near complete response will undergo a watch-and-wait strategy or local resection, and those with an incomplete response will undergo radical surgery. The primary endpoint is the cCR rate in phase II and 5-year overall survival in phase III. Secondary endpoints include postoperative anal, urinary, and sexual function. A total of 105 patients (phase II, 40 patients; phase III, 65 patients) will be enrolled over 3.5 years.

Conclusion
This trial will determine whether total neoadjuvant therapy and a watch-and-wait strategy is an effective alternative to radical surgery for early-stage rectal cancer in patients with cT2–3 N0 M0 and tumour size less than or equal to 5 cm.

Registration number
jRCTs031220288 (https://jrct.niph.go.jp/en-latest-detail/jRCTs031220288).
Revisiting a Positive Living Group Climate as a Citizenship Climate: A Socio-Spatial Perspective on Residential Youth Care
Authors: Remmery Matthias , Allemeersch Simon , Roose Rudi , Roets Griet 
Published: November 2023

Abstract
The concept of a positive living group climate is currently used as a key strategy to substantially realise the citizenship of youngsters in residential youth care. The concept focuses mainly on what happens inside the residential youth care facility, as the interpersonal relationships between the professionals and the youngsters are identified as the main component of a positive living group climate. How the youngsters practise and experience their citizenship in their everyday lives is also socio-spatially shaped and accommodated outside the residential youth care facility. We implement a multi-method qualitative research approach to explore how the pedagogical climate in residential youth care is socio-spatially shaped and accommodated as a living environment. The findings show that residential youth care is embedded in a wider social living environment in which youngsters navigate physically and socially through different relationships, circumstances and pedagogical milieus. This results in a synergy between dynamics in residential youth care and the wider social living environment, in which meaningful pedagogical interventions can take place. We consider it necessary to deepen and broaden the concept of a positive living group climate in residential youth care, revisiting the pedagogical climate as a citizenship climate.
Caspase cleavage of gasdermin E causes neuronal pyroptosis in HIV-associated neurocognitive disorder
Authors: Fernandes Jason P , Branton William G , Cohen Eric A , Koopman Gerrit , Kondova Ivanela , Gelman Benjamin B , Power Christopher 
Published: November 2023

Abstract
Despite effective antiretroviral therapies, 20–30% of persons with treated HIV infection develop a neurodegenerative syndrome termed HIV-associated neurocognitive disorder (HAND).
HAND is driven by HIV expression coupled with inflammation in the brain but the mechanisms underlying neuronal damage and death are uncertain. The inflammasome-pyroptosis axis coordinates an inflammatory type of regulated lytic cell death that is underpinned by the caspase-activated pore-forming gasdermin proteins. The mechanisms driving neuronal pyroptosis were investigated herein in models of HAND, using multi-platform molecular and morphological approaches that included brain tissues from persons with HAND and simian immunodeficiency virus (SIV)-infected non-human primates as well as cultured human neurons.
Neurons in the frontal cortices from persons with HAND showed increased cleaved gasdermin E (GSDME), which was associated with β-III tubulin degradation and increased HIV levels. Exposure of cultured human neurons to the HIV-encoded viral protein R (Vpr) elicited time-dependent cleavage of GSDME and Ninjurin-1 (NINJ1) induction with associated cell lysis that was inhibited by siRNA suppression of both proteins. Upstream of GSDME cleavage, Vpr exposure resulted in activation of caspases-1 and 3. Pretreatment of Vpr-exposed neurons with the caspase-1 inhibitor, VX-765, reduced cleavage of both caspase-3 and GSDME, resulting in diminished cell death. To validate these findings, we examined frontal cortical tissues from SIV-infected macaques, disclosing increased expression of GSDME and NINJ1 in cortical neurons, which was co-localized with caspase-3 detection in animals with neurological disease. Thus, HIV infection of the brain triggers the convergent activation of caspases-1 and -3, which results in GSDME-mediated neuronal pyroptosis in persons with HAND.
These findings demonstrate a novel mechanism by which a viral infection causes pyroptotic death in neurons while also offering new diagnostic and therapeutic strategies for HAND and other neurodegenerative disorders.
Mitogenomics clarifies the position of the Nearctic magpies (Pica hudsonia and Pica nuttalli) within the Holarctic magpie radiation
Authors: Kryukov Alexey P , Kryukov Kirill A , Collier Kathleen , Fang Bohao , Edwards Scott V 
Published: November 2023

Abstract
Partial separation of a peripheral population may lead to its divergence and, potentially, speciation due to genetic drift followed by selection and geographic isolation. This process may cause taxonomic uncertainty because reproductive isolation in allopatry cannot be verified directly. The two Nearctic allopatric species of magpies (Aves, Corvidae: Pica) serve as a good example of these problems. The Black-billed magpie Pica hudsonia is widely distributed in North America, whereas the Yellow-billed Magpie Pica nuttalli is endemic to a restricted range in California. Their relationships with Palearctic species have been little studied. We obtained complete mitochondrial genomes of both Nearctic magpie species, along with the Eurasian Magpie (Pica pica) and the Oriental Magpie (Pica serica), 20 mitogenomes in total. Phylogenetic analysis reveals a basal position of P. serica, and P. pica as a sister clade to the two Nearctic species. P. hudsonia and P. nuttalli form reciprocal monophyletic subclades, showing recent divergence between and within them. Our data show that the Nearctic magpie lineage diverged from the common ancestor with P. pica, with a single migration wave via the Beringia. Within the Nearctic, we hypothesize a peripatric mode of speciation among Pica taxa due to the divergence and separation of the small marginal population in California below the Sierra-Nevada mountains. Diversifying amino acid substitutions in ND4-ND5-ND6 genes along the branch leading to the New World clade may indicate selection for heat-tolerance. Considering the clear phenotypic differences between P. hudsonia and P. nuttalli, our data, showing their reciprocal monophylies and genetic distinctness, is consistent with the two-species taxonomy.
LeishMANIAdb: a comparative resource for Leishmania proteins
Authors: Tusnády Gábor E , Zeke András , Kálmán Zsófia E , Fatoux Marie , Ricard-Blum Sylvie , Gibson Toby J , Dobson Laszlo 
Published: November 2023

Abstract
Leishmaniasis is a detrimental disease causing serious changes in quality of life and some forms can lead to death. The disease is spread by the parasite Leishmania transmitted by sandfly vectors and their primary hosts are vertebrates including humans. The pathogen penetrates host cells and secretes proteins (the secretome) to repurpose cells for pathogen growth and to alter cell signaling via host–pathogen protein–protein interactions). Here, we present LeishMANIAdb, a database specifically designed to investigate how Leishmania virulence factors may interfere with host proteins. Since the secretomes of different Leishmania species are only partially characterized, we collated various experimental evidence and used computational predictions to identify Leishmania secreted proteins to generate a user-friendly unified web resource allowing users to access all information available on experimental and predicted secretomes. In addition, we manually annotated host–pathogen interactions of 211 proteins and the localization/function of 3764 transmembrane (TM) proteins of different Leishmania species. We also enriched all proteins with automatic structural and functional predictions that can provide new insights in the molecular mechanisms of infection. Our database may provide novel insights into Leishmania host–pathogen interactions and help to identify new therapeutic targets for this neglected disease.
Database URL: https://leishmaniadb.ttk.hu/
Data-Driven Envelopment with Privacy-Policy Tying
Authors: Condorelli Daniele , Padilla Jorge 
Published: November 2023

Abstract
We present a theory of monopoly protection by means of entry in adjacent markets that have a common customer base (i.e., envelopment). A firm dominant in its market enters a data-rich secondary market and engages in predatory pricing and privacy-policy tying. We define the latter as conditioning service provision to the subscription of a privacy policy that allows bundling of user data across all sources. Acquiring data from the secondary market confers an advantage in the data-intensive primary market that shields the dominant firm from entry, thus harming consumers. We discuss potential remedies, including data unbundling and portability.
Isolation and identification of specific lytic bacteriophages as a biocontrol agent against Serratia odorifera PBA-IAUF-1 and Kluyvera intermedia PBA-IAUF-6 causing bacterial canker in the grape and Siberian pear
Authors: Parsafar Somayeh , Beheshti Maal Keivan , Akkafi Hamid Reza , Rahimzadeh Torabi Ladan 
Published: November 2023

Abstract
Bacterial canker, a prevalent disease among fruit trees, is a significant concern. The use of phage therapy is presently seen as a dependable biological strategy to control bacterial diseases in fruits. The objective of this research was to use various biochemical and molecular techniques to determine the types of bacteria responsible for causing cankers in various fruits. Additionally, their ability to cause disease in the fruit tissues was assessed, the specific bacteriophages targeting these bacteria were isolated and identified. The bacteria were separated from different parts of the infected fruits like grapes and Siberian pears. The selection of fruit tissues showing signs of canker disease was performed, and the validation of the isolates’ pathogenicity was confirmed following Koch’s principles. Subsequently, in order to establish a conclusive identification of the bacterial species, molecular identification was conducted through the sequencing of a specific fragment within the 16S rRNA following amplification by PCR by using universal primers, RW01 and DG74. Isolation and titration of phages specific to fruit spoilage bacteria was done by spot and double-layer agar method, and the growth curve of the isolated bacteriophage was drawn. The phages were detected by transmission electron microscopy (TEM). The results of the study proved the presence of canker causing agents, Kluyvera intermedia PBA-IAUF-6 with the code Sh6 in the Siberian pears, and Serratia odorifera PBA-IAUF-1 with the code Rz3 in the grape fruits, which were deposited in GenBank with the accession numbers of KU878579 and KU168605, respectively. Isolation of the specific bacteriophages to the S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 bacterial strains were done from the effluent of South Isfahan wastewater treatment plant and Caspian Sea water, respectively. The titer of the specific phage to S. odorifera PBA-IAUF-1 and K. intermedia PBA-IAUF-6 was detected in the samples as 2.2 × 10−5 and 5 × 10−11 PFU/ml, respectively. An electron micrograph of a bacteriophage that targets two different bacterial strains revealed phages with a geometrically shaped head and a flexible tail, which resembled viruses from the Siphoviridae family.
Noise correlation analysis: the role of the inflection points in the formation of zero-time waves
Authors: Xia Yingjie , Feng Xuping , Chen Xiaofei 
Published: November 2023

SUMMARY
The cross-correlation function (CCF) of seismic noise recorded at two stations often exhibits a prominent burst of energy near zero time. However, the excitation mechanism of such unexpected signals remains unclear. In this study, we demonstrate that this phenomenon arises from constructive interference of body waves radiating from sources near the mid-vertical plane between two receivers. This interference is driven by the occurrence of an inflection point effect in the traveltime difference between waves reaching the two receivers. When noise source distribution is asymmetric, the cumulative effect of such sources results in the generation of zero-time waves. It is noteworthy that a noise source distribution that is either uniform or follows a cosϕ pattern, with ϕ denoting the azimuth from the centre of the receiver pair, can counteract the formation of these waves. Additionally, our investigation reveals that this constructive interference does not occur in the correlation of 2-D surface waves. We used numerical simulation to support our findings. In conclusion, this study offers a theoretical explanation for the emergence of zero-time waves on the CCF and provides efficient means of investigating the extraction of inter-receiver waves with uneven noise source distribution.