Miracle-dz/UniFAR-FTUs huggingface dataset:
DeepLoc 2.0: multi-label subcellular localization prediction using protein language models

Abstract The prediction of protein subcellular localization is of great relevance for proteomics research. Here, we propose an update to the popular tool DeepLoc with multi-localization prediction and improvements in both performance and interpretability. For training and validation, we curate eukaryotic and human multi-location protein datasets with stringent homology partitioning and enriched with sorting signal information compiled from the literature. We achieve state-of-the-art performance in DeepLoc 2.0 by using a pre-trained protein language model. It has the further advantage that it uses sequence input rather than relying on slower protein profiles. We provide two means of better interpretability: an attention output along the sequence and highly accurate prediction of nine different types of protein sorting signals. We find that the attention output correlates well with the position of sorting signals. The webserver is available at services.healthtech. dtu.dk/service.php? DeepLoc-2.0.
How Robust is Neural Machine Translation to Language Imbalance in Multilingual Tokenizer Training?

A multilingual tokenizer is a fundamental component of multilingual neural machine translation. It is trained from a multilingual corpus. Since a skewed data distribution is considered to be harmful, a sampling strategy is usually used to balance languages in the corpus. However, few works have systematically answered how language imbalance in tokenizer training affects downstream performance. In this work, we analyze how translation performance changes as the data ratios among languages vary in the tokenizer training corpus. We find that while relatively better performance is often observed when languages are more equally sampled, the downstream performance is more robust to language imbalance than we usually expected. Two features, UNK rate and closeness to the character level, can warn of poor downstream performance before performing the task. We also distinguish language sampling for tokenizer training from sampling for model training and show that the model is more sensitive to the latter.
Fast-neutron-induced fission of 
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We report the measurement of the TKE release in the fast neutron induced fission of $^{240}$Pu and $^{242}$Pu. The results are compared to the predictions of the GEF model, the CGMF model, and the model of Denisov and Sedykh as well as previous experimental work on these reactions. Our absolute measurements of the TKE release are in good agreement with the previous measurements of Nethaway \textit{et al.} for the interaction of 14.8 MeV neutrons with $^{240}$Pu \cite{Nethaway} and of Winkelmann and Aumann for the interaction of 15 MeV neutrons with $^{242}$Pu \cite{Winkelmann}. The general trends of the measured TKE values agree with phenomenological models but the variances of the TKE distributions are significantly less than predicted by various models. The mean post neutron emission TKE release decreases non- linearly with increasing neutron energy and can be represented as TKE(MeV) = 175.8 $\pm$ 0.3 - (2. 4 $\pm$ 0.8)log$_{10}$E$_n$ - (1.4 $\pm$0.4)log$_{10}$E$_{n}^2$ for $^{240}$Pu and TKE(MeV) = 177.1 $\pm$ 0.3 - (1.2 $\pm$ 0.9)log$_{10}$E$_n$ - (1.8 $\pm$0.5)log$_{10}$E$_{n}^2$ for $^{242}$Pu.
Paneth Cells Protect against Acute Pancreatitis via Modulating Gut Microbiota Dysbiosis

We demonstrate that AP patients and experimental AP mice exhibited a dysfunction of Paneth cells. Our in vivo research showed that the severity of AP was exacerbated by the long-term dysfunction of Paneth cells, which was associated with gut microbiota disorder. ABSTRACT Acute pancreatitis (AP) is usually accompanied by intestinal failure, but its mechanism is still unclear. In AP patients, the functions of Paneth cells (lysozyme, HD5, Reg3γ, and Wnt3a) decreased. Compared with AP mice, injuries and inflammation of the pancreas and ileum were aggravated in AP mice treated with dithizone (Dith) (Dith+AP mice). Intestinal permeability and bacterial translocation were also increased. 16S rRNA sequencing showed that the gut microbiota of Dith mice and Dith+AP mice exhibited a marked increase in the pathogenic bacterium Helicobacter and a significant decrease in the probiotic bacterium Blautia. Lysozyme gavage in Dith+AP mice effectively alleviated injuries of the pancreas and small intestine. The beneficial effect of lysozyme was associated with a significant increase in the probiotic bacterium Blautia and a virtual absence of the pathogenic bacterium Helicobacter. The severity of AP in antibiotic-treated mice (ABX mice) was significantly aggravated when receiving feces from Dith mice and was markedly alleviated when receiving feces from lysozyme-gavaged mice. In vitro, lysozyme increased the proliferation of enteroids by promoting the activation of the Wnt pathway and Lgr5 expression in intestinal stem cells. IMPORTANCE We demonstrate that AP patients and experimental AP mice exhibited a dysfunction of Paneth cells. Our in vivo research showed that the severity of AP was exacerbated by the long-term dysfunction of Paneth cells, which was associated with gut microbiota disorder. Restoring part of Paneth cell functions through lysozyme supplementation alleviated the severity of AP and gut microbiota dysbiosis. This study provides novel insight into the link of pancreas-gut interactions in the pathogenesis of AP, providing a new direction for the clinical treatment of intestinal complications during AP.
Polymicrobial Interactions of Oral Microbiota: a Historical Review and Current Perspective

The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. ABSTRACT The oral microbiota is enormously diverse, with over 700 microbial species identified across individuals that play a vital role in the health of our mouth and our overall well-being. In addition, as oral diseases such as caries (cavities) and periodontitis (gum disease) are mediated through interspecies microbial interactions, this community serves as an important model system to study the complexity and dynamics of polymicrobial interactions. Here, we review historical and recent progress in our understanding of the oral microbiome, highlighting how oral microbiome research has significantly contributed to our understanding of microbial communities, with broad implications in polymicrobial diseases and across microbial community ecology. Further, we explore innovations and challenges associated with analyzing polymicrobial systems and suggest future directions of study. Finally, we provide a conceptual framework to systematically study microbial interactions within complex communities, not limited to the oral microbiota.
Mental Health and Wellness of Service Providers Working with People Experiencing Homelessness in Canada: A National Survey from the Second Wave of the COVID-19 Pandemic

Objective: This study examined the scope of common mental health problems and perceived impacts of the COVID-19 pandemic among direct service providers working with people experiencing homelessness in Canada. Method: This cross-sectional study used an online survey that was disseminated to homeless service, supportive housing, and harm reduction organizations and networks. Data were collected on depression, anxiety, stress, post-traumatic stress, compassion satisfaction and fatigue, and substance use problems as well as pandemic-related changes in mental health and wellness. A total of 701 service providers completed the survey and were included in data analysis. Descriptive statistics were used to examine the primary research questions, with hierarchical multiple regression models also being fit to explore mental health and wellness differences by occupational service setting. Results: Most direct service providers (79.5%) working with people experiencing homelessness reported a decline in their mental health during the pandemic. There were high rates of common mental health problems within the sample that are largely consistent with those found among health-care workers during the pandemic. Occupational service settings were not associated with the severity of mental health problems, indicating pervasive issues across the workforce, though providers who were younger and spent more time in direct service roles were at greater risk. Conclusions: The common mental health problems and negative impacts of the pandemic among service providers working with people experiencing homelessness highlight a highly vulnerable workforce that could benefit from improved access to supports. Given the similarities between our findings and other studies examining essential workforces, it is recommended that initiatives that provide accessible mental health care to the health-care workforce during the pandemic be expanded to include homeless and social service providers.
Clinical and radiological outcomes of combined modular prothesis and cortical strut for revision proximal femur in giant cell tumor of bone patients

Background Femoral bone deficiency is a challenging problem in revision proximal femoral replacement. The purpose of this study is to evaluate the clinical and radiological outcomes of revision proximal femoral replacement as a salvage treatment for severe bone loss after oncologic proximal replacement surgery in patient with benign giant cell tumor of bone. Methods 16 patients (6 men and 10 women) were included in this retrospective study, with a mean age of 46.6 year at the time of revision surgery. All patients underwent revision proximal femoral replacement with the use of modular prosthesis and cortical strut allografts. The modified Harris Hip Score, Short Form 36, and musculoskeletal Tumor Society Score were used for patient evaluation. Regular follow-up was performed to evaluate the recurrence and metastases rate, limb function, and long-term complications of patients. Results The average follow-up was 46.3 months (range, 26–75 months), during which there was no local recurrence and metastases of patient. At the latest follow-up, the mean modified Harris Hip Score was 70.6 points, which was significantly improved compared with that of preoperative (p < 0.05). The final follow-up results of Short Form 36, Musculoskeletal Tumor Society Score, and limb-length discrepancy were also significantly improved compared to that of preoperative (p < 0.05). At the latest follow-up, the implanted femoral stems were all stable and all cortical strut allografts were also incorporated to their own bone. Conclusion Using modular prosthesis and cortical strut allografts in revision, proximal femur replacement is an acceptable procedure for relatively young patient with severe proximal femoral bone loss after oncologic surgery with benign giant cell tumor of bone. More attentions should be paid to reduce the risk of complications in these complex reconstructions.
Graphene toxicity as a double-edged sword of risks and exploitable opportunities: a critical analysis of the most recent trends and developments

Increased production volumes and a broadening application spectrum of graphene have raised concerns about its potential adverse effects on human health. Numerous reports demonstrate that graphene irrespective of its particular form exerts its effects on a widest range of living organisms, including prokaryotic bacteria and viruses, plants, micro- and macro-invertebrates, mammalian and human cells and whole animals in vivo. However, the available experimental data is frequently a matter of significant divergence and even controversy. Therefore, we provide here a critical analysis of the most recent (2015–2016) reports accumulated in the graphene-related materials biocompatibility and toxicology field in order to elucidate the cutting edge achievements, emerging trends and future opportunities in the area. Experimental findings from the diverse in vitro and in vivo model systems are analysed in the context of the most likely graphene exposure scenarios, such as respiratory inhalation, ingestion route, parenteral administration and topical exposure through the skin. Key factors influencing the toxicity of graphene and its complex derivatives as well as potential risk mitigation approaches exploiting graphene physicochemical properties, surface modifications and possible degradation pathways are also discussed along with its emerging applications for healthcare, diagnostics and innovative therapeutic approaches.
A design of high‐gain array antenna with novel metamaterial structures for millimeter‐wave femtocell implementation

A novel method based on the metamaterial concept has been proposed to increase the gain of a planar array antenna without increasing the dimensions for millimeter‐wave femtocell implementation which can easily replace expensive macrocells. To implement the proposed method and present its advantages, 16 novel metamaterial unit‐cells named split cylinder metamaterial resonators (SCMRs) have been used to increase the gain of a millimeter‐wave two‐layer array antenna. The dimensions of each SCMR are equal to 0.067 mm3 or 0.0001 λg3, where λg is the guided wavelength at 27.5 GHz. Providing an effective metamaterial environment by the proposed SCMRs increases the gain of the antenna by more than 10 dB in the operating frequencies compared to a sample array antenna in which no metamaterial structures is used. The proposed SCMRs at frequencies of 24.5–32.5 GHz, with the creation of negative permeability and permittivity, have created a metamaterial environment. The frequency range covered by the proposed antenna is 26.5–28.5 GHz for millimeter‐wave femtocell applications. The average gain of the proposed antenna in the operating frequency band is equal to 17 dB. Also, the radiation efficiency at 27.5 GHz is 86%. The final dimensions of the proposed antenna are equal to 0.047 λg3 at 27.5 GHz. To confirm the accuracy of the full‐wave simulation, the proposed two‐layer array antenna was fabricated and its characteristics were measured. There is an acceptable fit between the simulated and measured results. It should be noted that the most important advantage of the SCMR is the improvement of antenna performance without increasing the dimensions.
A systematic review: metabolomics‐based identification of altered metabolites and pathways in the skin caused by internal and external factors

The skin's ability to function optimally is affected by many diverse factors. Metabolomics has a great potential to improve our understanding of the underlying metabolic changes and the affected pathways. Therefore, the objective of this study was to review the current state of the literature and to perform further metabolic pathway analysis on the obtained data. The aim was to gain an overview of the metabolic changes under altered conditions and to identify common and different patterns as a function of the investigated factors. A cross‐study comparison of the extracted studies from different databases identified 364 metabolites, whose concentrations were considerably altered by the following factor groups: irradiation, xenobiotics, ageing and skin diseases (mainly psoriasis). Using metabolic databases and pathway analysis tools, the individual metabolites were assigned to the corresponding metabolic pathways and the most strongly affected signalling pathways were identified. All factors induced oxidative stress. Thus, antioxidant defence systems, especially coenzyme Q10 (ageing) and the glutathione system (irradiation, ageing, xenobiotics), were impacted. Lipid metabolism was also impacted by all factors studied. The carnitine shuttle as part of β‐oxidation was activated by all factor groups except ageing. Glycolysis, Krebs (TCA) cycle and purine metabolism were mainly affected by irradiation and xenobiotics. The pentose phosphate pathway was activated, and Krebs cycle was downregulated in response to oxidative stress. In summary, it can be ascertained that mainly energy metabolism, lipid metabolism, antioxidative defence and DNA repair systems were impacted by the factors studied.
Behavior and Immune Response of Conventional and Slow-Growing Broilers to Salmonella Typhimurium

Fast growth rate in broiler chickens comes with welfare concerns and the contribution of growth rate to pathogen resistance and sickness behavior is relatively unknown. The objective of this study was to evaluate physiological and behavioral responses of conventional (CONV) and slow-growing (SG) male broilers challenged with Salmonella Typhimurium. CONV (n = 156) and SG (n = 156) chicks were raised in a pen with wood litter shavings until day 7 of age, when birds were transferred to 24 isolators (n = 11 chicks/isolator). On day 14 of age, half of the birds (n = 12 isolators) were challenged with S. Typhimurium (ST) and the other half (n = 12 isolators) received a control (C). On days 7, 13, 17, 21, and 24, body weight was recorded, and blood, jejunum and ileum sections were collected from 2 birds/isolator (n = 48 birds/sampling) to measure plasma IgA and IgG and intestinal histomorphology, respectively. On days 12, 16, 21, and 23, video was recorded to evaluate bird postures (sitting, standing, or locomoting) and behaviors (eating, drinking, preening, stretching, sham foraging, allopreening, and aggression). CONV birds were 70 g heavier (p = 0.03) on day 21 and 140 g heavier (p = 0.007) on day 24 than SG. On day 7, CONV jejunum villus height and crypt depth were 22 and 7 μm greater (p ≤ 0.001), respectively, than SG. On day 24, ST ileum villus height was 95 μm shorter (p = 0.009) than C. IgA increased after day 17 for all birds and at day 21, CONV IgA was greater (p = 0.01) than SG. Although SG IgG was 344 μg/ml greater (p = 0.05) than CONV on day 7, CONV IgG increased with age (p < 0.0001) to greater (p ≤ 0.03) concentrations than SG on day 21 and day 24 by 689 μg/ml and 1,474 μg/ml, respectively, while SG IgG remained at similar concentrations after day 13. Generally, a greater proportion of birds sham foraged as they aged (p < 0.0001). A greater proportion of CONV tended to sit (p = 0.09) and fewer locomoted (p < 0.0001) than SG as they aged. The results illustrate conventional and slow-growing broilers differ in their behavior, immunity, and response to Salmonella.
Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe

Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.
Force From Filaments: The Role of the Cytoskeleton and Extracellular Matrix in the Gating of Mechanosensitive Channels

The senses of proprioception, touch, hearing, and blood pressure on mechanosensitive ion channels that transduce mechanical stimuli with high sensitivity and speed. This conversion process is usually called mechanotransduction. From nematode MEC-4/10 to mammalian PIEZO1/2, mechanosensitive ion channels have evolved into several protein families that use variant gating models to convert different forms of mechanical force into electrical signals. In addition to the model of channel gating by stretching from lipid bilayers, another potent model is the opening of channels by force tethering: a membrane-bound channel is elastically tethered directly or indirectly between the cytoskeleton and the extracellular molecules, and the tethering molecules convey force to change the channel structure into an activation form. In general, the mechanical stimulation forces the extracellular structure to move relative to the cytoskeleton, deforming the most compliant component in the system that serves as a gating spring. Here we review recent studies focusing on the ion channel mechanically activated by a tethering force, the mechanotransduction-involved cytoskeletal protein, and the extracellular matrix. The mechanosensitive channel PIEZO2, DEG/ENaC family proteins such as acid-sensing ion channels, and transient receptor potential family members such as NompC are discussed. State-of-the-art techniques, such as polydimethylsiloxane indentation, the pillar array, and micropipette-guided ultrasound stimulation, which are beneficial tools for exploring the tether model, are also discussed.
Efficacy of Metribuzin Doses on Physiological, Growth, and Yield Characteristics of Wheat and Its Associated Weeds

Weeds cause a serious constraint to wheat productivity. Chemical weed control is considered the most effective method to control weeds; however, a suitable dose and combination of herbicide with adjuvants play a vital role in controlling weeds and producing maximum wheat production. A field study was conducted to investigate the effectiveness of various doses of metribuzin alone or in combination with adjuvants [Bio-power (alkyl ether sulfates and sodium salts) and Ad-500 (fatty alcohol ethoxylate)] on the growth and yield of wheat and its associated weeds. Metribuzin at 175, 140, and 105 g a.i ha–1, each in combination with adjuvants (Bio-power or Ad-500) at 400 ml ha–1, were sprayed. A weedy check was also included as a control treatment. The wheat crop was infested with Fumaria indica, Melilotus indica, Anagallis arvensis, and Phalaris minor, and metribuzin with or without adjuvant was sprayed at two- to four-leaf stage of the weeds. The photosynthetic activity, weed population of each weed, and biomass of each weed was significantly affected by all herbicides along with the adjuvant. However, maximum inhibition of tested weeds was observed where metribuzin at 175 g a.i ha–1 + Bio-power at 400 ml ha–1 were sprayed. Metribuzin sprayed at 175 g a.i ha–1 with or without Bio-power recorded a maximum 1,000-grain weight, biological yield, and grain yield. Conclusively, metribuzin sprayed at 175 g a.i ha–1 + Bio-power at 400 at ml ha–1 have the potential to improve wheat yield by inhibiting weed growth, and Bio-power was superior to Ad-500 in improving the efficacy of metribuzin against weeds of wheat crop.