bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population estimates and sex ratio of the Critically Endangered Antioquia Brushfinch Atlapetes blancae
Authors: Chaparro-Herrera Sergio , Gomez Juan Pablo , Restrepo Arias Marcela , Ponciano José Miguel 
Published: February 2024

Summary
Antioquia Brushfinch Atlapetes blancae is a recently rediscovered Colombian microendemic species with a restricted distribution. Although the species might use a variety of habitats, current information suggests that it is a shrubland specialist. It is categorised as “Critically Endangered” because due to habitat loss its population has been estimated to be smaller than 50 individuals. Such estimates are based on indirect measurements of its population and assumptions regarding its restricted range/habitat. We provide the first direct population estimates and adult sex ratio for seven localities, using mark-resighting techniques. Individuals were captured using mist-nets, bled, and colour banded. Subsequently, we performed censuses along transects to record banded and non-banded individuals. Population estimates were obtained using the classic closed population mark-resighting model. In addition, we used the abundance–area relationship to estimate population size at other sites where the species has been previously recorded. Finally, individuals were sexed by amplifying the Z and W-linked Chromo-Helicase DNA-binding gene (CHD) genes. In total, we banded 55 individuals at four locations. Summarising across the seven sampled localities, we found that the population is most likely composed of 109 individuals in the 122 ha sampled. Based on the abundance–area relationship, we estimated that the population of Antioquia Brushfinch could be as large as 405 individuals in 322 ha of suitable habitat. We found that male/female sex ratio was 0.45 (95% confidence interval [CI] 0.32–0.6) and that it was not significantly biased. Our results suggest that the population of Antioquia Brushfinch is at least eight times larger than suggested by secondary information. We found that populations are properly structured at least regarding sex ratio, although we caution for further research on sex biases of immature and juvenile individuals. We recommend that future studies should focus on population trends and the impact of habitat transformation on the demography of this iconic species.
Evaluation of three prediction formulas of 24-hour urinary sodium excretion in Chinese residents: a systematic review and meta-analysis
Authors: Qi Zijing , Tang Shuai , Wu Beike , Li Yanxing , Yang Hongmei , Wang Kunbo , Li Zhifang 
Published: February 2024

Abstract

Objective:
To determine the appropriateness of three widely used formulas estimating 24-h urinary Na (24hUNa) from spot urine samples in the Chinese population.

Design:
Systematic review and meta-analysis.

Setting:
Literature review was conducted to identify studies for estimating 24hUNa using the Kawasaki, Tanaka and INTERSALT formulas simultaneously in PubMed, Embase and the Cochrane library databases. The mean difference (MD) and correlation coefficients (r) between measures and estimates from different formulas were assessed.

Participants:
Information extraction and quality assessment were performed in thirteen studies involving 8369 subjects.

Results:
Two studies which affected the overall robustness were excluded in the ‘leave-one-out’ sensitivity analyses. Within the final meta-analysis included eleven studies and 7197 participants, 36·07 mmol/d (95 %CI 16·89, 55·25) of MD was observed in the Kawasaki formula, and –19·62 mmol/d (95 %CI –37·37, –1·87) in the Tanaka formula and –35·78 mmol/d (95 %CI –50·76, –20·80) in the INTERSALT formula; a pooled r-Fisher’s Z of 0·39 (95 %CI 0·32, 0·45) in the Kawasaki formula, 0·43 (95 %CI 0·37, 0·49) in the Tanaka formula and 0·36 (95 %CI 0·31, 0·42) in the INTERSALT formula. Subgroup analyses were conducted to explore the possible factors affecting the accuracy of the formula estimation from three mainly aspects: population types, Na intake levels and urine specimen types.

Conclusions:
The meta-analysis suggested that the Tanaka formula performed a more accurate estimate in Chinese population. Time of collecting spot urine specimens and Na intake level of the sample population might be the main factors affecting the accuracy of the formula estimation.
Stable, intense supercontinuum light generation at 1 kHz by electric field assisted femtosecond laser filamentation in air
Authors: Liu Yaoxiang , Yin Fukang , Wang Tie-Jun , Leng Yuxin , Li Ruxin , Xu Zhizhan , Chin See Leang 
Published: February 2024

AbstractSupercontinuum (SC) light source has advanced ultrafast laser spectroscopy in condensed matter science, biology, physics, and chemistry. Compared to the frequently used photonic crystal fibers and bulk materials, femtosecond laser filamentation in gases is damage-immune for supercontinuum generation. A bottleneck problem is the strong jitters from filament induced self-heating at kHz repetition rate level. We demonstrated stable kHz supercontinuum generation directly in air with multiple mJ level pulse energy. This was achieved by applying an external DC electric field to the air plasma filament. Beam pointing jitters of the 1 kHz air filament induced SC light were reduced by more than 2 fold. The stabilized high repetition rate laser filament offers the opportunity for stable intense SC generation and its applications in air.
Diagnostic uplift through the implementation of short tandem repeat analysis using exome sequencing
Authors: Yoon Jihoon G. , Lee Seungbok , Cho Jaeso , Kim Narae , Kim Sheehyun , Kim Man Jin , Kim Soo Yeon , Moon Jangsup , Chae Jong-Hee 
Published: February 2024

AbstractTo date, approximately 50 short tandem repeat (STR) disorders have been identified; yet, clinical laboratories rarely conduct STR analysis on exomes. To assess its diagnostic value, we analyzed STRs in 6099 exomes from 2510 families with mostly suspected neurogenetic disorders. We employed ExpansionHunter and REViewer to detect pathogenic repeat expansions, confirming them using orthogonal methods. Genotype-phenotype correlations led to the diagnosis of thirteen individuals in seven previously undiagnosed families, identifying three autosomal dominant disorders: dentatorubral-pallidoluysian atrophy (n = 3), spinocerebellar ataxia type 7 (n = 2), and myotonic dystrophy type 1 (n = 2), resulting in a diagnostic gain of 0.28% (7/2510). Additionally, we found expanded ATXN1 alleles (≥39 repeats) with varying patterns of CAT interruptions in twelve individuals, accounting for approximately 0.19% in the Korean population. Our study underscores the importance of integrating STR analysis into exome sequencing pipeline, broadening the application of exome sequencing for STR assessments.
Early onset diagnosis in Alzheimer’s disease patients via amyloid-β oligomers-sensing probe in cerebrospinal fluid
Authors: An Jusung , Kim Kyeonghwan , Lim Ho Jae , Kim Hye Yun , Shin Jinwoo , Park InWook , Cho Illhwan , Kim Hyeong Yun , Kim Sunghoon , McLean Catriona , Choi Kyu Yeong , Kim YoungSoo , Lee Kun Ho , Kim Jong Seung 
Published: February 2024

AbstractAmyloid-β (Aβ) oligomers are implicated in the onset of Alzheimer’s disease (AD). Herein, quinoline-derived half-curcumin-dioxaborine (Q-OB) fluorescent probe was designed for detecting Aβ oligomers by finely tailoring the hydrophobicity of the biannulate donor motifs in donor-π-acceptor structure. Q-OB shows a great sensing potency in dynamically monitoring oligomerization of Aβ during amyloid fibrillogenesis in vitro. In addition, we applied this strategy to fluorometrically analyze Aβ self-assembly kinetics in the cerebrospinal fluids (CSF) of AD patients. The fluorescence intensity of Q-OB in AD patients’ CSF revealed a marked change of log (I/I0) value of 0.34 ± 0.13 (cognitive normal), 0.15 ± 0.12 (mild cognitive impairment), and 0.14 ± 0.10 (AD dementia), guiding to distinguish a state of AD continuum for early diagnosis of AD. These studies demonstrate the potential of our approach can expand the currently available preclinical diagnostic platform for the early stages of AD, aiding in the disruption of pathological progression and the development of appropriate treatment strategies.
R-Spondin 2 governs Xenopus left-right body axis formation by establishing an FGF signaling gradient
Authors: Lee Hyeyoon , Camuto Celine Marie , Niehrs Christof 
Published: February 2024

AbstractEstablishment of the left-right (LR, sinistral, dextral) body axis in many vertebrate embryos relies on cilia-driven leftward fluid flow within an LR organizer (LRO). A cardinal question is how leftward flow triggers symmetry breakage. The chemosensation model posits that ciliary flow enriches a signaling molecule on the left side of the LRO that promotes sinistral cell fate. However, the nature of this sinistralizing signal has remained elusive. In the Xenopus LRO, we identified the stem cell growth factor R-Spondin 2 (Rspo2) as a symmetrically expressed, sinistralizing signal. As predicted for a flow-mediated signal, Rspo2 operates downstream of leftward flow but upstream of the asymmetrically expressed gene dand5. Unexpectedly, in LR patterning, Rspo2 acts as an FGF receptor antagonist: Rspo2 via its TSP1 domain binds Fgfr4 and promotes its membrane clearance by Znrf3-mediated endocytosis. Concordantly, we find that at flow-stage, FGF signaling is dextralizing and forms a gradient across the LRO, high on the dextral- and low on the sinistral side. Rspo2 gain- and loss-of function equalize this FGF signaling gradient and sinistralize and dextralize development, respectively. We propose that leftward flow of Rspo2 produces an FGF signaling gradient that governs LR-symmetry breakage.
Risk of SARS-CoV-2 reinfection during multiple Omicron variant waves in the UK general population
Authors: Wei Jia , Stoesser Nicole , Matthews Philippa C. , Khera Tarnjit , Gethings Owen , Diamond Ian , Studley Ruth , Taylor Nick , Peto Tim E. A. , Walker A. Sarah , Pouwels Koen B. , Eyre David W. ,   the COVID-19 Infection Survey team, Rourke Emma , Thomas Tina , Pienaar Dawid , Preece Joy , Crofts Sarah , Lloyd Lina , Bowen Michelle , Ayoubkhani Daniel , Black Russell , Felton Antonio , Crees Megan , Jones Joel , Sutherland Esther , Crook Derrick W. , Pritchard Emma , Vihta Karina-Doris , Howarth Alison , Marsden Brian D. , Chau Kevin K. , Ferreira Lucas Martins , Dejnirattisai Wanwisa , Mongkolsapaya Juthathip , Hoosdally Sarah , Cornall Richard , Stuart David I. , Screaton Gavin , Lythgoe Katrina , Bonsall David , Golubchik Tanya , Fryer Helen , Newton John N. , Bell John I. , Cox Stuart , Paddon Kevin , James Tim , House Thomas , Robotham Julie , Birrell Paul , Jordan Helena , Sheppard Tim , Athey Graham , Moody Dan , Curry Leigh , Brereton Pamela , Jarvis Ian , Godsmark Anna , Morris George , Mallick Bobby , Eeles Phil , Hay Jodie , VanSteenhouse Harper , Lee Jessica , White Sean , Evans Tim , Bloemberg Lisa , Allison Katie , Pandya Anouska , Davis Sophie , Conway David I. , MacLeod Margaret , Cunningham Chris 
Published: February 2024

AbstractSARS-CoV-2 reinfections increased substantially after Omicron variants emerged. Large-scale community-based comparisons across multiple Omicron waves of reinfection characteristics, risk factors, and protection afforded by previous infection and vaccination, are limited. Here we studied ~45,000 reinfections from the UK’s national COVID-19 Infection Survey and quantified the risk of reinfection in multiple waves, including those driven by BA.1, BA.2, BA.4/5, and BQ.1/CH.1.1/XBB.1.5 variants. Reinfections were associated with lower viral load and lower percentages of self-reporting symptoms compared with first infections. Across multiple Omicron waves, estimated protection against reinfection was significantly higher in those previously infected with more recent than earlier variants, even at the same time from previous infection. Estimated protection against Omicron reinfections decreased over time from the most recent infection if this was the previous or penultimate variant (generally within the preceding year). Those 14–180 days after receiving their most recent vaccination had a lower risk of reinfection than those >180 days from their most recent vaccination. Reinfection risk was independently higher in those aged 30–45 years, and with either low or high viral load in their most recent previous infection. Overall, the risk of Omicron reinfection is high, but with lower severity than first infections; both viral evolution and waning immunity are independently associated with reinfection.
A Gamma-adapted subunit vaccine induces broadly neutralizing antibodies against SARS-CoV-2 variants and protects mice from infection
Authors: Coria Lorena M. , Rodriguez Juan Manuel , Demaria Agostina , Bruno Laura A. , Medrano Mayra Rios , Castro Celeste Pueblas , Castro Eliana F. , Del Priore Sabrina A. , Hernando Insua Andres C. , Kaufmann Ingrid G. , Saposnik Lucas M. , Stone William B. , Prado Lineia , Notaro Ulises S. , Amweg Ayelen N. , Diaz Pablo U. , Avaro Martin , Ortega Hugo , Ceballos Ana , Krum Valeria , Zurvarra Francisco M. , Sidabra Johanna E. , Drehe Ignacio , Baqué Jonathan A. , Li Causi Mariana , De Nichilo Analia V. , Payes Cristian J. , Southard Teresa , Vega Julio C. , Auguste Albert J. , Álvarez Diego E. , Flo Juan M. , Pasquevich Karina A. , Cassataro Juliana 
Published: February 2024

AbstractIn the context of continuous emergence of SARS-CoV-2 variants of concern (VOCs), one strategy to prevent the severe outcomes of COVID-19 is developing safe and effective broad-spectrum vaccines. Here, we present preclinical studies of a RBD vaccine derived from the Gamma SARS-CoV-2 variant adjuvanted with Alum. The Gamma-adapted RBD vaccine is more immunogenic than the Ancestral RBD vaccine in terms of inducing broader neutralizing antibodies. The Gamma RBD presents more immunogenic B-cell restricted epitopes and induces a higher proportion of specific-B cells and plasmablasts than the Ancestral RBD version. The Gamma-adapted vaccine induces antigen specific T cell immune responses and confers protection against Ancestral and Omicron BA.5 SARS-CoV-2 challenge in mice. Moreover, the Gamma RBD vaccine induces higher and broader neutralizing antibody activity than homologous booster vaccination in mice previously primed with different SARS-CoV-2 vaccine platforms. Our study indicates that the adjuvanted Gamma RBD vaccine is highly immunogenic and a broad-spectrum vaccine candidate.
Targeting ALK averts ribonuclease 1-induced immunosuppression and enhances antitumor immunity in hepatocellular carcinoma
Authors: Liu Chunxiao , Zhou Chenhao , Xia Weiya , Zhou Yifan , Qiu Yufan , Weng Jialei , Zhou Qiang , Chen Wanyong , Wang Ying-Nai , Lee Heng-Huan , Wang Shao-Chun , Kuang Ming , Yu Dihua , Ren Ning , Hung Mien-Chie 
Published: February 2024

AbstractTumor-secreted factors contribute to the development of a microenvironment that facilitates the escape of cancer cells from immunotherapy. In this study, we conduct a retrospective comparison of the proteins secreted by hepatocellular carcinoma (HCC) cells in responders and non-responders among a cohort of ten patients who received Nivolumab (anti-PD-1 antibody). Our findings indicate that non-responders have a high abundance of secreted RNase1, which is associated with a poor prognosis in various cancer types. Furthermore, mice implanted with HCC cells that overexpress RNase1 exhibit immunosuppressive tumor microenvironments and diminished response to anti-PD-1 therapy. RNase1 induces the polarization of macrophages towards a tumor growth-promoting phenotype through activation of the anaplastic lymphoma kinase (ALK) signaling pathway. Targeting the RNase1/ALK axis reprograms the macrophage polarization, with increased CD8+ T- and Th1- cell recruitment. Moreover, simultaneous targeting of the checkpoint protein PD-1 unleashes cytotoxic CD8+ T-cell responses. Treatment utilizing both an ALK inhibitor and an anti-PD-1 antibody exhibits enhanced tumor regression and facilitates long-term immunity. Our study elucidates the role of RNase1 in mediating tumor resistance to immunotherapy and reveals an RNase1-mediated immunosuppressive tumor microenvironment, highlighting the potential of targeting RNase1 as a promising strategy for cancer immunotherapy in HCC.
A sequence-aware merger of genomic structural variations at population scale
Authors: Zheng Zeyu , Zhu Mingjia , Zhang Jin , Liu Xinfeng , Hou Liqiang , Liu Wenyu , Yuan Shuai , Luo Changhong , Yao Xinhao , Liu Jianquan , Yang Yongzhi 
Published: February 2024

AbstractMerging structural variations (SVs) at the population level presents a significant challenge, yet it is essential for conducting comprehensive genotypic analyses, especially in the era of pangenomics. Here, we introduce PanPop, a tool that utilizes an advanced sequence-aware SV merging algorithm to efficiently merge SVs of various types. We demonstrate that PanPop can merge and optimize the majority of multiallelic SVs into informative biallelic variants. We show its superior precision and lower rates of missing data compared to alternative software solutions. Our approach not only enables the filtering of SVs by leveraging multiple SV callers for enhanced accuracy but also facilitates the accurate merging of large-scale population SVs. These capabilities of PanPop will help to accelerate future SV-related studies.
Imaging the state-to-state charge-transfer dynamics between the spin-orbit excited Ar+(2P1/2) ion and N2
Authors: Zhang Guodong , Lu Dandan , Guo Hua , Gao Hong 
Published: February 2024

AbstractAr++N2 → Ar+N2+ has served as a paradigm for charge-transfer dynamics studies during the last several decades. Despite significant experimental and theoretical efforts on this model system, state-resolved experimental investigations on the microscopic charge-transfer mechanism between the spin-orbit excited Ar+(2P1/2) ion and N2 have been rare. Here, we measure the first quantum state-to-state differential cross sections for Ar++N2 → Ar+N2+ with the Ar+ ion prepared exclusively in the spin-orbit excited state 2P1/2 on a crossed-beam setup with three-dimensional velocity-map imaging. Trajectory surface-hopping calculations qualitatively reproduce the vibrationally dependent rotational and angular distributions of the N2+ product. Both the scattering images and theoretical calculations show that the charge-transfer dynamics of the spin-orbit excited Ar+(2P1/2) ion differs significantly from that of the spin-orbit ground Ar+(2P3/2) when colliding with N2. Such state-to-state information makes quantitative understanding of this benchmark charge-transfer reaction within reach.
Dual Higgs modes entangled into a soliton lattice in CuTe
Authors: Kwon SeongJin , Jung Hyunjin , Lee SangJin , Cho Gil Young , Kong KiJeong , Won ChoongJae , Cheong Sang-Wook , Yeom Han Woong 
Published: February 2024

AbstractRecently discovered Higgs particle is a key element in the standard model of elementary particles and its analogue in materials, massive Higgs mode, has elucidated intriguing collective phenomena in a wide range of materials with spontaneous symmetry breaking such as antiferromagnets, cold atoms, superconductors, superfluids, and charge density waves (CDW). As a straightforward extension beyond the standard model, multiple Higgs particles have been considered theoretically but not yet for Higgs modes. Here, we report the real-space observations, which suggest two Higgs modes coupled together with a soliton lattice in a solid. Our scanning tunneling microscopy reveals the 1D CDW state of an anisotropic transition metal monochalcogenide crystal CuTe is composed of two distinct but degenerate CDW structures by the layer inversion symmetry broken. More importantly, the amplitudes of each CDW structure oscillate in an out-of-phase fashion to result in a regular array of alternating domains with repeating phase-shift domain walls. This unusual finding is explained by the extra degeneracy in CDWs within the standard Landau theory of the free energy. The multiple and entangled Higgs modes demonstrate how novel collective modes can emerge in systems with distinct symmetries broken simultaneously.
Approaching a fully-polarized state of nuclear spins in a solid
Authors: Millington-Hotze Peter , Dyte Harry E. , Manna Santanu , Covre da Silva Saimon F. , Rastelli Armando , Chekhovich Evgeny A. 
Published: February 2024

AbstractMagnetic noise of atomic nuclear spins is a major source of decoherence in solid-state spin qubits. In theory, near-unity nuclear spin polarization can eliminate decoherence of the electron spin qubit, while turning the nuclei into a useful quantum information resource. However, achieving sufficiently high nuclear polarizations has remained an evasive goal. Here we implement a nuclear spin polarization protocol which combines strong optical pumping and fast electron tunneling. Nuclear polarizations well above 95% are generated in GaAs semiconductor quantum dots on a timescale of 1 minute. The technique is compatible with standard quantum dot device designs, where highly-polarized nuclear spins can simplify implementations of qubits and quantum memories, as well as offer a testbed for studies of many-body quantum dynamics and magnetism.
Malaria seroepidemiology in very low transmission settings in the Peruvian Amazon
Authors: Fernandez-Camacho Bryan , Peña-Calero Brian , Guillermo-Roman Martina , Ruiz-Cabrejos Jorge , Barboza Jose Luis , Bartolini-Arana Lucia , Barja-Ingaruca Antony , Rodriguez-Ferrucci Hugo , Soto-Calle Veronica E. , Nelli Luca , Byrne Isabel , Hill Monica , Dumont Elin , Grignard Lynn , Tetteh Kevin , Wu Lindsey , Llanos-Cuentas Alejandro , Drakeley Chris , Stresman Gillian , Carrasco-Escobar Gabriel 
Published: February 2024

AbstractDespite progress towards malaria reduction in Peru, measuring exposure in low transmission areas is crucial for achieving elimination. This study focuses on two very low transmission areas in Loreto (Peruvian Amazon) and aims to determine the relationship between malaria exposure and proximity to health facilities. Individual data was collected from 38 villages in Indiana and Belen, including geo-referenced households and blood samples for microscopy, PCR and serological analysis. A segmented linear regression model identified significant changes in seropositivity trends among different age groups. Local Getis-Ord Gi* statistic revealed clusters of households with high (hotspots) or low (coldspots) seropositivity rates. Findings from 4000 individuals showed a seropositivity level of 2.5% (95%CI: 2.0%-3.0%) for P. falciparum and 7.8% (95%CI: 7.0%-8.7%) for P. vivax, indicating recent or historical exposure. The segmented regression showed exposure reductions in the 40–50 age group (β1 = 0.043, p = 0.003) for P. vivax and the 50–60 age group (β1 = 0.005, p = 0.010) for P. falciparum. Long and extreme distance villages from Regional Hospital of Loreto exhibited higher malaria exposure compared to proximate and medium distance villages (p < 0.001). This study showed the seropositivity of malaria in two very low transmission areas and confirmed the spatial pattern of hotspots as villages become more distant.