Miracle-dz/UniFAR-FTUs huggingface dataset:
Megascopic processes reflected in the microscopic realm: sedimentary and biotic dynamics of the Middle Ordovician “orthoceratite limestone” at Kinnekulle, Sweden

Abstract The Middle Ordovician (Dapingian–middle Darriwilian) “orthoceratite limestone” is documented in its traditional type area at Kinnekulle in the province of Västergötland in southern Sweden. Detailed field studies combined with systematic qualitative and quantitative analyses of carbonate microfacies at high stratigraphic resolution show that this suite of cool-water carbonate rocks is more variable than is suggested by its overall homogeneous macroscopic appearance. Long-term changes in carbonate textures and fossil grain assemblages, together with pervasive rhythmic/cyclic patterns, suggest a strong influence from sea level on microfacies characteristics. Assessment of the results in light of regional facies patterns indicates that the cool-water “orthoceratite limestone” behaved much like “model” siliciclastic sedimentary systems, in that carbonate texture varied with depositional depth as particle size of siliclastics does. Carbonate texture thus appears to reflect absolute depth well, whereas grain assemblages record high-frequency cycles of changes in both sea level and substrate conditions. A relative sea level curve compiled from the collective data shows excellent agreement with previously published curves based on different proxies. The most important factor for the long-term establishment and regional dominance of the “orthoceratite limestone” throughout much of the Early and Middle Ordovician appears to have been a limited terrigenous sediment input to the Baltoscandian paleobasin. Hence, much of the regional facies zonation may reflect distance from weathering sources rather than bathymetric conditions.
A coordinated retrieval method for sea surface salinity based on SMOS and ocean color data

A coordinated retrieval method for sea surface salinity based on SMOS and ocean color data was developed. The method retrieved sea surface salinity in open sea based on SMOS data, and those with much RFIs in the coastal area using ocean color data, aCDOM. Tight relationships between surface water salinity and in situ aCDOM were found during the cruises in the Yangtze River estuary on April 2013 and Hangzhou Bay in May 2014, distributions of aCDOM revealed gradual downward trends of magnitudes, as water flowed down the Yangtze River estuary into the ECS coast. A dilution process was detected as water flowed down the Yangtze River and into the ECS coast. Thus, a salinity inversion model from the negative relationship between salinity and aCDOM was developed firstly. Then we matched the SSS products with different spatial resolution retrieved based on SMOS and ocean color and combined them. In the end, we compared the SSS measurements between those based on only SMOS data and those based on method in this paper, and found that the method can make up the phenomenon of lack of data effectively.
Oral Health-related Quality of Life Among Denture Stomatitis Patients with Implant Overdenture Treated with Photodynamic Therapy.

PURPOSE This study aimed to assess the impact of photodynamic therapy (PDT) on the oral health-related quality of life (OHRQoL) among denture stomatitis patients with implant overdenture prostheses (IODs). MATERIALS AND METHODS The patients were recruited from a specialist dental practice according to selection criteria. The Candida spp. were identified and confirmed by the microbiological culture technique. Candida counts were estimated as colony-forming units (CFU/ml) at baseline, 15, 30, and 60 days. PDT was carried out twice a week with 72 h intervals for a period of 4 weeks. A structured questionnaire was used for data collection. It included the demographic details of the patients, including age, gender, education, marital and socioeconomic status (SES), oral habits, and smoking status. In addition, the Oral Health Impact Profile-EDENT (OHIP-EDENT) scale was added to assess the OHRQoL of all patients before and after PDT treatment. The data were analysed using descriptive statistics, the t-test and the Shapiro-Wilk test; statistical signifcance was set at p < 0.05. RESULTS At baseline, the overall mean Candida CFU/ml were quite high in the implant overdenture (IODs) samples, 37.12 ± 15.8, as compared to palatal mucosa samples with 5.1 ± 2.3. After PDT treatment, a statistically significant reduction was noted in the mean Candida CFU/ml on both surfaces at all follow-up visits. It was observed that all domains of OHIP-EDENT except for physical disability and handicap showed statistically significant improvement in mean scores after PDT treatment. FL, P1, P2, D2, and D3 had statistically significant mean score improvements of 2.2, 3.1, 2.2, 1.4, and 0.7, respectively. Furthermore, after PDT treatment, the total OHIP-EDENT score showed a statistically significant improvement of 11.6. CONCLUSION PDT treatment has a positive impact on the OHRQoL for patients with denture stomatitis. It can be used as an effective treatment option for the treatment of denture stomatitis in IOD patients.
Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads

Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.
Zero-Shot Video Grounding With Pseudo Query Lookup and Verification

Video grounding, the process of identifying a specific moment in an untrimmed video based on a natural language query, has become a popular topic in video understanding. However, fully supervised learning approaches for video grounding that require large amounts of annotated data can be expensive and time-consuming. Recently, zero-shot video grounding (ZS-VG) methods that leverage pre-trained object detectors and language models to generate pseudo-supervision for training video grounding models have been developed. However, these approaches have limitations in recognizing diverse categories and capturing specific dynamics and interactions in the video context. To tackle these challenges, we introduce a novel two-stage ZS-VG framework called Lookup-and-Verification (LoVe), which treats the pseudo-query generation procedure as a video-to-concept retrieval problem. Our approach allows for the extraction of diverse concepts from an open-concept pool and employs a verification process to ensure the relevance of the retrieved concepts to the objects or events of interest in the video proposals. Comprehensive experimental results on the Charades-STA, ActivityNet-Captions, and DiDeMo datasets demonstrate the effectiveness of the LoVe framework.
First occurrence of the Red Sea goatfish, Parupeneus forsskali (Fourmanoir Guz, 1976) in the coastal waters of Egyptian Mediterranean Sea

This study discusses the first recorded occurrence of the Red Sea goatfish, Parupeneus forsskali in the Egyptian Mediterranean waters, to the best of the authors’ understanding. On 31 January 2016, a single specimen of this species was captured from Alexandria coastal waters (31°16'N; 30°10'E), Mediterranean Sea, Egypt. The collected specimen represents the first record of P. forsskali in the Egyptian Mediterranean waters. This specimen has a total length of 26.5 cm, fork length of 23.0 cm and standard length of 21.5 cm and weighed 228.4 g (total weight). The finding of this paper confirms the establishment of this Lessepsian immigrant along the eastern Mediterranean. Key words: Parupeneus forsskali, Lessepsian immigrant, Mediterranean, Egypt.
Espacios de Banach no separables, compacidad y renormamiento / Antonio Avilés López; directores, Bernardo Cascales Salinas y José Orihuela Calatayud.

La tesis consta de cuatro capitulos, El primero de ellos esta dedicado a los compactos de Eberlein uniformes, es decir subconjuntos debil compactos de espacios de Hilbert. Se prueba que la bola de un espacio de Hilbert en la topologia debil es imagen continua de un producto numerable de compactificaciones por un punto de conjuntos discretos, lo que combinado con resultados de Murray Bell implica que el reticulo de abiertos de dicha bola cumple diversas propiedades de tipo Ramsey. Se construye ademas un norma en el espacio de Hilbert no separable diferente de la norma hilbertiana pero equivalente a ella cuya bola en la topologia debil no verica estas propiedades de Ramsey y por tanto no es homeomorfo a la bola en la norma hilbertiana. Otro ejemplo de compacto de Eberlein uniforme es la familia compacta de los subconjuntos de cardinalidad menor que natural n de un conjunto dado, asi como los espacios que se expresan como productos numerables de este tipo de compactos. Se estudia tambien en el primer capitulo la clasificacion topologica y la clasificacion de los espacios de C(K) de compactos K que son productos numerables como los anteriormente descritos. En el segundo capitulo, se estudia en el invariante cardinal de un espacio de Banach dado por el menor numero de subconjuntos debil compactos necesarios para generar el espacio. Se estudia la relacion de este invariante con otros como el numero de Lindelof o los indices de K-analiticidad y K-determinacion, demostrandose entre otros resultados que existen espacios de Banach debilmente Lindelof determinados generados por un numero arbitrariamente alto de debil compactos, mientras que todo espacio debilmente numerablemente determinado esta generado por un continuo de debil compactos. Tambien se estudia la relacion entre el numero de debil compactos que generan un espacio y sus subespacios, y la relacion con el caracter de densidad. A modo de ejemplo, un subespac
What is the role of the hippocampus and parahippocampal gyrus in the persistence of tinnitus?

Abstract The hippocampus and parahippocampal gyrus have been implicated as part of a tinnitus network by a number of studies. These structures are usually considered in the context of a “limbic system,” a concept typically invoked to explain the emotional response to tinnitus. Despite this common framing, it is not apparent from current literature that this is necessarily the main functional role of these structures in persistent tinnitus. Here, we highlight a different role that encompasses their most commonly implicated functional position within the brain—that is, as a memory system. We consider tinnitus as an auditory object that is held in memory, which may be made persistent by associated activity from the hippocampus and parahippocampal gyrus. Evidence from animal and human studies implicating these structures in tinnitus is reviewed and used as an anchor for this hypothesis. We highlight the potential for the hippocampus/parahippocampal gyrus to facilitate maintenance of the memory of the tinnitus percept via communication with auditory cortex, rather than (or in addition to) mediating emotional responses to this percept.
Strategies to mitigate moral distress as reported by eldercare professionals

ABSTRACT Eldercare workers experience higher levels of moral distress than other health and social care service workers. Moral distress is a psychological response to a morally challenging event. Very little is known about moral distress in the context of eldercare and about the mechanisms of preventing or mitigating moral distress. This qualitative study was conducted as part of the “Ensuring the availability of staff and the attractiveness of the sector in eldercareservices” project in Finland in 2021. The data were from 39 semi-structured interviews. This qualitative interview data were examined using two-stage content analysis. The key finding of this study, as reported by eldercare professionals, is that strategies to mitigate moral distress can be found at all organizational levels : organizational, workplace and individual. The tools that emerged from the interviews fell into four main categories:) organizational support and education 2) peer support 3) improving self-care and competence and 4) defending patients. The main identified categories confirmed the earlier findings but the qualitative, rich research interview data provided new insights into a little-studied topic: mitigating moral distress in eldercare. The main conclusion is that, in order to mitigate moral distress, ethical competence needs to be strengthened at all organizational levels.
PlasmidEC and gplas2: an optimized short-read approach to predict and reconstruct antibiotic resistance plasmids in Escherichia coli

Accurate reconstruction of Escherichia coli antibiotic resistance gene (ARG) plasmids from Illumina sequencing data has proven to be a challenge with current bioinformatic tools. In this work, we present an improved method to reconstruct E. coli plasmids using short reads. We developed plasmidEC, an ensemble classifier that identifies plasmid-derived contigs by combining the output of three different binary classification tools. We showed that plasmidEC is especially suited to classify contigs derived from ARG plasmids with a high recall of 0.941. Additionally, we optimized gplas, a graph-based tool that bins plasmid-predicted contigs into distinct plasmid predictions. Gplas2 is more effective at recovering plasmids with large sequencing coverage variations and can be combined with the output of any binary classifier. The combination of plasmidEC with gplas2 showed a high completeness (median=0.818) and F1-Score (median=0.812) when reconstructing ARG plasmids and exceeded the binning capacity of the reference-based method MOB-suite. In the absence of long-read data, our method offers an excellent alternative to reconstruct ARG plasmids in E. coli.
Integrated optical gyroscope, and a method of manufacturing

光集積ジャイロであって、取付プレート、上側基板及び下側基板を備えた多層型の光コイルを有し、上側基板、下側基板は取付プレートに接着されている。 上側基板は上側導波管コイルを、下側基板は下側導波管コイルを有する。 カプラは、入力ポートと第１、第２、第３の出力ポートとを有する。 第１の光ファイバは、上側導波コイルを下側導波コイルに結合する。 コイルは結合されて共通の回転感度を有する。 第２の光ファイバはカプラの第１出力ポートを上側導波管コイルに接続する。 第３の光ファイバはカプラの第２出力ポートを下側導波管コイルに接続する。 光源はカプラの第１入力ポートに光波を入れる。 カプラは光波を実質的に等しい第１及び第２の出力波に分ける。 第１の波は上側及び下側の導波管に第１の回転感度を有する波を形成し、第２の波は反対方向に同じことを行う。 変調器手段は第１の回転感度を有する波及び第２の回転感度を有する波の位相を変調する。 検知手段は検知した電気信号を提供する。
Adjusting Central and Eastern North America Ground‐Motion Intensity Measures between Sites with Different Reference‐Rock Site Conditions

Abstract Adjustment factors are provided for converting ground‐motion intensity measures between central and eastern North America (CENA) sites with different reference‐rock site conditions ( V S 30 =760, 2000, and 3000 m/s) for moment magnitudes ranging from 2 to 8, rupture distances ranging from 2 to 1200 km, Fourier amplitude spectra (FAS) for frequencies ranging from 0.01 to 100 Hz, response spectra for periods ranging from 0.01 to 10.0 s, peak ground acceleration, and peak ground velocity. The adjustment factors are given for a wide range of the site diminution parameters ( κ 0 ) for sites with V S 30 =760 m/s and for a κ 0 of 0.006 s for two harder rock sites. Fourteen CENA velocity profiles with V S 30 values within a factor of 1.1 of 760 m/s were used to derive average FAS amplification factors as a function of frequency, which were then used in simulations of peak ground‐motion parameters and response spectra to derive the adjustment factors. The amplification function differs from that used in western North America (e.g., Campbell and Boore, 2016) in having a peak near 9 Hz, due to the resonance of motions in the relatively thin low‐velocity material over hard rock that characterizes many CENA sites with V S 30 near 760 m/s. We call these B/C sites, because this velocity marks the boundary between National Earthquake Hazards Reduction Program site classes B and C (Building Seismic Safety Council, 2004). The adjustments for short‐period motions are sensitive to the value of κ 0 , but there are very few if any determinations of κ 0 for CENA B/C sites. For this reason, we determined κ 0 from multiple recordings at Pinyon Flat Observatory (PFO), California, which has a velocity‐depth profile similar to those of CENA B/C sites. The PFO and other results from the literature suggest that appropriate values of κ 0 for CENA B/C sites are expected to lie between 0.01 and 0.03 s. Electronic Supplement: Zip files with parameters used by Stochastic‐Method SIMulation (SMSIM) and ratios of the ground‐motion intensity measures between hard‐rock sites and National Earthquake Hazards Reduction Program (NEHRP) B/C sites.
INTERNATIONAL SCIENTIFIC COMMITTEE FOR TUNA AND TUNA-LIKE SPECIES IN THE NORTH PACIFIC OCEAN (ISC) An Evaluation of the Natural Mortality Schedule Assumed in the PBF 2008 Stock Assessment and Proposed Changes

The stock status of Northern Pacific bluefin tuna (PBF), Thunnus orientalis, was recently evaluated by the PBF Working Group (WG) of the International Scientific Committee (ISC) for Tuna and Tuna like Species. The stock status remains uncertain and the WG is investigating the possibility that there may be a model mis-specification. This paper focuses on natural mortality. It reviews the scientific process leading to the PBF natural mortality (M) schedule assumed for the 2008 PBF assessment. It also provides a critical evaluation of the assumptions and proposes an alternative natural mortality schedule for PBF. In the absence of direct estimates of M for PBF beyond age-0 (1+ years), the WG adopted a vector based on assumptions made for southern bluefin tuna (SBT). This choice should be re-visited and revised considering the differences that exist between the life-history of PBF and SBT. The adoption for PBF of the SBT estimate of M=0.12 yr for the 4+ year old adult fish seems the most problematic. The later is based on the long life-span of SBT (maximum age of 42) which does not seem to be the case for PBF (maximum observed age of 21 years). In addition, while the mean age at maturity for SBT varies from age 8-12 years, PBF begins to mature at age 3 and are fully mature at age 5. It seems reasonable to assume that such an early investment on reproduction would result in higher natural mortality levels for mature PBF. An alternative M estimate for the adult fish (3+ year) could be taken as the median value (M=0.27) obtained across a large suite of life-history based methods. Estimates of natural mortality for ages 1 and 2 also
Fair Classifiers Without Fair Training: An Influence-Guided Data Sampling Approach

A fair classifier should ensure the benefit of people from different groups, while the group information is often sensitive and unsuitable for model training. Therefore, learning a fair classifier but excluding sensitive attributes in the training dataset is important. In this paper, we study learning fair classifiers without implementing fair training algorithms to avoid possible leakage of sensitive information. Our theoretical analyses validate the possibility of this approach, that traditional training on a dataset with an appropriate distribution shift can reduce both the upper bound for fairness disparity and model generalization error, indicating that fairness and accuracy can be improved simultaneously with simply traditional training. We then propose a tractable solution to progressively shift the original training data during training by sampling influential data, where the sensitive attribute of new data is not accessed in sampling or used in training. Extensive experiments on real-world data demonstrate the effectiveness of our proposed algorithm.
MuLan: Multimodal-LLM Agent for Progressive Multi-Object Diffusion

Existing text-to-image models still struggle to generate images of multiple objects, especially in handling their spatial positions, relative sizes, overlapping, and attribute bindings. In this paper, we develop a training-free Multimodal-LLM agent (MuLan) to address these challenges by progressive multi-object generation with planning and feedback control, like a human painter. MuLan harnesses a large language model (LLM) to decompose a prompt to a sequence of sub-tasks, each generating only one object conditioned on previously generated objects by stable diffusion. Unlike existing LLM-grounded methods, MuLan only produces a high-level plan at the beginning while the exact size and location of each object are determined by an LLM and attention guidance upon each sub-task. Moreover, MuLan adopts a vision-language model (VLM) to provide feedback to the image generated in each sub-task and control the diffusion model to re-generate the image if it violates the original prompt. Hence, each model in every step of MuLan only needs to address an easy sub-task it is specialized for. We collect 200 prompts containing multi-objects with spatial relationships and attribute bindings from different benchmarks to evaluate MuLan. The results demonstrate the superiority of MuLan in generating multiple objects over baselines. The code is available on https://github.com/measure-infinity/mulan-code.
Parallel Structures in Pre-training Data Yield In-Context Learning

Pre-trained language models (LMs) are capable of in-context learning (ICL): they can adapt to a task with only a few examples given in the prompt without any parameter update. However, it is unclear where this capability comes from as there is a stark distribution shift between pre-training text and ICL prompts. In this work, we study what patterns of the pre-training data contribute to ICL. We find that LMs' ICL ability depends on $\textit{parallel structures}$ in the pre-training data -- pairs of phrases following similar templates in the same context window. Specifically, we detect parallel structures by checking whether training on one phrase improves prediction of the other, and conduct ablation experiments to study their effect on ICL. We show that removing parallel structures in the pre-training data reduces LMs' ICL accuracy by 51% (vs 2% from random ablation). This drop persists even when excluding common patterns such as n-gram repetitions and long-range dependency, showing the diversity and generality of parallel structures. A closer look at the detected parallel structures indicates that they cover diverse linguistic tasks and span long distances in the data.