Miracle-dz/UniFAR-FTUs huggingface dataset:
Isolation and draft genome sequence of Enterobacter asburiae strain i6 amenable to genetic manipulation

Enterobacter asburiae is a species of Gram-negative bacteria that is found in soil, water, and sewage. E. asburiae is generally considered to be an opportunistic pathogen, but has also been reported as a plant growth-promoting bacterium (PGPB), which may have beneficial effects on plant growth and development. However, genetic analysis of E. asburiae has been limited, possibly due to its redundant enzymes that digest exogenous DNA in the cell. Here, an E. asburiae strain i6 was isolated from soil in Nara, Japan. This strain was amenable to transformation and the one-step gene inactivation method based on λ Red recombinase. The transformation efficiency of the i6 strain with the 10 kb plasmid DNA pCF430 was at least four orders of magnitude higher than that of the previously sequenced E. asburiae strain ATCC 35953, which could not be transformed with the same plasmid DNA. A draft genome sequence of the i6 strain was determined and deposited into the database, allowing several factors that may determine transformation efficiency to be perturbed and tested. Together with the amenability of the i6 strain to genetic manipulation, the information from the i6 genome will facilitate characterization and fine-tuning of the beneficial and detrimental traits of this species.
Determination of ω-end functionalities in tailored poly(2-alkyl-2-oxazoline)s by liquid chromatography and mass spectrometry

The in-depth analytical characterization of polymers, in particular regarding intended biomedical applications, is becoming increasingly important to elucidate their structure–property relationships. Specifically, end group analysis of e.g. polymers featuring a ‘stealth effect’ towards the immune system is of particular importance because of their use in coupling reactions to bioactive compounds. Herein, we established a liquid chromatography (LC) protocol to analyse bicyclo[6.1. 0]nonyne-functionalized poly(2-alkyl-2–oxazoline)s (POx)s as promising functional polymers that can be applied in strain-promoted click reactions. This work involved the synthesis of poly(2-methyl-2-oxazoline) (PMeOx) and poly(2-ethyl-2-oxazoline) (PEtOx) by living cationic ring-opening polymerization (CROP) with different molar masses ranging from 2 up to 17.5 kDa and, to our knowledge, the first liquid chromatographic analysis of PMeOx. The developed analytical protocol enables the quantitative determination of post-polymerization reaction sequences with respect to the conversion of the ω-end groups. All synthesized polymers were straightforwardly analysed on a C18-derivatized silica monolithic column under reversed-phase chromatographic conditions with a binary mobile phase gradient comprising a mixture of acetonitrile and water. Subsequent mass spectrometry of collected elution fractions enabled the confirmation of the desired ω-end group functionalities and the identification of synthetic by-products.
The contextual awareness, response and evaluation (CARE) diabetes project: study design for a quantitative survey of diabetes prevalence and non-communicable disease risk in Ga Mashie, Accra, Ghana

ABSTRACT Diabetes is estimated to affect between 3.3% and 8.3% of adults in Ghana, and prevalence is expected to rise. The lack of cost-effective diabetes prevention programmes designed specifically for the Ghanaian population warrants urgent attention. The Contextual Awareness, Response and Evaluation (CARE): Diabetes Project in Ghana is a mixed methods study that aims to understand diabetes in the Ga Mashie area of Accra, identify opportunities for community-based intervention and inform future diabetes prevention and control strategies. This paper presents the study design for the quantitative survey within the CARE project. This survey will take place in the densely populated Ga Mashie area of Accra, Ghana. A household survey will be conducted using simple random sampling to select households from 80 enumeration areas identified in the 2021 Ghana Population and Housing Census. Trained enumerators will interview and collect data from permanent residents aged ≥ 25 years. Pregnant women and those who have given birth in the last six months will be excluded. Data analysis will use a combination of descriptive and inferential statistics, and all analyses will account for the cluster sampling design. Analyses will describe the prevalence of diabetes, other morbidities, and associated risk factors and identify the relationship between diabetes and physical, social, and behavioural parameters. This survey will generate evidence on drivers and consequences of diabetes and facilitate efforts to prevent and control diabetes and other NCDs in urban Ghana, with relevance for other low-income communities.
Viruses of some garlic ecotypes in Croatia

Recent, there is increasing demand for autochthonous ecotypes of garlic (Allium sativum L.) in Croatia. Many local ecotypes of garlic are developed due to specific environmental conditions and producer's selection. However, the average yield of garlic is not in the European average range, since the classical vegetative propagation from cloves usually results with virus infections that cause significant yield reduction. Viruses are considered significant garlic’s pathogens. The research was set up to determine infection rate in plant material of different garlic ecotypes grown from cloves in different regions. Plants were collected from commercial fields in Zadar County (coastal part of Croatia) and Vukovar-Srijem County (eastern Croatia) and were tested by enzyme-linked immunosorbent assay (ELISA) on the presence of three viruses: Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV) and Garlic common latent virus (GCLV). As a potential source of antigen leaf tissue was used and tests were conducted according to manufacturer’s instructions (Bioreba AG, Switzerland). In plants from Zadar County dominant was OYDV, followed by GCLV and LYSV. All tested plants originating from Vukovar-Srijem County were infected with three tested viruses. Out of 316 analyzed plants only 4 (1.3%) showed to be free from viruses included in survey. Plants infected with OYDV showed symptoms of leaf yellowing and reduced growth, while those infected with LYSV expressed yellow stripes. Symptoms were most evident at the beginning of vegetation. Due to high infection rate, deteriorated sanitary status, and increased interest in use and production of local garlic ecotypes, work on sanitary selection will be important part of revitalization program.
Pyrite Formation and Its Controls in Black Shales of the Buxin Formation(Lower Eocene) from the Sanshui Basin,Guangdong

Analyses of TOC/S,TOC/DOP,S/Fe relationships and S-TOC-Femultiple linear regression were carried out to determine limiting factors for pyrite formation in black shales of the Honggang Member(Lower Eocene Bu-xin Formation) in the Sanshui Basin.Submember A,showing lower organic carbon and higher iron contents than the other submembers,deposited in oxygenated bottom waters.Bacterial sulfate reduction took place below the sediment-water interface,and pyrite was formed diagenetically and organic carbon was limited.Submember B and C are characterized by large variations in organic carbon content.Organic-rich(TOC4%) rocks deposited under anoxic environments,in which H_(2)S presented above the sediment water interface as well as within the sediments.Pyrite was formed syngenetically and confined by the duration during which iron detritus reacted with H_(2)S in the water column and by the availability of dissolved sulfate that decreased due to an increasing input of fresh waters.For organic-poor(TOC4%) sediments,pyrite was of syngenetic and diagenetic.Organic carbon-limited diagenetic pyrite added to the earlier formed syngenetic pyrite,which was controlled by the time that iron minerals remained in contact with H_(2)S in anoxic waters.
Evolution of the mantle beneath the eastern North China Craton during the Cenozoic: Linking geochemical and geophysical observations

Recent discoveries related to the geochemistry of Cenozoic basalts and the geophysics of the deep mantle beneath eastern Eurasia make it possible to place constraints on the relationship between the seismic tomography of subcontinental mantle domains and their geochemical heterogeneities. Basalts with ocean island basalt‐like trace elements erupted during (56–23 Ma) and after (≤23 Ma) rifting of the eastern North China Craton (NCC) show evidence for the mixing of an isotopically depleted source and an EMI (Enriched mantle type I) pyroxenitic mantle. NCC rifting‐stage basalts exhibit anomalously low MgO and Fe2O3T and high SiO2 and Al2O3, as well as low Dy/Yb and Y/Yb and high εHf at a given εNd, as compared to the postrifting basalts. Temporal compositional variations and their association with basin subsidence indicate that heterogeneity in the eastern NCC asthenospheric mantle is the primary driver for intraplate magmatism in this region. The specific magmatic sources shifted in terms of depth, related to lithospheric thinning and thickening in the eastern NCC. The NCC EMI mantle domain most likely developed due to ancient events, is persistent through time, and is not related to dehydration of the stagnant Pacific slab in the mantle transition zone. Based on the chemical signatures of postrifting basalts, contributions from the Pacific slab are likely to be carbonatite rich. Mantle metasomatism by carbonatite melts from the Pacific slab and the interaction of these melts at shallower depths with EMI pyroxenitic mantle domains to trigger melting are contributors to the observed low P wave velocity zone beneath eastern Eurasia.
An obligate microsporidian parasite modulates defense against opportunistic bacterial infection in the yellow fever mosquito, Aedes aegypti

ABSTRACT The ability of Aedes aegypti mosquitoes to transmit vertebrate pathogens depends on multiple factors, including the mosquitoes’ life history traits, immune response, and microbiota (i.e., the microbes associated with the mosquito throughout its life). The microsporidium Edhazardia aedis is an obligate intracellular parasite that specifically infects Ae. aegypti mosquitoes and severely affects mosquito survival and other life history traits critical for pathogen transmission. In this work, we investigated how E. aedis impacts bacterial infection with Serratia marcescens in Ae. aegypti mosquitoes. We measured development, survival, and bacterial load in both larval and adult stages of mosquitoes. In larvae, E. aedis exposure was either horizontal or vertical and S. marcescens was introduced orally. Regardless of the route of transmission, E. aedis exposure resulted in significantly higher S. marcescens loads in larvae. E. aedis exposure also significantly reduced larval survival but subsequent exposure to S. marcescens had no effect. In adult females, E. aedis exposure was only horizontal and S. marcescens was introduced orally or via intrathoracic injection. In both cases, E. aedis infection significantly increased S. marcescens bacterial loads in adult female mosquitoes. In addition, females infected with E. aedis and subsequently injected with S. marcescens suffered 100% mortality which corresponded with a rapid increase in bacterial load. These findings suggest that exposure to E. aedis can influence the establishment and/or replication of other microbes in the mosquito. This has implications for understanding the ecology of mosquito immune defense and potentially disease transmission by mosquito vector species. IMPORTANCE The microsporidium Edhazardia aedis is a parasite of the yellow fever mosquito, Aedes aegypti. This mosquito transmits multiple viruses to humans in the United States and around the world, including dengue, yellow fever, and Zika viruses. Hundreds of millions of people worldwide will become infected with one of these viruses each year. E. aedis infection significantly reduces the lifespan of Ae. aegypti and is therefore a promising novel biocontrol agent. Here, we show that when the mosquito is infected with this parasite, it is also significantly more susceptible to infection by an opportunistic bacterial pathogen, Serratia marcescens. This novel discovery suggests the mosquito’s ability to control infection by other microbes is impacted by the presence of the parasite.
PENINGKATAN KEMAMPUAN BERPIKIR KRITIS DENGAN PEMBELAJARAN BERBASIS SCIENTIFIC APPROACH SISWA KELAS X SMA PANJURA MALANG

ABSTRAKSiswa kelas X di SMA Panjura Malang, mengalami kesulitan dalam memahami mata pelajaran biologi. Metode yang digunakan dalam mata pelajaran biologi masih menggunakan metode ceramah dan rendahnya kemampuan berpikir siswa disebabkan karena pembelajaran biologi selama ini cenderung hanya mengasah aspek mengingat dan memahami. Penelitian ini bertujuan untuk mengetahui ada tidaknya pengaruh pembelajaranberbasis Scientific Approach terhadap kemampuan berpikir kritis siswa. Variabel dalam penelitian ini terdiri dari pembelajaran berbasis Scientific Approach sebagai variabel independent, kemampuan berpikir kritis siswa sebagai variabel dependent. Metode pengambilan data yaitu dengan menggunakan metode tes tertulis berupa soal uraian untuk kemampuan berpikir kritis sesuai dengan indikator kemampuan berpikir kritis siswa. Validitas instrumen ini menggunakan pengujian validitas dan reliabilitas butir soal dengan pengujian tingkat kesukaran dan daya pembeda soal. Teknik analisis data untuk menguji hipotesis menggunakan analisis uji t-test pada taraf signifikansi 5%. Hasil penelitian menunjukan bahwa pembelajaran berbasis Scientific Approach memberikan pengaruh terhadap kemampuan berpikir kritis siswa kelas X SMA Panjura Malang yang dibuktikan dengan hasil menggunakan uji statistika yaitu uji t. Hal ini membuktikan bahwa penggunaan pembelajaran berbasis Scientific Approach bisa digunakan dalam pembelajaran karena dapat memberikan pengaruh positif dan signifikan terhadap kemampuan berpikir siswa.Kata Kunci: Pembelajaran, Scientific Approach, kemampuan berpikir kritis.
PI3K/mTOR is a therapeutically targetable genetic dependency in diffuse intrinsic pontine glioma

Diffuse midline glioma (DMG), including tumors diagnosed in the brainstem (diffuse intrinsic pontine glioma; DIPG), are uniformly fatal brain tumors that lack effective treatment. Analysis of CRISPR/Cas9 loss-of-function gene deletion screens identified PIK3CA and MTOR as targetable molecular dependencies across patient derived models of DIPG, highlighting the therapeutic potential of the blood-brain barrier–penetrant PI3K/Akt/mTOR inhibitor, paxalisib. At the human-equivalent maximum tolerated dose, mice treated with paxalisib experienced systemic glucose feedback and increased insulin levels commensurate with patients using PI3K inhibitors. To exploit genetic dependence and overcome resistance while maintaining compliance and therapeutic benefit, we combined paxalisib with the antihyperglycemic drug metformin. Metformin restored glucose homeostasis and decreased phosphorylation of the insulin receptor in vivo, a common mechanism of PI3K-inhibitor resistance, extending survival of orthotopic models. DIPG models treated with paxalisib increased calcium-activated PKC signaling. The brain penetrant PKC inhibitor enzastaurin, in combination with paxalisib, synergistically extended the survival of multiple orthotopic patient-derived and immunocompetent syngeneic allograft models; benefits potentiated in combination with metformin and standard-of-care radiotherapy. Therapeutic adaptation was assessed using spatial transcriptomics and ATAC-Seq, identifying changes in myelination and tumor immune microenvironment crosstalk. Collectively, this study has identified what we believe to be a clinically relevant DIPG therapeutic combinational strategy.
Rotational Motion Due to Skin Shear Deformation at Wrist and Elbow

The hanger reflex is an illusion phenomenon that induces strong force perception and rotational motion, and it occurs in multiple parts of the body. A potential application of this phenomenon is in upper limb rehabilitation for patients with upper-limb paralysis involving arm rotation. However, the only upper limb movements that have been confirmed in this phenomenon are the inward and outward movements of the wrist, which limits the applicable tasks. Therefore, we attempted to apply the hanger reflex to the elbow and use it simultaneously with the wrist. This phenomenon occurs due to shear deformation of the skin, so shear deformation was presented to the skin on the elbow. When shear deformation of the skin was presented to the elbow in the same manner as in previous studies applied to the wrist, movement and force perception of pronation and supination of the elbow were confirmed. The results of an experiment in which the hanger reflex was simultaneously presented to the elbow and wrist showed that each region independently perceived motion and force.
Are All Gay Men at Risk of Developing HIV/AIDS? Why China’s Mass HIV Testing Has Majorly Targeted Gay Men in the Era of Biomedicalization

Global HIV/AIDS responses have been increasingly biomedically dominated over the past years. In line with this shifting paradigm, China has prioritized mass HIV testing as a practical approach to controlling its HIV/AIDS epidemics among at-risk populations, especially gay men and other men who have sex with men (MSM). This study analyzed why China’s mass HIV testing mainly targeted gay men by understanding the perspectives of public health professionals, community-based organization (CBO) workers, and gay men. In addition, this study revealed the tensions and unintended consequences of HIV/AIDS prevention and the representation of gay men in China. The study involved fieldwork conducted in a major city in Eastern China from 2015 to 2019. Semi-structured interviews were held with participants from the three abovementioned groups (N = 25). The study identified four processes concerning why gay men are mainly targeted for HIV testing. Some public health professionals believe that being a gay man is equivalent to having HIV/AIDS risks. In addition, this study particularly noted tensions between public health professionals and gay men, including gay men–identified CBO workers, over whether mass HIV testing should target gay men or anyone who engaged in sexual risk behaviors. This study argued that a particular focus on gay men due to pursuing biomedical advances in HIV/AIDS prevention seems to have unintendedly stereotyped gay men based on the presumptions that they are at risk of developing HIV/AIDS. In addition, this study corresponded to the broader social scientific discussion concerning whether HIV/AIDS intervention should target specific sexual risk practices or sexual identity/population.
The Japanese nationwide cohort data of proton beam therapy for liver oligometastasis in breast cancer patients

Abstract A nationwide multicenter cohort study on particle therapy was launched by the Japanese Society for Radiation Oncology in Japan in May 2016. We analyzed the outcome of proton beam therapy (PBT) for liver oligometastasis in breast cancers. Cases in which PBT was performed at all Japanese proton therapy facilities between May 2016 and February 2019 were enrolled. The patients were selected based on the following criteria: the primary cancer was controlled, liver recurrence without extrahepatic tumors and no more than three liver lesions. Fourteen females, with a median age of 57 years (range, 44–73) and 22 lesions, were included. The median lesion size, fraction (fr) size and biological effective dose were 44 (20–130) mm, 6.6 (2–8) gray (Gy) (relative biological effectiveness)/fr and 109.6 (52.7–115.2) Gy, respectively. The median follow-up period was 22.8 (4–54) months. The 1-, 2- and 3-year local control (LC) rates of liver metastasis from breast cancer were 100% for all. The 1-, 2- and 3-year overall survival rates were 85.7, 62.5 and 62.5%, respectively. The 1-, 2- and 3-year progression-free survival (PFS) rates were 50.0%, 33.3%, and 16.7%, respectively. The median PFS time was 16 months. Only one patient did not complete PBT due to current disease progression. One patient had Grade 3 radiation-induced dermatitis. None of the patients experienced radiation-induced liver failure during the acute or late phase. Owing to the low incidence of adverse events and the high LC rate, PBT appears to be a feasible option for liver oligometastasis in breast cancers.
The origin of different bending stiffness between double-stranded RNA and DNA revealed by magnetic tweezers and simulations

Abstract The subtle differences in the chemical structures of double-stranded (ds) RNA and DNA lead to significant variations in their biological roles and medical implications, largely due to their distinct biophysical properties, such as bending stiffness. Although it is well known that A-form dsRNA is stiffer than B-form dsDNA under physiological salt conditions, the underlying cause of this difference remains unclear. In this study, we employ high-precision magnetic-tweezer experiments along with molecular dynamics simulations and reveal that the relative bending stiffness between dsRNA and dsDNA is primarily determined by the structure- and salt-concentration-dependent ion distribution around their helical structures. At near-physiological salt conditions, dsRNA shows a sparser ion distribution surrounding its phosphate groups compared to dsDNA, causing its greater stiffness. However, at very high monovalent salt concentrations, phosphate groups in both dsRNA and dsDNA become fully neutralized by excess ions, resulting in a similar intrinsic bending persistence length of approximately 39 nm. This similarity in intrinsic bending stiffness of dsRNA and dsDNA is coupled to the analogous fluctuations in their total groove widths and further coupled to the similar fluctuation of base-pair inclination, despite their distinct A-form and B-form helical structures.
SILICON-SUBSTITUTED CALCIUM PHOSPHATES FOR BONE TISSUE ENGINEERING APPLICATIONS

Silicon-substituted calcium phosphate (CP) powders were prepared by wet precipitation method, at 50°C, using CaCO3, (NH2)2CO-H3PO4), and Si(OCH2CH3)4 as reagents. Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and Rietveld refinement were used to characterize the samples. The raw precipitated powders were composed of carbonated hydroxyapatite and octacalcium phosphate. After heat treatment at 1200°C well crystalline phases of β-tricalcium phosphate (β-TCP, Ca3(PO4)2) and α-tricalcium phosphate (α-TCP) were detected.