bluuebunny/crossref_metadata_2025 huggingface dataset:
An ecological investigation on lichens and other lithobionts colonizing rock art in Valle Camonica (UNESCO WHS n. 94) addresses preventive conservation strategies
Authors: Favero-Longo Sergio E. , Matteucci Enrica , Castelli Daniele , Iacomussi Paola , Martire Luca , Ruggiero Maria Giuseppina , Segimiro Alessandro
Published: September 2023

Environmental control strategies are commonly practised to limit biodeterioration issues threatening indoor cultural heritage objects, while they are still poorly exploited for the conservation of outdoor stone heritage surfaces, including rock art. In this study, we evaluated the environmental factors driving the diversity and abundance of lithobiontic communities in the Rock Engravings National Park of Naquane (UNESCO WHS n. 94, Italy). The survey considered 23 rocks that had been cleaned in the last three (3YC) or twelve (12YC) years or more than 40 years ago (NRC). A cyanobacteria-dominated biofilm and lichens (37 taxa) were the most widespread and abundant lithobiontic components, prevailing on 3YC–12YC and NRC rocks, respectively. On the latter, a turnover of xerophytic and meso-hygrophytic lichen communities was observed. On 3YC–12YC rocks lichen colonization, if present, was limited to nitrophytic species, including common epiphytes from surrounding trees and a small number of meso-hygrophytic species, with a prevalence of asexual reproductive strategies. Multivariate analyses including environmental parameters (canonical correspondence analyses) indicated that tree cover and the presence of bare or vegetated ground upstream of the rocks, probably prolonging wetness and providing nutrients by water transport, are the factors mostly related to the microbial and lichen recolonization of 3YC–12YC surfaces. On this basis, an experiment on preventive conservation was conducted, consisting of a new cleaning of a strongly recolonized 3YC surface combined with the building of a small wall to protect part of the rock from prolonged water fluxes. The fluorimetric and colorimetric monitoring of the rock surface, carried out 40 months after this new cleaning intervention, displayed recolonization on the unprotected area only, indicating the potential of preventive conservation strategies in outdoor environments.
A distinctive new species of Biatora (Ramalinaceae, Lecanorales) described from native European forests
Authors: Palice Zdeněk , Malíček Jiří , Vondrák Jan , Printzen Christian
Published: September 2023

A unique crustose lichen species was recently documented from various types of preserved forests across boreal and temperate Europe (Norway, Ukraine, the Czech Republic) and the Caucasus (Russia). It is formally described here as the new species Biatora amylacea. A phylogeny based on ITS and mtSSU sequences demonstrates that it belongs to an isolated group within the core of Biatora s. lat., together with the recently described B. radicicola. It is a distinctive taxon within the genus on account of its amyloid exciple, otherwise known only from members of the Biatora rufidula group. The new species is also characterized by amyloid thalline hyphae and the production of soredia with a blue-green pigment. This microlichen may serve as a bioindicator species of old-growth forests.
Species–area relationship in lichens tested in protected areas across Italy
Authors: Gheza Gabriele , Di Nuzzo Luca , Giordani Paolo , Chiarucci Alessandro , Benesperi Renato , Bianchi Elisabetta , Canali Giulia , Francesconi Luana , Vallese Chiara , Nascimbene Juri
Published: September 2023

The species–area relationship (SAR) states that species richness increases with the increase of the sampled area, although other factors can influence the pattern. SARs have been tested on many different organisms, but only rarely on lichens. We aimed to test the SAR, across a wide range of area sizes, for three main substratum-related guilds of lichens, namely epiphytic, epilithic and epigaeic. The test was performed using data from lichen inventories carried out in 44 protected areas of various sizes across Italy. We found a positive correlation of species richness with area size for all three guilds, better fitted by the logarithmic function for epilithic lichens and by the power function for epiphytic and epigaeic lichens. Our results support the fundamental role of area size as the main driver for lichen diversity, suggesting that in an area-based conservation framework, larger protected areas are fundamental to support high lichen species richness. However, finer scale investigations are also required to better elucidate whether and how other environmental factors could interact with area size and modify SAR patterns. Exhaustive lichen inventories could be useful information sources to more robustly test such relationships, and therefore better inform conservation practices.
The Woman between Us: Sarah Nakimu Nalwanga and the Founding of Uganda’s Anglican Tradition
Authors: Teketwe Kimeze
Published: September 2023

There has always been a debate about the location and role of women during the persecution of Christians under Mwanga II’s first reign as Kabaka of Buganda. Kabaka is the Luganda equivalent of the English word king. The debate is partly fueled by a total absence of women from the pictures of Ugandans historically referred to as the Uganda Martyrs. This paper uses archival research to tell the story of an African woman who, in her adult life, married two devout Anglicans, in whose lives she was actively involved, laying a foundation for Uganda’s Anglican tradition. Evidence shows the first Anglican baptism, teacher and burial in Uganda are traced to her first marriage, which ended in early 1884 with the death of her husband from smallpox. Nakimu Nalwanga Sarah would have been the first martyr if not for the timely discovery that she was Mwanga’s relative. Still, as a punishment, she was ordered to witness the cruel burning of the first martyrs on January 31, 1885. She married again in a marriage that produced Uganda’s first catechist, deacon and priest. Her second husband was part of a team that completed the translation of the first Luganda Bible in 1895.
Recovery-Colleges in Deutschland
Authors: Stiehl Simon , Schulz Michael , Omundo Jared
Published: September 2023

Was ist zu diesem Thema bereits bekannt?

Recovery Colleges (RC) sind liberale, peer-gestützte Bildungseinrichtungen zur Förderung der individuellen, psychischen Gesundheitskompetenz und Zufriedenheit von Menschen mit beziehungsweise ohne seelischen Krisenerfahrungen.

Wie wird eine neue Perspektive eingebracht?

Abseits der Exploration von Recovery, Häufigkeiten von RCs in Deutschland und positivem Nutzen von Recovery Colleges, wird in diesem Beitrag der Fokus auf die zu wenig beschriebenen Prinzipien, Kernelemente sowie Strukturen von deutschsprachigen College-Einrichtungen im Zuge einer wahrlichen recovery-orientierten Praxis gerichtet.

Was sind die Auswirkungen für die Praxis?

Aufgrund der vorgestellten Prinzipien und Kernmerkmalen von RCs, kann für die Bildungseinrichtungen ein hoher Grad an recovery-orientierter Praxis festgestellt werden, welcher den Nutzenden von RCs und somit der psychosozialen Versorgungsstruktur in der Gemeinde zugutekommt.
Land Cover Control on the Drivers of Evaporation and Sensible Heat Fluxes: An Observation‐Based Synthesis for the Netherlands
Authors: Jansen Femke A. , Jongen Harro J. , Jacobs Cor M. J. , Bosveld Fred C. , Buzacott Alexander J. V. , Heusinkveld Bert G. , Kruijt Bart , van der Molen Michiel , Moors Eddy , Steeneveld Gert‐Jan , van der Tol Christiaan , van der Velde Ype , Voortman Bernard , Uijlenhoet Remko , Teuling Adriaan J.
Published: September 2023

Land cover controls the land‐atmosphere exchange of water and energy through the partitioning of solar energy into latent and sensible heat. Observations over all land cover types at the regional scale are required to study these turbulent flux dynamics over a landscape. Here, we aim to study how the control of daily and midday latent and sensible heat fluxes over different land cover types is distributed along three axes: energy availability, water availability and exchange efficiency. To this end, observations from 19 eddy covariance flux tower sites in the Netherlands, covering six different land cover types located within the same climatic zone, were used in a regression analysis to explain the observed dynamics and find the principle drivers. The resulting relative position of these sites along the three axes suggests that land cover partly explains the variance of daily and midday turbulent fluxes. We found that evaporation dynamics from grassland, peatland swamp and cropland sites could mostly be explained by energy availability. Forest evaporation can mainly be explained by water availability, urban evaporation by water availability and exchange efficiency, and open water evaporation can almost entirely be explained by exchange efficiency. We found that the sensible heat flux is less sensitive to land cover type. This demonstrates that the land‐atmosphere interface plays an active role in the shedding of sensible heat. Our results contribute to a better understanding of the dynamics of evaporation over different land cover types and may help to optimize, and potentially simplify, models to predict evaporation.
Interpretable Machine Learning Reveals Potential to Overcome Reactive Flood Adaptation in the Continental US
Authors: Veigel Nadja , Kreibich Heidi , Cominola Andrea
Published: September 2023

Floods cause average annual losses of more than US$30 billion in the US and are estimated to significantly increase due to global change. Flood resilience, which currently differs strongly between socio‐economic groups, needs to be substantially improved by proactive adaptive measures, such as timely purchase of flood insurance. Yet, knowledge about the state and uptake of private adaptation and its drivers is so far scarce and fragmented. Based on interpretable machine learning and large insurance and socio‐economic open data sets covering the whole continental US we reveal that flood insurance purchase is characterized by reactive behavior after severe flood events. However, we observe that the Community Rating System helps overcome this behavior by effectively fostering proactive insurance purchase, irrespective of socio‐economic backgrounds in the communities. Thus, we recommend developing additional targeted measures to help overcome existing inequalities, for example, by providing special incentives to the most vulnerable and exposed communities.
Effects of the Relative Dynamics of Ionospheric Irregularities and GPS Satellites on Receiver Tracking Loop Performance
Authors: Biswas Trisani , Paul Ashik
Published: September 2023

Transionospheric satellite signals are exposed to perturbation, caused by irregularities generated in the ionosphere. However, the characteristics of the satellite motion can have an additional impact on signal perturbation, in addition to the effects of irregularity structures, that drift from west to east during geomagnetic quiet conditions. This paper reports the effect of Global Positioning System satellite geometry, on tracking loop performance of ground‐based receivers, during occurrence of ionospheric scintillations. Observations are made from station Calcutta (22.58°N, 88.38°E geographic; magnetic dip 34.54°), located near the northern crest of Equatorial Ionization Anomaly, during three different solar activity periods (March 2014, March 2015, and March 2022). Efforts have been made to study the correlation of east‐west component of satellite velocity at Ionospheric Pierce Point (IPP) with duration of loss‐of‐lock and rate of signal fading (<−10 dB), from ground scintillation pattern observations. Results of this study show 75%–78% correlation between duration of loss‐of‐lock and eastward component of satellite velocity, for all three period of observation. Subsequently, shorter duration of loss‐of‐lock has been observed corresponding to satellite velocity being westward. Signal fading rate is found to decrease with increasing satellite velocity, having median value of the fading rate cumulative distribution percentage, corresponding to satellite velocity of 16.69, 31.76, and 19.14 m/s respectively during March 2014, March 2015, and March 2022. Results of this study also indicate direction and component of satellite velocity at IPP to be a dominant cause of signal outage, even during periods of weak to moderate scintillations.
Depletion of G9A attenuates imiquimod-induced psoriatic dermatitis via targeting EDAR-NF-κB signaling in keratinocyte
Authors: Fang Zhiqin , Wang Yutong , Huang Bo , Chen Xiang , Jiang Rundong , Yin Mingzhu
Published: September 2023

Psoriasis is a common and recurrent inflammatory skin disease characterized by inflammatory cells infiltration of the dermis and excessive proliferation, reduced apoptosis, and abnormal keratosis of the epidermis. In this study, we found that G9A, an important methyltransferase that mainly mediates the mono-methylation (me1) and di-methylation (me2) of histone 3 lysine 9 (H3K9), is highly expressed in lesions of patients with psoriasis and imiquimod (IMQ)-induced psoriasis-like mouse model. Previous studies have shown that G9A is involved in the pathogenesis of various tumors by regulating apoptosis, proliferation, differentiation, and invasion. However, the role of G9A in skin inflammatory diseases such as psoriasis remains unclear. Our data so far suggest that topical administration of G9A inhibitor BIX01294 as well as keratinocyte-specific deletion of G9A greatly alleviated IMQ-induced psoriatic alterations in mice for the first time. Mechanistically, the loss function of G9A causes the downregulation of Ectodysplasin A receptor (EDAR), consequently inhibiting the activation of NF-κB pathway, resulting in impaired proliferation and increased apoptosis of keratinocytes, therefore ameliorating the psoriatic dermatitis induced by IMQ. In total, we show that inhibition of G9A improves psoriatic-like dermatitis mainly by regulating cell proliferation and apoptosis rather than inflammatory processes, and that this molecule may be considered as a potential therapeutic target for keratinocyte hyperproliferative diseases such as psoriasis.
Analysis of 72,469 UK Biobank exomes links rare variants to male-pattern hair loss
Authors: Henne Sabrina Katrin , Aldisi Rana , Sivalingam Sugirthan , Hochfeld Lara Maleen , Borisov Oleg , Krawitz Peter Michael , Maj Carlo , Nöthen Markus Maria , Heilmann-Heimbach Stefanie
Published: September 2023

Male-pattern hair loss (MPHL) is common and highly heritable. While genome-wide association studies (GWAS) have generated insights into the contribution of common variants to MPHL etiology, the relevance of rare variants remains unclear. To determine the contribution of rare variants to MPHL etiology, we perform gene-based and single-variant analyses in exome-sequencing data from 72,469 male UK Biobank participants. While our population-level risk prediction suggests that rare variants make only a minor contribution to general MPHL risk, our rare variant collapsing tests identified a total of five significant gene associations. These findings provide additional evidence for previously implicated genes (EDA2R, WNT10A) and highlight novel risk genes at and beyond GWAS loci (HEPH, CEPT1, EIF3F). Furthermore, MPHL-associated genes are enriched for genes considered causal for monogenic trichoses. Together, our findings broaden the MPHL-associated allelic spectrum and provide insights into MPHL pathobiology and a shared basis with monogenic hair loss disorders.
Intrinsic 1$${T}^{{\prime} }$$ phase induced in atomically thin 2H-MoTe2 by a single terahertz pulse
Authors: Shi Jiaojian , Bie Ya-Qing , Zong Alfred , Fang Shiang , Chen Wei , Han Jinchi , Cao Zhaolong , Zhang Yong , Taniguchi Takashi , Watanabe Kenji , Fu Xuewen , Bulović Vladimir , Kaxiras Efthimios , Baldini Edoardo , Jarillo-Herrero Pablo , Nelson Keith A.
Published: September 2023

The polymorphic transition from 2H to 1$${T}^{{\prime} }$$

T

′

-MoTe2, which was thought to be induced by high-energy photon irradiation among many other means, has been intensely studied for its technological relevance in nanoscale transistors due to the remarkable improvement in electrical performance. However, it remains controversial whether a crystalline 1$${T}^{{\prime} }$$

T

′

phase is produced because optical signatures of this putative transition are found to be associated with the formation of tellurium clusters instead. Here we demonstrate the creation of an intrinsic 1$${T}^{{\prime} }$$

T

′

lattice after irradiating a mono- or few-layer 2H-MoTe2 with a single field-enhanced terahertz pulse. Unlike optical pulses, the low terahertz photon energy limits possible structural damages. We further develop a single-shot terahertz-pump-second-harmonic-probe technique and reveal a transition out of the 2H-phase within 10 ns after photoexcitation. Our results not only provide important insights to resolve the long-standing debate over the light-induced polymorphic transition in MoTe2 but also highlight the unique capability of strong-field terahertz pulses in manipulating quantum materials.
A branching model of lineage differentiation underpinning the neurogenic potential of enteric glia
Authors: Laddach Anna , Chng Song Hui , Lasrado Reena , Progatzky Fränze , Shapiro Michael , Erickson Alek , Sampedro Castaneda Marisol , Artemov Artem V. , Bon-Frauches Ana Carina , Amaniti Eleni-Maria , Kleinjung Jens , Boeing Stefan , Ultanir Sila , Adameyko Igor , Pachnis Vassilis
Published: September 2023

Glial cells have been proposed as a source of neural progenitors, but the mechanisms underpinning the neurogenic potential of adult glia are not known. Using single cell transcriptomic profiling, we show that enteric glial cells represent a cell state attained by autonomic neural crest cells as they transition along a linear differentiation trajectory that allows them to retain neurogenic potential while acquiring mature glial functions. Key neurogenic loci in early enteric nervous system progenitors remain in open chromatin configuration in mature enteric glia, thus facilitating neuronal differentiation under appropriate conditions. Molecular profiling and gene targeting of enteric glial cells in a cell culture model of enteric neurogenesis and a gut injury model demonstrate that neuronal differentiation of glia is driven by transcriptional programs employed in vivo by early progenitors. Our work provides mechanistic insight into the regulatory landscape underpinning the development of intestinal neural circuits and generates a platform for advancing glial cells as therapeutic agents for the treatment of neural deficits.
Genotypic diversity and unrecognized antifungal resistance among populations of Candida glabrata from positive blood cultures
Authors: Badrane Hassan , Cheng Shaoji , Dupont Christopher L. , Hao Binghua , Driscoll Eileen , Morder Kristin , Liu Guojun , Newbrough Anthony , Fleres Giuseppe , Kaul Drishti , Espinoza Josh L. , Clancy Cornelius J. , Nguyen M. Hong
Published: September 2023

The longstanding model is that most bloodstream infections (BSIs) are caused by a single organism. We perform whole genome sequencing of five-to-ten strains from blood culture (BC) bottles in each of ten patients with Candida glabrata BSI. We demonstrate that BCs contain mixed populations of clonal but genetically diverse strains. Genetically distinct strains from two patients exhibit phenotypes that are potentially important during BSIs, including differences in susceptibility to antifungal agents and phagocytosis. In both patients, the clinical microbiology lab recovered a fluconazole-susceptible index strain, but we identify mixed fluconazole-susceptible and –resistant populations. Diversity in drug susceptibility is likely clinically relevant, as fluconazole-resistant strains were subsequently recovered by the clinical laboratory during persistent or relapsing infections. In one patient, unrecognized respiration-deficient small colony variants are fluconazole-resistant and significantly attenuated for virulence during murine candidiasis. Our data suggest a population-based model of C. glabrata genotypic and phenotypic diversity during BSIs.
3D covalent organic framework membrane with fast and selective ion transport
Authors: Zhu Tianhao , Kong Yan , Lyu Bohui , Cao Li , Shi Benbing , Wang Xiaoyao , Pang Xiao , Fan Chunyang , Yang Chao , Wu Hong , Jiang Zhongyi
Published: September 2023

3D ionic covalent organic framework (COF) membranes, which are envisioned to be able to break the trade-off between ion conductivity and ion selectivity, are waiting for exploitation. Herein, we report the fabrication of a 3D sulfonic acid-functionalized COF membrane (3D SCOF) for efficient and selective ion transport, using dual acid-mediated interfacial polymerization strategy. The 3D SCOF membranes possess highly interconnected ion transport channels, ultramicroporous pore sizes (0.97 nm), and abundant sulfonate groups (with a high ion exchange capacity of 4.1 mmol g−1), leading to high proton conductivity of 843 mS cm−1 at 90 °C. When utilized in osmotic energy conversion, a high power density of 21.2 W m−2, and a remarkable selectivity of 0.976 and thus an exceptional energy conversion efficiency of 45.3% are simultaneously achieved. This work provides an alternative approach to 3D ionic COF membranes and promotes the applications of 3D COFs in ion transport and separation.
Distinct sub-second dopamine signaling in dorsolateral striatum measured by a genetically-encoded fluorescent sensor
Authors: Salinas Armando G. , Lee Jeong Oen , Augustin Shana M. , Zhang Shiliang , Patriarchi Tommaso , Tian Lin , Morales Marisela , Mateo Yolanda , Lovinger David M.
Published: September 2023

The development of genetically encoded dopamine sensors such as dLight has provided a new approach to measuring slow and fast dopamine dynamics both in brain slices and in vivo, possibly enabling dopamine measurements in areas like the dorsolateral striatum (DLS) where previously such recordings with fast-scan cyclic voltammetry (FSCV) were difficult. To test this, we first evaluated dLight photometry in mouse brain slices with simultaneous FSCV and found that both techniques yielded comparable results, but notable differences in responses to dopamine transporter inhibitors, including cocaine. We then used in vivo fiber photometry with dLight in mice to examine responses to cocaine in DLS. We also compared dopamine responses during Pavlovian conditioning across the striatum. We show that dopamine increases were readily detectable in DLS and describe transient dopamine kinetics, as well as slowly developing signals during conditioning. Overall, our findings indicate that dLight photometry is well suited to measuring dopamine dynamics in DLS.
Conformational dynamics of cohesin/Scc2 loading complex are regulated by Smc3 acetylation and ATP binding
Authors: Kaushik Aditi , Than Thane , Petela Naomi J. , Voulgaris Menelaos , Percival Charlotte , Daniels Peter , Rafferty John B. , Nasmyth Kim A. , Hu Bin
Published: September 2023

The ring-shaped cohesin complex is a key player in sister chromatid cohesion, DNA repair, and gene transcription. The loading of cohesin to chromosomes requires the loader Scc2 and is regulated by ATP. This process is hindered by Smc3 acetylation. However, the molecular mechanism underlying this inhibition remains mysterious. Here, using Saccharomyces cerevisiae as a model system, we identify a novel configuration of Scc2 with pre-engaged cohesin and reveal dynamic conformations of the cohesin/Scc2 complex in the loading reaction. We demonstrate that Smc3 acetylation blocks the association of Scc2 with pre-engaged cohesin by impairing the interaction of Scc2 with Smc3’s head. Lastly, we show that ATP binding induces the cohesin/Scc2 complex to clamp DNA by promoting the interaction between Scc2 and Smc3 coiled coil. Our results illuminate a dynamic reconfiguration of the cohesin/Scc2 complex during loading and indicate how Smc3 acetylation and ATP regulate this process.
SENP6 regulates localization and nuclear condensation of DNA damage response proteins by group deSUMOylation
Authors: Claessens Laura A. , Verlaan-de Vries Matty , de Graaf Ilona J. , Vertegaal Alfred C. O.
Published: September 2023

The SUMO protease SENP6 maintains genomic stability, but mechanistic understanding of this process remains limited. We find that SENP6 deconjugates SUMO2/3 polymers on a group of DNA damage response proteins, including BRCA1-BARD1, 53BP1, BLM and ERCC1-XPF. SENP6 maintains these proteins in a hypo-SUMOylated state under unstressed conditions and counteracts their polySUMOylation after hydroxyurea-induced stress. Co-depletion of RNF4 leads to a further increase in SUMOylation of BRCA1, BARD1 and BLM, suggesting that SENP6 antagonizes targeting of these proteins by RNF4. Functionally, depletion of SENP6 results in uncoordinated recruitment and persistence of SUMO2/3 at UVA laser and ionizing radiation induced DNA damage sites. Additionally, SUMO2/3 and DNA damage response proteins accumulate in nuclear bodies, in a PML-independent manner driven by multivalent SUMO-SIM interactions. These data illustrate coordinated regulation of SUMOylated DNA damage response proteins by SENP6, governing their timely localization at DNA damage sites and nuclear condensation state.
BAP1 promotes osteoclast function by metabolic reprogramming
Authors: Rohatgi Nidhi , Zou Wei , Li Yongjia , Cho Kevin , Collins Patrick L. , Tycksen Eric , Pandey Gaurav , DeSelm Carl J. , Patti Gary J. , Dey Anwesha , Teitelbaum Steven L.
Published: September 2023

Treatment of osteoporosis commonly diminishes osteoclast number which suppresses bone formation thus compromising fracture prevention. Bone formation is not suppressed, however, when bone degradation is reduced by retarding osteoclast functional resorptive capacity, rather than differentiation. We find deletion of deubiquitinase, BRCA1-associated protein 1 (Bap1), in myeloid cells (Bap1∆LysM), arrests osteoclast function but not formation. Bap1∆LysM osteoclasts fail to organize their cytoskeleton which is essential for bone degradation consequently increasing bone mass in both male and female mice. The deubiquitinase activity of BAP1 modifies osteoclast function by metabolic reprogramming. Bap1 deficient osteoclast upregulate the cystine transporter, Slc7a11, by enhanced H2Aub occupancy of its promoter. SLC7A11 controls cellular reactive oxygen species levels and redirects the mitochondrial metabolites away from the tricarboxylic acid cycle, both being necessary for osteoclast function. Thus, in osteoclasts BAP1 appears to regulate the epigenetic-metabolic axis and is a potential target to reduce bone degradation while maintaining osteogenesis in osteoporotic patients.
Hypoxanthine phosphoribosyl transferase 1 metabolizes temozolomide to activate AMPK for driving chemoresistance of glioblastomas
Authors: Yin Jianxing , Wang Xiefeng , Ge Xin , Ding Fangshu , Shi Zhumei , Ge Zehe , Huang Guang , Zhao Ningwei , Chen Dongyin , Zhang Junxia , Agnihotri Sameer , Cao Yuandong , Ji Jing , Lin Fan , Wang Qianghu , Zhou Qigang , Wang Xiuxing , You Yongping , Lu Zhimin , Qian Xu
Published: September 2023

Temozolomide (TMZ) is a standard treatment for glioblastoma (GBM) patients. However, TMZ has moderate therapeutic effects due to chemoresistance of GBM cells through less clarified mechanisms. Here, we demonstrate that TMZ-derived 5-aminoimidazole-4-carboxamide (AICA) is converted to AICA ribosyl-5-phosphate (AICAR) in GBM cells. This conversion is catalyzed by hypoxanthine phosphoribosyl transferase 1 (HPRT1), which is highly expressed in human GBMs. As the bona fide activator of AMP-activated protein kinase (AMPK), TMZ-derived AICAR activates AMPK to phosphorylate threonine 52 (T52) of RRM1, the catalytic subunit of ribonucleotide reductase (RNR), leading to RNR activation and increased production of dNTPs to fuel the repairment of TMZ-induced-DNA damage. RRM1 T52A expression, genetic interruption of HPRT1-mediated AICAR production, or administration of 6-mercaptopurine (6-MP), a clinically approved inhibitor of HPRT1, blocks TMZ-induced AMPK activation and sensitizes brain tumor cells to TMZ treatment in mice. In addition, HPRT1 expression levels are positively correlated with poor prognosis in GBM patients who received TMZ treatment. These results uncover a critical bifunctional role of TMZ in GBM treatment that leads to chemoresistance. Our findings underscore the potential of combined administration of clinically available 6-MP to overcome TMZ chemoresistance and improve GBM treatment.
Epigenomic analysis of formalin-fixed paraffin-embedded samples by CUT&Tag
Authors: Henikoff Steven , Henikoff Jorja G. , Ahmad Kami , Paranal Ronald M. , Janssens Derek H. , Russell Zachary R. , Szulzewsky Frank , Kugel Sita , Holland Eric C.
Published: September 2023

For more than a century, formalin-fixed paraffin-embedded (FFPE) sample preparation has been the preferred method for long-term preservation of biological material. However, the use of FFPE samples for epigenomic studies has been difficult because of chromatin damage from long exposure to high concentrations of formaldehyde. Previously, we introduced Cleavage Under Targeted Accessible Chromatin (CUTAC), an antibody-targeted chromatin accessibility mapping protocol based on CUT&Tag. Here we show that simple modifications of our CUTAC protocol either in single tubes or directly on slides produce high-resolution maps of paused RNA Polymerase II at enhancers and promoters using FFPE samples. We find that transcriptional regulatory element differences produced by FFPE-CUTAC distinguish between mouse brain tumors and identify and map regulatory element markers with high confidence and precision, including microRNAs not detectable by RNA-seq. Our simple workflows make possible affordable epigenomic profiling of archived biological samples for biomarker identification, clinical applications and retrospective studies.
A de novo evolved gene contributes to rice grain shape difference between indica and japonica
Authors: Chen Rujia , Xiao Ning , Lu Yue , Tao Tianyun , Huang Qianfeng , Wang Shuting , Wang Zhichao , Chuan Mingli , Bu Qing , Lu Zhou , Wang Hanyao , Su Yanze , Ji Yi , Ding Jianheng , Gharib Ahmed , Liu Huixin , Zhou Yong , Tang Shuzhu , Liang Guohua , Zhang Honggen , Yi Chuandeng , Zheng Xiaoming , Cheng Zhukuan , Xu Yang , Li Pengcheng , Xu Chenwu , Huang Jinling , Li Aihong , Yang Zefeng
Published: September 2023

The role of de novo evolved genes from non-coding sequences in regulating morphological differentiation between species/subspecies remains largely unknown. Here, we show that a rice de novo gene GSE9 contributes to grain shape difference between indica/xian and japonica/geng varieties. GSE9 evolves from a previous non-coding region of wild rice Oryza rufipogon through the acquisition of start codon. This gene is inherited by most japonica varieties, while the original sequence (absence of start codon, gse9) is present in majority of indica varieties. Knockout of GSE9 in japonica varieties leads to slender grains, whereas introgression to indica background results in round grains. Population evolutionary analyses reveal that gse9 and GSE9 are derived from wild rice Or-I and Or-III groups, respectively. Our findings uncover that the de novo GSE9 gene contributes to the genetic and morphological divergence between indica and japonica subspecies, and provide a target for precise manipulation of rice grain shape.
Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis
Authors: Li Shuai , Lian Wen-Hui , Han Jia-Rui , Ali Mukhtiar , Lin Zhi-Liang , Liu Yong-Hong , Li Li , Zhang Dong-Ya , Jiang Xian-Zhi , Li Wen-Jun , Dong Lei
Published: September 2023

Deserts occupy one-third of the Earth’s terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as “microbial dark matter”. Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.
AdsorbML: a leap in efficiency for adsorption energy calculations using generalizable machine learning potentials
Authors: Lan Janice , Palizhati Aini , Shuaibi Muhammed , Wood Brandon M. , Wander Brook , Das Abhishek , Uyttendaele Matt , Zitnick C. Lawrence , Ulissi Zachary W.
Published: September 2023

Computational catalysis is playing an increasingly significant role in the design of catalysts across a wide range of applications. A common task for many computational methods is the need to accurately compute the adsorption energy for an adsorbate and a catalyst surface of interest. Traditionally, the identification of low-energy adsorbate-surface configurations relies on heuristic methods and researcher intuition. As the desire to perform high-throughput screening increases, it becomes challenging to use heuristics and intuition alone. In this paper, we demonstrate machine learning potentials can be leveraged to identify low-energy adsorbate-surface configurations more accurately and efficiently. Our algorithm provides a spectrum of trade-offs between accuracy and efficiency, with one balanced option finding the lowest energy configuration 87.36% of the time, while achieving a ~2000× speedup in computation. To standardize benchmarking, we introduce the Open Catalyst Dense dataset containing nearly 1000 diverse surfaces and ~100,000 unique configurations.
Large sliding regulation in van der waals layered nonlinear optical ternary chalcogenides
Authors: Wu Qingchen , Kang Lei , Wu Jian , Lin Zheshuai
Published: September 2023

Interlayer sliding modulation in van der Waals (vdW) layered materials opens opportunities to seek tunable applications for photonics and optoelectronics at the nanoscale. In this work, focusing on ternary chalcogenides, dozens of typical vdW layered materials with the formula of A2MZ4(A, M = metal cation; Z = S/Se) were systematically classified and studied to illustrate the interlayer sliding modulation performance on nonlinear optical (NLO) effect and underlying mechanism. Based on first-principles analysis, the screened Cd2GeSe4exhibits large second harmonic generation (SHG) deviation (>36 times between high- and low-SHG states) under sliding among all studied materials. This phenomenon arises from the polarization modulation induced by the vdW interlayer charge redistribution of two tetrahedral primitives in the ternary edge-sharing tetrahedral structures. Our findings present a strategy to substantially modulate NLO properties by altering the interlayer charge coupling which is commonly thought to be very weak in vdW layered materials.
Optimal energy and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803
Authors: Kugler Amit , Stensjö Karin
Published: September 2023

Understanding energy and redox homeostasis and carbon partitioning is crucial for systems metabolic engineering of cell factories. Carbon metabolism alone cannot achieve maximal accumulation of metabolites in production hosts, since an efficient production of target molecules requires energy and redox balance, in addition to carbon flow. The interplay between cofactor regeneration and heterologous production in photosynthetic microorganisms is not fully explored. To investigate the optimality of energy and redox metabolism, while overproducing alkenes—isobutene, isoprene, ethylene and 1-undecene, in the cyanobacterium Synechocystis sp. PCC 6803, we applied stoichiometric metabolic modelling. Our network-wide analysis indicates that the rate of NAD(P)H regeneration, rather than of ATP, controls ATP/NADPH ratio, and thereby bioproduction. The simulation also implies that energy and redox balance is interconnected with carbon and nitrogen metabolism. Furthermore, we show that an auxiliary pathway, composed of serine, one-carbon and glycine metabolism, supports cellular redox homeostasis and ATP cycling. The study revealed non-intuitive metabolic pathways required to enhance alkene production, which are mainly driven by a few key reactions carrying a high flux. We envision that the presented comparative in-silico metabolic analysis will guide the rational design of Synechocystis as a photobiological production platform of target chemicals.
Multimodal video and IMU kinematic dataset on daily life activities using affordable devices
Authors: Martínez-Zarzuela Mario , González-Alonso Javier , Antón-Rodríguez Míriam , Díaz-Pernas Francisco J. , Müller Henning , Simón-Martínez Cristina
Published: September 2023

Human activity recognition and clinical biomechanics are challenging problems in physical telerehabilitation medicine. However, most publicly available datasets on human body movements cannot be used to study both problems in an out-of-the-lab movement acquisition setting. The objective of the VIDIMU dataset is to pave the way towards affordable patient gross motor tracking solutions for daily life activities recognition and kinematic analysis. The dataset includes 13 activities registered using a commodity camera and five inertial sensors. The video recordings were acquired in 54 subjects, of which 16 also had simultaneous recordings of inertial sensors. The novelty of dataset lies in: (i) the clinical relevance of the chosen movements, (ii) the combined utilization of affordable video and custom sensors, and (iii) the implementation of state-of-the-art tools for multimodal data processing of 3D body pose tracking and motion reconstruction in a musculoskeletal model from inertial data. The validation confirms that a minimally disturbing acquisition protocol, performed according to real-life conditions can provide a comprehensive picture of human joint angles during daily life activities.
Metagenomic data from surface seawater of the east coast of South Korea
Authors: Lim Yeonjung , Yang Seung-Jo , Kang Ilnam , Cho Jang-Cheon
Published: September 2023

The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth’s oceans, thereby meriting its recognition as a “miniature ocean”. The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued. Here, we present a monthly time-series metagenomic dataset spanning a one-year period in 2009, obtained from surface (10 m) seawater samples collected off the coast of the East Sea. The dataset encompasses 12 metagenomes, amounting 195 Gbp, with 14.73–22.52 Gbp per sample. This dataset is accompanied by concurrently measured physicochemical parameters. Our anticipation is that these metagenomes will facilitate extensive investigations aimed at elucidating various aspects of the marine microbial ecosystems in the East Sea.
The pre-Jurassic Meng-Shaan paleochannel and its control on the accumulation model of Yan 10 reservoir in Central Ordos Basin
Authors: Guo Chunling , Liu Jianchao , Fu Guomin , Chen Lijun , Wang Feng , Huang Zhe , Qiao Li , Wang Longjun
Published: September 2023

In the setting of the increasing density of exploration wells, and the decreasing scale and increasing difficulty of discovering Jurassic paleogeomorphology reservoirs, it is urgent to deepen the fine depiction of pre-Jurassic paleogeomorphology features and to analyze their controlling effect on reservoirs. Based on abundant logging data combined with indoor microscopic observation and experimental testing, the paper applies the theory of reservoir configuration analysis for the first time to the single-channel period division of the pre-Jurassic Meng-Shaan paleochannel which deposited with the braided channel sand bodies. Meanwhile, it reveals the controlling effect of hydrocarbon accumulation and the distribution characteristics of the Yan 101 reservoir as ' paleogeomorphology and sedimentary facies combination' to determine the type, 'migration channel' to determine the distributing range, and 'low-amplitude structure' to determine the trap in the study area, and also the reservoir accumulation modes in different channel ranges have established. In conclusion, the single-channel boundary of the Meng-Shaan paleochannel in different periods controls the path of oil and gas migration, thus controlling the distribution range and reservoir type of the Yan 10 reservoir. Moreover, depending on the production data we derived that it should prefer the composite trap reservoir of the Fuxian period and the Yan 102 period, as well as the structural reservoir on the periphery of the Yan 102 period single-channel for the further exploration of the Yan 10 paleogeomorphology reservoirs within the development range of the Meng-Shaan ancient river. In particular, the lithologic trap reservoirs within the Fuxian period channel and the Meng-Shaan main channel, such as the reservoirs of the 'Source' of the secondary channel type and the paleochannel type, which could as a replacement accumulation model for increasing reserves and production.
Shoreline response to sea-level rise according to equilibrium beach profiles
Authors: Luque Pau , Gómez-Pujol Lluís , Ribas Francesca , Falqués Albert , Marcos Marta , Orfila Alejandro
Published: September 2023

Shoreline position is a key parameter of a beach state, often used as a descriptor of the response of the system to changes in external forcing, such as sea-level rise. Changes in shoreline position are the result of coupled hydrodynamic and morphodynamic processes happening in the nearshore and acting at different temporal scales. Due to this complexity, methodologies aimed at reproducing shoreline evolution at decadal time scale require many simplifications. Simpler methods usually consider an equilibrium beach profile whose shape depends only on beach morphology, and whose location varies depending on incoming forcing. Here, we derive a general equation for shoreline evolution using equilibrium beach profiles. We particularize it based on several common assumptions, and evaluate changes on shoreline position caused by sea-level rise, combined with simultaneous wave and high-frequency sea-level forcing. We compare our model against other analytical equilibrium beach profile-based models and with a dynamic model explicitly computing sediment transport. Results indicate that: (i) it is necessary to consider the area of the emerged beach subject to marine forcing rather than focusing only on the submerged part, (ii) the rates of shoreline recession may change for narrow beaches, defined as those for which marine forcings act onto all of their aerial surface, and (iii) Bruun’s Rule can describe beach shoreline evolution, but the uncertainty in selecting the landward boundary of the active profile entails a huge uncertainty in the magnitude of shoreline evolution. This problematic uncertainty can be drastically reduced if instantaneous forcing conditions are used instead of the arbitrary emerged/submerged active profile boundaries typically defined by only one statistic parameter of extreme conditions.
Ambient data-driven SSO online monitoring of type-3 wind turbine generator integrated power systems based on MMPF-KF method
Authors: Chen Xi , Wu Xi , Zhou Jinyu , Li Qingfeng , Wu Chenyu , Li Qiang , Ren Bixing , Xu Ke
Published: September 2023

Series compensation grids connected with type-3 wind turbine generator (WTG)-based wind farms have suffered numerous subsynchronous oscillation (SSO) events worldwide. For early alerting of SSO and effective development of protection and control strategies, it is critical to monitor and identify SSO accurately and quickly. Ambient data is continuously available, which is useful for online monitoring. This paper proposes an ambient data-driven SSO online monitoring method based on the Kalman filter (KF) combined with the multi-model partitioning filter (MMPF). The KF is utilized to fit the measured ambient data with an auto regressive (AR) model. Then, the damping factor (or damping ratio) and frequency in the SSO mode can be acquired by solving the roots of the characteristic polynomial corresponding to the AR model. Moreover, the MMPF is an effective model order selection method applied to the KF for better identification. The performance of the MMPF-KF method is demonstrated by simulations and real-time experiments. The results of case studies validate the effectiveness of the proposed method under various conditions.
Average booking curves draw exponential functions
Authors: Shintani Masaru , Umeno Ken
Published: September 2023

The booking curve time series in perishable asset industries, including hotels, has been studied to manage a demand-supply condition or revenue management (RM). However, due to changing times, e.g., economy and technology, many RM practitioners have put their efforts into catching on to peoples’ booking pattern shifts, representing macroscopic changes in booking curves. We investigate macroscopic aspects of booking curves with actual sales data across six properties in the hotel and car-rental industries for two years, considering the difference in the economic environment characterized before and during the COVID-19 epidemic. We explain a new cross-industry and cross-economic-environment universal statistical law: average booking curves draw exponential functions (the ABCDEF law). We provide a basis for the ABCDEF law from three perspectives; data validation, modeling in the statistical physics framework, and empirical justification for the causality of the model. The ABCDEF law derives informative statistics to quantitatively measure peoples’ buying behavior even in time or society changes, which is expected to contribute to management in various industries.