Miracle-dz/UniFAR-FTUs huggingface dataset:
Étude de Brevibacterium aurantiacum, une bactérie d'affinage de fromage : de son métabolisme du soufre à son interaction avec Kluyveromyces lactis

L'objectif de ce travail etait d'etudier une bacterie d'affinage de cet ecosysteme, Brevibacterium aurantiacum (BA). La mise en place d'outils moleculaires pour l'etude de la biodiversite du genre Brevibacterium. L'approche par MLST avec 9 genes de menage est un nouvel outil prometteur pour l'identification des Brevibacteriaceae, nous avons identifie une nouvelle espece appartenant aux souches d'interet technologique, B. antiquum. L'approche par puce ADN a permis d'etudier la biodiversite au sein de l'espece de BA, les resultats montrent que 13% et 15% du genome de la souche sequencee sont absents et/ou divergents dans les souches BL2 et ATCC 9175. Nous avons ensuite realise une reconstruction du metabolisme du soufre chez BA ATCC 9175 et etudie sa regulation en fonction de differentes sources de soufre en utilisant des approches omics. Les resultats montrent une repression des voies d'assimilation du sulfate et de la biosynthese de la cysteine en presence de cystine et une repression des voies de biosynthese de la methionine via l'homocysteine et la voie de transulfuration par la methionine. Enfin, lors d'un ajout de methionine dans le milieu, nous observons une induction coordonnee des genes codant pour la methionine gamma-lyase et un transporteur de la methionine suggerant la presence d'un regulateur specifique pour cette voie. Enfin, nous avons etudie le comportement de BA en presence ou en absence d'une levure d'affinage de fromage Kluyveromyces lactis (KL) par des approches biochimiques et transcriptomiques. Chez BA, on observe une modification du metabolisme carbone et de l'azote, de la voie de biosynthese des pigments.
A systematic review and meta-analysis based on Asian cohort

Several studies have investigated the relationship between Manganese (Mn) levels and hepatocellular carcinoma (HCC), but the results were inconsistent. Thus, we conducted a systematic review and meta-analysis to evaluate the association between Mn levels and HCC. Nine studies focusing on hair Mn levels, 6 studies on serumMn levels and 6 studies on tissue Mn levels were identified in a systematic search of PubMed, CNKI, Wanfang and SinoMed databases. Standard mean differences (SMD) with the corresponding 95% confidence intervals (CI) were pooled to compare theMn levels between HCC and controls. In serum, theMn levels in HCCwere significantly lower than in healthy controls (SMD (95%CI): 0.941 ( 1.559, 0.323)). In hair, the Mn levels in HCCwere slightly lower than in healthy controls, but not significant (SMD (95% CI): 0.168 ( 0.766, 0.430)). In tissue, the Mn levels in tumors were significantly lower than in adjacent normal tissues (SMD (95% CI): 4.867 ( 7.143, 2.592)). Subgroup analysis showed consistent results. In conclusion, this meta-analysis suggested an inverse association between Mn levels and HCC. Abbreviations: AAS = atomic absorption spectrometry, CI = confidence interval, HCC = hepatocellular carcinoma, HCV = hepatitis C virus, ICP-AES = inductively coupled plasma atomic emission spectrometry, Mn = Manganese, MnSOD = Manganese superoxide dismutase, NOS = Newcastle-Ottawa Scale, SMD = standard mean difference.
Caractérisation moléculaire et physiologique des facteurs de réponse à l’éthylène (ERF) chez la tomate (Solanum lycopersicon)

La phytohormone ethylene, controle de nombreux processus physiologique durant le developpement des plantes, ainsi que la reponse aux stress biotiques et abiotiques. Les ERF (Facteurs de Reponse a l’Ethylene) sont les derniers facteurs de transcription de la voie de transduction de cette hormone. Ils sont par leur nombre, de bons candidats pour expliquer la diversite de reponse a l’ethylene. Dans cette etude 28 ERF de tomates ont ete isoles, caracterises et renommes. Des etudes d’interaction ADN/proteine montrent que l’environnement du cis-element est determinant pour l’interaction GCC/ERF. Des experiences d’expression transitoire des ERF ont permis de demontrer que leur activite transcriptionnelle est independante de leur classe d’appartenance. Leur profil d’expression suggere une specificite de reponse au cours du developpement vegetatif ou de la maturation, ainsi qu’un role preponderant dans l’initiation du fruit. L’analyse fonctionnelle est illustree par deux exemples. D’une part, la surexpression de SlERF2 dans la tomate induit une germination precoce des graines ou il a ete montre que la MANNANASE2, un marqueur de la germination, est fortement induit dans les graines transgeniques. D’autre part, la surexpression d’ATERF13 fusionne a un domaine represseur dominant induit une insensibilite partielle a l’ethylene et une hypersensibilite au stress salin. ABSTRACT: The phytohormone ethylene controls many physiological aspects of the plant development and stress response. ERFs (Ethylene Response Factors) are the last transcription factors of the ethylene transduction pathway. By their number, they are good candidates to explain the diversity of ethylene response. In this work 28 tomato ERFs have been isolated, characterized and renamed. DNA/protein interaction studies indicate that flanking regions of the ciselement are decisive for the GCC/ERF binding. Transient expression studies of ERFs demonstrated that the transcriptional activity is independent of the class they belong to. The study of their expression pattern revealed a specific response for some ERFs during the vegetative growth whereas others are preferentially expressed in fruit, from fruit set to ripening. The physiological significance of the ERFs is addressed through two examples. First, over-expression of the SlERF2 gene in the tomato resulted in premature seed germination in which MANNANASE2, a germination marker, is dramatically enhanced in the transgenic seeds. Second, over-expression of AtERF13 fused to a dominant repressor domain induces a partial insensitivity to ethylene and hypersensitivity to salt stress.
Measuring Actin Dynamics Through Image Analysis and Modeling

1 1 Actin polymerization and the lamellipodium 3 1.1 BACKGROUND . 3 1.1.1 Actin is part of the machinery of crawling cells . 3 1.1.2 Basics of actin polymerization . 4 1.1. 3 Regulation of actin polymerization . 7 1.1. 4 Dendritic nucleation model . 10 1.1. 5 Fluorescence microscopy methods to study dynamics at the leading edge. 11 1.2 MOTIVATION AND OUTLINE . 14 1.2. 1 Extracting filament structures from fluorescence microscopy images . 14 1.2. 2 Particle tracking in fluorescence microscopy . 15 1.2. 3 Theoretical model of actin turnover in the lamellipodium . 16 2 Extracting filament structures from fluorescent microscopy images 17 2.
Radiographic abnormalities and asbestos exposure: Libby, Montana.

Peipins et al. (2003) described the study conducted by the Agency for Toxic Substances and Disease Registry (ATSDR 2001, 2002a) to analyze the association between the prevalence of radiographic abnormalities and asbestos exposure pathways for residents of Libby, Montana. Although Peipins et al. presented many detailed results, they failed to explicitly state the obvious conclusion of their analysis: excess risk of asbestos-related disease for Libby residents is a consequence of occupational exposure, and risk associated with low-level exposure is negligible. This finding is extremely important for guiding future public health assessments of exposure to vermiculite from the Libby mine and exposure to amphibole asbestos in general. Peipins et al. (2003) made a clear case for the importance of occupational exposure. They reported the following statistically significant factors for predicting pleural abnormalities: being a former mine worker; being older; having been a household contact of a mine worker; and being male. These results associate pleural abnormalities with high occupational exposure groups—mine workers and household contacts of mine workers. Only one environmental exposure pathway was statistically significant— played in vermiculite pile, which may involve exposures as high as occupational exposures. The ATSDR data (ATSDR 2001, 2002a) indicate that 17.8% of the 6,668 subjects with X-ray films had pleural abnormalities. This percentage appears large in comparison to 6.7% of subjects with pleural abnormalities in the internal control group (no exposure). However, occupational exposures inflate the difference. I reanalyzed the data by forming three exposure groups: mine workers, residents with other occupational or domestic exposure, and residents with no occupational or domestic exposure (the “environmental exposure only” group) (Price B. In press). Pleural abnormalities were recorded for 51% of mine workers, 19.9% of residents with other occupational or domestic exposure, and 9.1% of residents with no occupational or domestic exposure. These results again demonstrate the importance of occupational exposure for pleural abnormalities. The percentage for the “environmental exposure only” group is close to the percentage for the internal controls. Other confounding factors mentioned by Peipins et al. (2003) could further reduce the difference. One of those factors is the false positive bias due to subpleural fat, which would be expected to be greater in the environmental exposure group than in the mine worker group (Price B. In press). Peipins et al. (2003) implied that asbestos exposure was high in Libby:
Invasive Species: Genetics, Characteristics and Trait Variation Along a Latitudinal Gradient

Globalization during the second half of the 20th century has accelerated the introduction and the spread of non-native species. Introduced species is considered the second largest threat to biodiversity after habitat destruction. It is therefore necessary to understand what makes introduced species successful in novel environments. Furthermore, introduced species provide unique opportunities to study the evolutionary processes that are involved in invasion success. We studied genetics, and evolution of higher phenotypic plasticity and local adaptation after introduction of one of the highly invasive species in Europe, Impatiens glandulifera, and compared trait variation in native and invasive Impatiens species along a latitudinal gradient in Europe. We found evidence of multiple introductions of the invasive I. glandulifera in Europe. Despite multiple introductions, there was a strong loss of genetic diversity in the invasive populations compared to native populations from Kashmir, India. Furthermore, loss of genetic diversity in the invasive populations does not constrain evolution of adaptive genetic differentiation. In another study, we did not find evidence that the species developed increased plasticity after introduction. A comparative study between a native, Impatiens noli-tangere, and an invasive species, Impatiens parviflora, showed that latitude has stronger effect on the performance of the invasive species in terms of plant height than on the native species. Surprisingly, the invasive species performed better under low nitrogen compared to high nitrogen conditions along the latitudinal gradient indicating that the invasive species is not constrained by low nitrogen conditions. All together these findings suggest that invasive species loose genetic variation, and do not adapt into more aggressive invasives, but they do evolve rapid adaptations to broad-scale environmental conditions in their introduced range
Studies on the practical production of docosaheｘaenoic acid using thraustochytrid microorganisms [an abstract of dissertation and a summary of dissertation review]

ドコサヘキサエン酸（DHA）はヒトの必須脂肪酸である。 DHAは脳や網膜のリン脂質成分として高い割合で含まれており、特に脳機能に関わるアルツハイマー型痴呆症やうつ病などの疾病に有効であるとされる。 DHAは海産魚介類に蓄積されているので、ヒトは主としてDHAをこれらの食品から摂取するが、サプリメントとして利用することも多い。 しかし、歴史的に魚介類の大消費国である日本国においても、食生活での魚離れが進んでいることなどから、現代人のDHAの摂取量は不足している。 DHAの原材料としてはもっぱら魚油が使用されているが、経年的な漁獲量の低下、海洋汚染に伴う魚油への重金属の蓄積などから、世界的にみればDHAの原材料は魚油から発酵生産による微生物油に移行ししつあるとみられる。 アメリカにおいては既に乳児用ミルクに魚油由来のDHAを添加することは法律で禁じられている。 日本では微生物由来のDHAはまだ生産されていない。 魚油に比べて高コストであることが最大の理由である。 DHAを多量に蓄積する微生物は海産性であり、その増殖にはNaClを必要とするので、海水を確保すること、海水中の高濃度のClイオンがステンレス製培養タンクの腐食の原因になることなどが高コスト化の要因である。 本研究ではDHA蓄積性スラウストキトリッド類微生物１２B株を材料にして、DHAの発酵生産技術を実用レベルにまで上げることを目的とし、海水を用いない培地の作成、DHA生産性の一層の向上条件を検討した。 また、１２B株の分類学的帰属についても調べた。 １２B株は従来、50％海水に、研究レベルで用いられる高品質の１％ペプトン、１％酵母エキス、８％ブドウ糖を加えたF培地で培養されている。 本研究では先ず、このペプトン、酵母エキス、ブドウ糖の濃度を一定にし、海水の主要塩類である、NaClとMgSO4の濃度を変えて１２B株の細胞収量への影響をみた。 培地中のNaCl濃度は0.1％まで低下させることが可能であり、0.1％NaCl存在下では1. 0％MgSO4で最大の細胞収量を得た。 F培地に用いる海水を0.1％NaClと1. 0％MgSO4で置き替えた培地（NM培地）での細胞、DHA収量（それぞれ18. 8 mg/ml, 2. 4 mg/ml）はF培地を用いた時の値（それぞれ11. 4 mg/ml, 0.7 mg/ml）を上回った。 0.1％NaClはステンレスの性状に影響をもたらさない。 培地調製の低コスト化をさらに推し進めるため、ペプトン、酵母エキス、ブドウ糖の全てを安価な工業用のものに置き換えた培地（INM培地）を調製した。 これを用いた場合の細胞、DHA収量はNM培地の値をさらに上回った。 INM培地は、その調製コストがF培地の場合の約30％と見積もられる（海水の採取や運搬、濾過のコスト、人件費などは除く）ことから、DHAの微生物発酵生産の実用性が高まったと考えられる。 １２B株は、18S rRNA遺伝子とミトコンドリアチトクロム酸化酵素サブユニットＩＩ遺伝子の塩基配列の相同性解析、及び生理・形態学的特徴によって、暫定的にAurantiochytrium 属の新種と同定した。
Diagnosis and management of xerostomia and hyposalivation

Xerostomia, the subjective complaint of dry mouth, and hyposalivation remain a significant burden for many individuals. Diagnosis of xerostomia and salivary gland hypofunction is dependent upon a careful and detailed history and thorough oral examination. There exist many options for treatment and symptom management: salivary stimulants, topical agents, saliva substitutes, and systemic sialogogues. The aim of this review is to investigate the current state of knowledge on management and treatment of patients affected by xerostomia and/or hyposalivation.
Influence of the Intensive Care Unit Environment on the Reliability of the Montreal Cognitive Assessment

Background: Neuropsychological screening becomes increasingly important for the evaluation of subarachnoid hemorrhage (SAH) and stroke patients. It is often performed during the surveillance period on the intensive (ICU), while it remains unknown, whether the distraction in this environment influences the results. We aimed to study the reliability of the Montreal Cognitive Assessment (MoCA) in the ICU environment. Methods: Consecutive stable patients with recent brain injury (tumor, trauma, stroke, etc.) were evaluated twice within 36 h using official parallel versions of the MoCA (ΔMoCA). The sequence of assessment was randomized into (a) busy ICU first or (b) quiet office first with subsequent crossover. For repeated MoCA, we determined sequence, period, location effects, and the intraclass correlation coefficient (ICC). Results: N = 50 patients were studied [n = 30 (60%) male], with a mean age of 57 years. The assessment's sequence [“ICU first” mean ΔMoCA −1.14 (SD 2.34) vs. “Office first” −0.73 (SD 1.52)] did not influence the MoCA (p = 0.47). On the 2nd period, participants scored 0.96 points worse (SD 2.01; p = 0.001), indicating no MoCA learning effect but a possible difference in parallel versions. There was no location effect (p = 0.31) with ΔMoCA between locations (Office minus ICU) of −0.32 (SD 2.21). The ICC for repeated MoCA was 0.87 (95% CI 0.79–0.92). Conclusions: The reliability of the MoCA was excellent, independent from the testing environment being ICU or office. This finding is helpful for patient care and studies investigating the effect of a therapeutic intervention on the neuropsychological outcome after SAH, stroke or traumatic brain injury.
Y-rituximab in CD20+ B-cell lymphoma as predicted by Zr-rituximab immuno-PET: impact of preloading with unlabelled rituximab

Purpose To compare using immuno-PET/CT the distribution of Zr-labelled rituximab without and with a preload of unlabelled rituximab to assess the impact of preloading with unlabelled rituximab on tumour targeting and radiation dose of subsequent radioimmunotherapy with Y-labelled rituximab in CD20+ B-cell lymphoma. Methods Five patients with CD20+ B-cell lymphoma and progressive disease were prospectively enrolled. All patients underwent three study phases: initial dosimetric phase with baseline Zr-rituximab PET/CT imaging without a cold preload, followed 3 weeks later by a second dosimetric phase with administration of a standard preload (250 mg/m) of unlabelled rituximab followed by injection of Zr-rituximab, and a therapeutic phase 1 week later with administration of unlabelled rituximab followed by Y-rituximab. PET/CT imaging and tracer uptake by organs and lesions were assessed. Results With a cold rituximab preload, the calculated wholebody dose of Y-rituximab was similar (mean 0.87 mSv/MBq, range 0.82–0.99mSv/MBq) in all patients.Without a preload, an increase in whole-body dose of 59% and 87%was noted in two patients with preserved circulating CD20+ B cells. This increase in radiation dose was primarily due to a 12.4-fold to 15-fold higher dose to the spleen without a preload. No significant change in whole-body dose was noted in the three other patients with B-cell depletion. Without a preload, consistently higher tumour uptake was noticed in patients with B-cell depletion. Conclusion Administration of the standard preload of unlabelled rituximab impairs radioconjugate tumour targeting in the majority of patients eligible for radioimmunotherapy, that is patients previously treated with rituximab-containing therapeutic regimens. This common practice may need to be reconsidered and further evaluated as the rationale for this high preload has its origin in the Bprerituximab era^. Clinical Trial Application: CTA 2011-005474-38 Trial Registry: EudraCT
BIO012831 1679..1687

The hexokinase 1 variant in mammalian spermatozoa (HK1S) has a unique N-terminus and this isoform atypically localizes to the plasma membrane. However, the mechanism of this process currently remains ambiguous. In this report, we show that fatty acylation underlies the specific sorting of HK1S. Employing chimeric reporter constructs, we first established that compartmentalization of HK1S does not function exclusively in sperm cells and that this feature is swappable to somatic HEK293 cells. Although the N-terminus lacks the classical consensus signature for myristoylation and the sequence-based predictions fail to predict myristoylation of HK1S, complementary experimental approaches confirmed that HK1S is myristoylated. Using live-cell confocal microscopy, we show that the mutation of a single amino acid, the myristoyl recipient Gly, impedes the prominent feature of plasmamembrane association and relocates the enzyme to the cytosol but not the nucleus. Additionally, substitutions of the putatively palmitoylated Cys is also reflected in a similar loss of compartmentalization of the protein. Taken together, our findings conclusively demonstrate that the N-terminal ‘MGQICQ’ motif in the unique GCS domain of HK1S acquires hydrophobicity by dual lipidic modifications, N-myristoylation and palmitoylation, to serve the requirements for membranous associations and thus its compartmentalization.
Characterization of the Interaction between Arabidopsis Toc159 and Toc33 GTPase Domains

Protein-protein interactions are critical for many biochemical processes and for cellular function. Understanding interactions between proteins and ligands, as well as other proteins are necessary for the modelling of biological systems. Protein import into chloroplasts is one such system where the understanding of interactions between members of the translocation complex is limited. The translocon at the outer envelope membrane of chloroplasts (Toe complex) consists of three core components: Toc75, Tocl59, and Toc34. Members of the Tocl59 and Toc34 gene families in Arabidopsis thaliana have been shown to assemble differentially into structurally and functionally distinct complexes. More specifically, there is evidence that complexes containing atTocl59 and atToc33 (the prefix "at" identifies the species of origin, Arabidopsis thaliana) import photosynthetic proteins, whereas complexes containing atTocl32/120 and atToc34 seem to preferentially import non-photosynthetic proteins. The interactions between atTocl59 and atToc33 or atTocl32 and atToc34 are mediated by their GTPase domains. The current research used recombinant GTPase domains to investigate the specifics of the interaction between atTocl59G and atToc33G in more detail using molecular and biophysical approaches. Methods included using blue-native PAGE, fluorescence spectroscopy and circular dichroism spectroscopy to characterize the interaction between atTocl59G and atToc33G. Objectives were to characterize the interaction between atTocl59G and atToc33G as well as attempt to manipulate the monomendimer equilibrium for individual proteins for the purpose of studying heterodimer formation. A secondary objective was to generate single tryptophan mutants of atTocl59G (W973F and W1056F) to more precisely characterize the interaction between proteins. Results indicate that only a small percentage of the total protein exists as heterodimers, making quantification using fluorescence spectroscopy and circular dichroism spectroscopy difficult. Nonetheless, it was demonstrated that heterodimer formation occurs between the G-domains of atTocl59 and atToc33. The data also suggest that higher order oligomers may form, which may be indicative of multiple interaction domains among proteins as previously suggested by stoichiometric studies on isolated Toe complexes. The effects of chelating agents, such as EDTA and
Zippy LL(1) parsing with derivatives

In this paper, we present an efficient, functional, and formally verified parsing algorithm for LL(1) context-free expressions based on the concept of derivatives of formal languages. Parsing with derivatives is an elegant parsing technique, which, in the general case, suffers from cubic worst-case time complexity and slow performance in practice. We specialise the parsing with derivatives algorithm to LL(1) context-free expressions, where alternatives can be chosen given a single token of lookahead. We formalise the notion of LL(1) expressions and show how to efficiently check the LL(1) property. Next, we present a novel linear-time parsing with derivatives algorithm for LL(1) expressions operating on a zipper-inspired data structure. We prove the algorithm correct in Coq and present an implementation as a part of Scallion, a parser combinators framework in Scala with enumeration and pretty printing capabilities.
'I have too much respect for my elders': Understanding South African Mobile Users' Perceptions of Privacy and Current Behaviors on Facebook and WhatsApp

Facebook usage is growing in developing countries, but we know little about how to tailor social media privacy settings to users in less well-resourced settings. To that end, we present findings from interviews of 52 current mobile social media users in South Africa. We found users’ primary privacyrelated concern was who else could see their posts and messages, not what data the platforms or advertisers collect about them. Second, users displayed general knowledge gaps on existing social media privacy settings and relied heavily on blocking and passwords for privacy and security protection. Third, users’ privacy and security-related behaviors were heavily influenced by living in high-crime areas. Based on these findings, we suggest future work to better serve users’ privacy and security needs in less well-resourced settings.