bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intersection of network medicine and machine learning towards investigating the key biomarkers and pathways underlying amyotrophic lateral sclerosis: a systematic review
Authors: Das Trishala , Kaur Harbinder , Gour Pratibha , Prasad Kartikay , Lynn Andrew M , Prakash Amresh , Kumar Vijay 
Published: November 2022

Abstract

Background
Network medicine is an emerging area of research that focuses on delving into the molecular complexity of the disease, leading to the discovery of network biomarkers and therapeutic target discovery. Amyotrophic lateral sclerosis (ALS) is a complicated rare disease with unknown pathogenesis and no available treatment. In ALS, network properties appear to be potential biomarkers that can be beneficial in disease-related applications when explored independently or in tandem with machine learning (ML) techniques.

Objective
This systematic literature review explores recent trends in network medicine and implementations of network-based ML algorithms in ALS. We aim to provide an overview of the identified primary studies and gather details on identifying the potential biomarkers and delineated pathways.

Methods
The current study consists of searching for and investigating primary studies from PubMed and Dimensions.ai, published between 2018 and 2022 that reported network medicine perspectives and the coupling of ML techniques. Each abstract and full-text study was individually evaluated, and the relevant studies were finally included in the review for discussion once they met the inclusion and exclusion criteria.

Results
We identified 109 eligible publications from primary studies representing this systematic review. The data coalesced into two themes: application of network science to identify disease modules and promising biomarkers in ALS, along with network-based ML approaches. Conclusion This systematic review gives an overview of the network medicine approaches and implementations of network-based ML algorithms in ALS to determine new disease genes, and identify critical pathways and therapeutic target discovery for personalized treatment.
OAF: a new member of the BRICHOS family
Authors: Sanchez-Pulido Luis , Ponting Chris P 
Published: November 2022

Abstract

Summary
The 10 known BRICHOS domain-containing proteins in humans have been linked to an unusually long list of pathologies, including cancer, obesity and two amyloid-like diseases. BRICHOS domains themselves have been described as intramolecular chaperones that act to prevent amyloid-like aggregation of their proteins' mature polypeptides. Using structural comparison of coevolution-based AlphaFold models and sequence conservation, we identified the Out at First (OAF) protein as a new member of the BRICHOS family in humans. OAF is an experimentally uncharacterized protein that has been proposed as a candidate biomarker for clinical management of coronavirus disease 2019 infections. Our analysis revealed how structural comparison of AlphaFold models can discover remote homology relationships and lead to a better understanding of BRICHOS domain molecular mechanism.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
Children’s syntax is supported by the maturation of BA44 at 4 years, but of the posterior STS at 3 years of age
Authors: Klein Cheslie C , Berger Philipp , Goucha Tomás , Friederici Angela D , Grosse Wiesmann Charlotte 
Published: November 2022

Abstract
Within the first years of life, children learn major aspects of their native language. However, the ability to process complex sentence structures, a core faculty in human language called syntax, emerges only slowly. A milestone in syntax acquisition is reached around the age of 4 years, when children learn a variety of syntactic concepts. Here, we ask which maturational changes in the child’s brain underlie the emergence of syntactically complex sentence processing around this critical age. We relate markers of cortical brain maturation to 3- and 4-year-olds’ sentence processing in contrast to other language abilities. Our results show that distinct cortical brain areas support sentence processing in the two age groups. Sentence production abilities at 3 years were associated with increased surface area in the most posterior part of the left superior temporal sulcus, whereas 4-year-olds showed an association with cortical thickness in the left posterior part of Broca’s area, i.e. BA44. The present findings suggest that sentence processing abilities rely on the maturation of distinct cortical regions in 3- compared to 4-year-olds. The observed shift to more mature regions involved in processing syntactically complex sentences may underlie behavioral milestones in syntax acquisition at around 4 years.
Development of neonatal brain functional centrality and alterations associated with preterm birth
Authors: Fenn-Moltu Sunniva , Fitzgibbon Sean P , Ciarrusta Judit , Eyre Michael , Cordero-Grande Lucilio , Chew Andrew , Falconer Shona , Gale-Grant Oliver , Harper Nicholas , Dimitrova Ralica , Vecchiato Katy , Fenchel Daphna , Javed Ayesha , Earl Megan , Price Anthony N , Hughes Emer , Duff Eugene P , O’Muircheartaigh Jonathan , Nosarti Chiara , Arichi Tomoki , Rueckert Daniel , Counsell Serena , Hajnal Joseph V , Edwards A David , McAlonan Grainne , Batalle Dafnis 
Published: November 2022

AbstractFormation of the functional connectome in early life underpins future learning and behavior. However, our understanding of how the functional organization of brain regions into interconnected hubs (centrality) matures in the early postnatal period is limited, especially in response to factors associated with adverse neurodevelopmental outcomes such as preterm birth. We characterized voxel-wise functional centrality (weighted degree) in 366 neonates from the Developing Human Connectome Project. We tested the hypothesis that functional centrality matures with age at scan in term-born babies and is disrupted by preterm birth. Finally, we asked whether neonatal functional centrality predicts general neurodevelopmental outcomes at 18 months. We report an age-related increase in functional centrality predominantly within visual regions and a decrease within the motor and auditory regions in term-born infants. Preterm-born infants scanned at term equivalent age had higher functional centrality predominantly within visual regions and lower measures in motor regions. Functional centrality was not related to outcome at 18 months old. Thus, preterm birth appears to affect functional centrality in regions undergoing substantial development during the perinatal period. Our work raises the question of whether these alterations are adaptive or disruptive and whether they predict neurodevelopmental characteristics that are more subtle or emerge later in life.
The dynamics of cortical interactions in visual recognition of object category: living versus nonliving
Authors: Usami Kiyohide , Matsumoto Riki , Korzeniewska Anna , Shimotake Akihiro , Matsuhashi Masao , Nakae Takuro , Kikuchi Takayuki , Yoshida Kazumichi , Kunieda Takeharu , Takahashi Ryosuke , Crone Nathan E , Ikeda Akio 
Published: November 2022

Abstract
Noninvasive brain imaging studies have shown that higher visual processing of objects occurs in neural populations that are separable along broad semantic categories, particularly living versus nonliving objects. However, because of their limited temporal resolution, these studies have not been able to determine whether broad semantic categories are also reflected in the dynamics of neural interactions within cortical networks. We investigated the time course of neural propagation among cortical areas activated during object naming in 12 patients implanted with subdural electrode grids prior to epilepsy surgery, with a special focus on the visual recognition phase of the task. Analysis of event-related causality revealed significantly stronger neural propagation among sites within ventral temporal lobe (VTL) at early latencies, around 250 ms, for living objects compared to nonliving objects. Differences in other features, including familiarity, visual complexity, and age of acquisition, did not significantly change the patterns of neural propagation. Our findings suggest that the visual processing of living objects relies on stronger causal interactions among sites within VTL, perhaps reflecting greater integration of visual feature processing. In turn, this may help explain the fragility of naming living objects in neurological diseases affecting VTL.
Monoclonal Antibodies as Long-Acting Products: What Are We Learning From Human Immunodeficiency Virus (HIV) and Coronavirus Disease 2019 (COVID-19)?
Authors: Caskey Marina , Kuritzkes Daniel R 
Published: November 2022

Abstract
Broadly neutralizing antibodies directed against human immunodeficiency virus (HIV) offer promise as long-acting agents for prevention and treatment of HIV. Progress and challenges are discussed. Lessons may be learned from the development of monoclonal antibodies to treat and prevent COVID-19.
It Pro’s on Crypto, Stablecoin and Blockchain
Authors: Runciman Brian 
Published: November 2022

Abstract
Cryptocurrency values are tanking, the government’s NFT and stablecoin plans have been met with scepticism, NFTs are widely termed a scam and, whilst blockchain has some use cases, it has green issues to rival big oil. Brian Runciman MBCS looks at a recent BCS survey.
Distributed Partial Simulation for Graph Pattern Matching
Authors: Aouar Aissam , Yahiaoui Saïd , Sadeg Lamia , Nouali-Taboudjemat Nadia , Beghdad Bey Kadda 
Published: November 2022

Abstract
Pattern matching in big graphs is important for different modern applications. Recently, this problem was defined in terms of multiple extensions of graph simulation, to reduce complexity and capture more meaningful results. These results were achieved through the relaxation of commonly used constraint in subgraph isomorphism pattern matching. Nevertheless, these graph simulation variant models are still too strict to provide results in many cases, especially when analyzed graphs contain anomalies and incomplete information. To deal with this issue, we introduce a new graph pattern matching (GPM) method, called partial simulation, capable of retrieving matches despite missing parts of the pattern graph, such as vertices and/or edges. Furthermore, considering the number and inequality of the outputs, we define a relevance function to compute a value expressing how each match vertex respects the pattern graph. Similarly, we define partial dual simulation GPM that returns vertices that satisfy a part of the dual simulation constraints and assigns a relevance value to them. Additionally, we provide distributed scalable algorithms to evaluate the proposed partial simulation methods based on the distributed vertex-centric programming paradigm. Finally, our experiments on real-world data graphs demonstrate the effectiveness of the proposed models and the efficiency of their associated algorithms.
How not to run international affairs
Authors: Toye Richard 
Published: November 2022

Abstract
This article explores three case-studies—the Munich crisis of 1938, the Suez crisis and war of 1956 and the Iraq war of 2003—as examples of ‘how not to run international affairs’. On the face of it, all three episodes were disasters. Irrespective of whether Munich was strategically correct, Neville Chamberlain's public presentation of the agreement was a clear miscalculation. Anthony Eden created an elaborate pretext for invading Egypt, which was nevertheless so see-through that it destroyed British credibility. Tony Blair appears to have persuaded himself into believing that Saddam had weapons of mass destruction, and basing his case for war upon this idea left him exposed when the weapons were shown not to exist. Whereas it is easy to say that these mistakes should not have been made, it is harder to suggest mechanisms that would prevent leaders falling prey to such delusions, when their immediate political interests appear to depend on them. The article concludes that in these three cases failure was over-determined; on the other hand, there are many everyday crises that foreign policy actors, who understand ‘how not to run international affairs’, succeed in preventing from turning into disasters.
How not to negotiate: the case of trade multilateralism
Authors: Narlikar Amrita 
Published: November 2022

Abstract
Trade multilateralism would not have featured as a case of ‘abject failure’ had this special issue been planned in 2001. But since then, the World Trade Organization (WTO) has unfortunately become an almost perfect example of how not to negotiate, even when one takes into account the limited successes of the 12th ministerial conference in June 2022. This article proceeds in four steps. The first section outlines the multiple levels of malfunction and breakdown in the organization. The second part argues that a variety of negotiation failures are responsible for the dire straits in which the WTO finds itself today. I identify three broad categories of bargaining failures in this member-driven organization: negotiation mishaps that have led to the Doha deadlocks; negotiation muddles that members have got themselves into while updating the institutional practices of the WTO; and failures on the part of the membership to find negotiated solutions to new systemic challenges. The third section reflects on the interaction of my own research with the world of policy. The fourth and concluding section presents the main ‘Dos’ and ‘Don'ts’ that follow from the analysis, and offers some further policy recommendations.
Genetic evidence for causal relationships between age at natural menopause and the risk of ageing-associated adverse health outcomes
Authors: Lankester Joanna , Li Jin , Salfati Elias Levy Itshak , Stefanick Marcia L , Chan Kei Hang Katie , Liu Simin , Crandall Carolyn J , Clarke Shoa L , Assimes Themistocles L 
Published: November 2022

AbstractBackgroundA later age at natural menopause (ANM) has been linked to several ageing-associated traits including an increased risk of breast and endometrial cancer and a decreased risk of lung cancer, osteoporosis and Alzheimer disease. However, ANM is also related to several proxies for overall health that may confound these associations.MethodsWe investigated the causal association of ANM with these clinical outcomes using Mendelian randomization (MR). Participants and outcomes analysed were restricted to post-menopausal females. We conducted a one-sample MR analysis in both the Women’s Health Initiative and UK Biobank. We further analysed and integrated several additional data sets of post-menopausal women using a two-sample MR design. We used ≤55 genetic variants previously discovered to be associated with ANM as our instrumental variable.ResultsA 5-year increase in ANM was causally associated with a decreased risk of osteoporosis [odds ratio (OR) = 0.80, 95% CI (0.70–0.92)] and fractures (OR = 0.76, 95% CI, 0.62–0.94) as well as an increased risk of lung cancer (OR = 1.35, 95% CI, 1.06–1.71). Other associations including atherosclerosis-related outcomes were null.ConclusionsOur study confirms that the decline in bone density with menopause causally translates into fractures and osteoporosis. Additionally, this is the first causal epidemiological analysis to our knowledge to find an increased risk of lung cancer with increasing ANM. This finding is consistent with molecular and epidemiological studies suggesting oestrogen-dependent growth of lung tumours.
Factors Associated With Vaccine-Induced T-Cell Immune Responses Against Severe Acute Respiratory Syndrome Coronavirus 2 in Kidney Transplant Recipients
Authors: Tometten Inga , Landmann Sinje , Kantauskaite Marta , Lamberti Joshua , Hillebrandt Jonas , Müller Lisa , Kittel Margarethe , Kolb Thilo , Ivens Katrin , Schmitz Michael , Voges Anja , Adams Ortwin , Andrée Marcel , Schaal Heiner , Lübke Nadine , Königshausen Eva , Rump Lars Christian , Stegbauer Johannes , Timm Jörg 
Published: November 2022

AbstractVaccination against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important prophylactic measure in kidney transplant recipients (KTRs), but the immune response is often impaired. Here, we examined the T-cell immune response against SARS-CoV-2 in 148 KTRs after 3 or 4 vaccine doses, including 35 KTRs with subsequent SARS-CoV-2 infection. The frequency of spike-specific T cells was lower in KTRs than in immunocompetent controls and was correlated with the level of spike-specific antibodies. Positive predictors for detection of vaccine-induced T cells were detection of spike-specific antibodies, heterologous immunization with messenger RNA and a vector vaccine, and longer time after transplantation. In vaccinated KTRs with subsequent SARS-CoV-2 infection, the T-cell response was greatly enhanced and was significantly higher than in vaccinated KTRs without SARS-CoV-2 infection. Overall, the data show a correlation between impaired humoral and T-cell immunity to SARS-CoV-2 vaccination and provide evidence for greater robustness of hybrid immunity in KTRs.
Housing Insecurity and Homelessness: Evidence from the United Kingdom
Authors: Fetzer Thiemo , Sen Srinjoy , Souza Pedro C L 
Published: November 2022

AbstractHomelessness and precarious living conditions are on the rise across much of the Western world. This paper exploits quasi-exogenous variation in the affordability of rents due to a cut in rent subsidies for low-income households in the United Kingdom in April 2011. Using comprehensive district-level administrative data, we show that the affordability shock caused a significant increase in financial distress, evictions, property crimes, insecure temporary housing arrangements, statutory homelessness, and actual rough sleeping. The most notable rise in statutory homelessness is driven by families with children, lone parents, individuals with existing health conditions, and as a result of having been evicted. We estimate that the fiscal savings were low and shifted toward the local administration: Savings by the central government were partially offset by an increase in council spending to meet statutory obligations for homelessness.
The formation mechanism of the typical hot dry rocks in Hunan Province, China
Authors: Ou Jian , Chen Liangjing , Zhang Baojian , Zhou Hua , Tang Xianchun , Bai Huaqing , Zhang Dailei , Gao Jun 
Published: November 2022

Abstract
Calculated by using the pipeline model, the burial depths of the 150 and 180°C hot dry rocks (HDRs) are 3.20–3.56 and 3.92–4.36 km in the Reshuiwei geothermal field, respectively, while those in the Huitang geothermal field are 3.13–3.50 and 3.84–4.28 km, respectively. Based on the analysis of the geophysical and terrestrial heat flow data, rock thermal generation rates, and the hydrochemical thermometric scale data, we summarized the formation mechanisms of the HDRs in Hunan Province: (i) the boundary deep faults in the welding area have made the intersection part of the deep faults an open tectonic environment, which is beneficial to the upwelling of deep-mantle-sourced thermal matter. (ii) The southeastern Hunan Province is the front region of the West Pacific subduction and retreat. Lithospheric thinning in this area is significant since the Mesozoic era, especially in the Dongting Lake basin, which was formed during extension and depression. This kind of regional lithospheric thinning is favorable for the lateral and upward migration and the intrusion of the deep-mantle-sourced hot substances. (iii) Rocks with high radioactive heat production rates are important crustal thermal sources for the formation of HDRs. Besides that, plutons with similar geological conditions are favorable for the formation of HDR resources. These plutons include the Baimashan pluton and its surrounding areas, and the eastern Dongting Lake plain. Moreover, the intermediate and acid granites distributed in the Chenzhou-Linwu deep fault are also part of the plutons, and the area where the Chenzhou-Linwu deep fault convergent with the Changde-Anren deep fault.
The Draft Italian Code of International Crimes
Authors: Fronza Emanuela , Meloni Chantal 
Published: November 2022

Abstract
In a major effort of coordination, on 31 May 2022, the Committee of Experts appointed by the Italian Minister of Justice delivered the draft Italian ‘Code of International Crimes’ (CIC), whose purpose is to fully implement the Rome Statute into the domestic legal system by adopting substantive legislation on international crimes. The aim of this article is to give an account of the work of the Committee, outlining the prospective legislation and presenting the choices made within the process of implementation. The draft Italian law analysed here represents one example of the different implementation processes which followed the adoption of the ICC Statute, both with respect to the chosen method of implementation — the adoption of an ad hoc code of international crimes — and with respect to some substantive choices, such as the introduction of the crime of cultural genocide and the responsibility of legal persons for international crimes. Ensuring coherence with the fundamental principles of the domestic legal system was of course of utmost importance and guided the entire Committee’s work, in light of the state’s margin of appreciation within the implementation process. In this sense, the implementation process underlying the draft CIC entailed both a transposition of concepts and elements of the ICC Statute into the domestic legal order (internationalization of national laws) and their adaptation to the specific features of the domestic system (nationalization of international criminal law).
Single-molecule localization microscopy based on denoising, interpolation and local maxima
Authors: Cheng Tao 
Published: November 2022

Abstract
A single fluorescent molecule is highly likely to be located at the center pixel position of a raw image diffused spot in an ideal situation. Even if the molecule and the center pixel position do not completely overlap, they are very close. A single-molecule localization method based on denoising, interpolation and local maxima (DIL) is proposed. The low-resolution raw image is denoised and interpolated, and a new image with a pixel size equal to that of the super-resolution image is attained. The local maxima of the new image are extracted. With this method, it is found that the local maxima positions can be regarded as the fluorescent molecule positions. Simulation results demonstrate that the DIL single-molecule localization accuracy reaches ∼18 nm when the Gaussian noise variance is equal to 0.01. Experimental results demonstrate that the DIL localization methodology is comparable to the Gaussian fitting algorithm and is faster.