Miracle-dz/UniFAR-FTUs huggingface dataset:
Impact of glaucoma on the spatial frequency processing of scenes in central vision

Abstract Glaucoma is an eye disease characterized by a progressive vision loss usually starting in peripheral vision. However, a deficit for scene categorization is observed even in the preserved central vision of patients with glaucoma. We assessed the processing and integration of spatial frequencies in the central vision of patients with glaucoma during scene categorization, considering the severity of the disease, in comparison to age-matched controls. In the first session, participants had to categorize scenes filtered in low-spatial frequencies (LSFs) and high-spatial frequencies (HSFs) as a natural or an artificial scene. Results showed that the processing of spatial frequencies was impaired only for patients with severe glaucoma, in particular for HFS scenes. In the light of proactive models of visual perception, we investigated how LSF could guide the processing of HSF in a second session. We presented hybrid scenes (combining LSF and HSF from two scenes belonging to the same or different semantic category). Participants had to categorize the scene filtered in HSF while ignoring the scene filtered in LSF. Surprisingly, results showed that the semantic influence of LSF on HSF was greater for patients with early glaucoma than controls, and then disappeared for the severe cases. This study shows that a progressive destruction of retinal ganglion cells affects the spatial frequency processing in central vision. This deficit may, however, be compensated by increased reliance on predictive mechanisms at early stages of the disease which would however decline in more severe cases.
Gravidity and Parity Definitions (Implications in Risk Assessment)

A nulliparous woman (nullip) has not given birth previously (regardless of outcome). A primagravida is in her first pregnancy. A primiparous woman has given birth once. The term 'primip' is often used interchangeably with primagravida, although technically incorrect, as a woman does not become primiparous until she has delivered her baby. A multigravida has been pregnant more than once. A multiparous woman (multip) has given birth more than once. A grand multipara is a woman who has already delivered five or more infants who have achieved a gestational age of 24 weeks or more, and such women are traditionally considered to be at higher risk than the average in subsequent pregnancies. A grand multigravida has been pregnant five times or more. A great grand multipara has delivered seven or more infants beyond 24 weeks of gestation.
Home improvements in later life: competing policy goals and the practices of older Dutch homeowners

Abstract Dutch policy-making has been framed by simultaneous efforts aimed at reforming the social care system and initiating an ambitious sustainable retrofitting programme of housing. In these processes, the willingness and ability of older people, living in owner-occupied housing, to adapt and improve their home or move to a suitable dwelling are crucial. However, our understanding of how and why older people undertake home improvements, and how these practices intersect with policy agendas is still limited. In this paper we draw on a qualitative study with 33 older Dutch homeowner households, to understand how older people conceive home improvements and investments, and their motivations for pursuing them (or not). We find that home improvement as well as moves through and into homeownership are usually deeply connected with ideas of a good life. That may involve adapting to decreasing mobility and cognitive functions, closer relations with children and grandchildren, traveling and hobbies, comfort, and even luxury. However, these practices often lack the coherence implied by policymakers and include intricate considerations of physical, mental, social, and financial well-being.
Towards Intention Understanding in Suicidal Risk Assessment with Natural Language Processing

Recent applications of natural language processing techniques to suicidal ideation detection and risk assessment frame the detection or assessment task as a text classiﬁcation problem. Recent advances have developed many models, especially deep learning models, to boost predictive performance. Though the performance (in terms of aggregated evaluation scores) is improving, this position paper urges that better intention understanding is required for reliable suicidal risk assessment with computational methods. This paper reﬂects the state of natural language processing applied to suicide-associated text classiﬁcation tasks, differentiates suicidal risk assessment and intention understanding, and points out potential limitations of sentiment features and pre-trained language models in suicidal intention understanding. Besides, it urges the necessity for sequential intention understanding and risk assessment, discusses some critical issues in evaluation such as uncertainty, and studies the lack of benchmarks.
Identification and characterization of bacterial glycogen-degrading enzymes in the vaginal microbiome

The healthy human vaginal microbiota is generally dominated by lactobacilli, and the transition to a more diverse community of anaerobic microbes is associated with health risks. Glycogen released by lysed epithelial cells is believed to be an important nutrient source in this environment. However, the mechanism by which vaginal bacteria metabolize glycogen is unclear, with evidence implicating both microbial and human enzymes. Here, we biochemically characterize six glycogen-degrading enzymes (GDEs) from vaginal bacteria that support the growth of amylase-deficient L. crispatus on glycogen. We reveal variations in the pH tolerance and susceptibility to inhibition between enzymes from different organisms. Analysis of vaginal microbiome datasets show these enzymes are expressed in all Community State Types. Finally, we confirm the presence and activity of bacterial GDEs in cervicovaginal fluid. This work establishes that bacterial GDEs can participate in the breakdown of glycogen, providing insight into metabolism that may shape the vaginal microbiota.
Behavioral measurements of motor readiness in mice

Motor planning facilitates rapid and precise execution of volitional movements. Although motor planning has been classically studied in humans and monkeys, the mouse has become an increasingly popular model system to study neural mechanisms of motor planning. It remains yet untested whether mice and primates share common behavioral features of motor planning. We combined videography and a delayed response task paradigm in an autonomous behavioral system to measure motor planning in non-body- restrained mice. Motor planning resulted in both reaction time savings and increased movement accuracy, replicating classic effects in primates. We found that motor planning was reflected in task-relevant body features. Both the specific actions prepared and the degree of motor readiness could be read out online during motor planning. The online readout further revealed behavioral evidence of simultaneous preparation for multiple actions under uncertain conditions. These results validate the mouse as a model to study motor planning, demonstrate body feature movements as a powerful real-time readout of motor readiness, and offer behavioral evidence that motor planning can be a parallel process that permits rapid selection of multiple prepared actions.
A theory of hippocampal theta correlations accounting for extrinsic and intrinsic sequences

Hippocampal place cell sequences have been hypothesized to serve as diverse purposes as the induction of synaptic plasticity, formation and consolidation of long-term memories, or navigation and planning. During spatial behaviors of rodents, sequential firing of place cells at the theta timescale (known as theta sequences) encodes running trajectories, which can be considered as 1-dimensional behavioral sequences of traversed locations. In a 2-dimensional space, however, each single location can be visited along arbitrary 1-dimensional running trajectories. Thus, a place cell will generally take part in multiple different theta sequences, raising questions about how this 2-dimensional topology can be reconciled with the idea of hippocampal sequences underlying memory of (1-dimensional) episodes. Here, we propose a computational model of cornu ammonis 3 (CA3) and dentate gyrus (DG), where sensorimotor input drives the direction-dependent (extrinsic) theta sequences within CA3 reflecting the 2-dimensional spatial topology, whereas the in-trahippocampal CA3-DG projections concurrently produce intrinsic sequences that are independent of the specific running trajectory. Consistent with experimental data, these intrinsic theta sequences are less prominent in the theta state, but we show that they can nevertheless be detected during theta activity, thereby serving as running-direction independent landmark cues. We hypothesize that the intrinsic sequences largely reflect replay and preplay activity during non-theta states.
Recognizing the opponent: the consolidation of long-term social memory in zebrafish males

Recognizing and remembering another individual in a social context could be beneficial for individual fitness. Especially in agonistic encounters, remembering an opponent and the previous fight could allow avoiding new conflicts. Considering this, we hypothesized that this type of social interaction forms a long-term recognition memory lasting several days. It has been shown that a second encounter 24 hours later between the same pair of zebrafish males is resolved with lower levels of aggression. Here, we evaluated if this behavioral change could last for longer intervals and a putative mechanism associated with memory storage: the recruitment of NMDA receptors. We found that if a pair of zebrafish males fight and 48 or 72 hours later fight again, they resolved the second encounter with lower levels of aggression. However, if immediately after the first encounter opponents were exposed to MK-801 (NMDA receptor antagonist), they resolve the second one with the same levels of aggression, that is, no reduction in aggressive behaviors was observed. These results suggest the formation of a long-term social memory related to recognizing a particular opponent and/or the outcome and features of a previous fight.
Nano-structured Hydrotrope-Caged Cytochrome c with Boosted Stability in Harsh Environments: A Molecular Insight

Green and nano-structured catalytic media are vital for bio-catalysis to attenuate the denaturation tendency of biocata-lysts under severe reaction conditions. Hydrotropes with multi-faceted physiochemical properties represent promising systems for sustainable protein packaging. Herein, the suitability of adenosine-5’-triphosphate (ATP) and cholinium sa-licylate ([Cho][Sal]) ionic liquid (IL) to form nano-structures and to nano-confine Cytochrome c (Cyt c) were demonstrat-ed to enhance the stability and activity under multiple stressors. Experimental and computational analyses were under-taken to explain the nano-structured phenomenon of ATP and IL, structural organizations of nano-confined Cyt c, and site-specific interactions that stabilize the protein structure. Both ATP and IL form nano-structures in aqueous media and could cage Cyt c via multiple nonspecific soft interactions. Remarkably, the engineered molecular nano-cages of ATP (5-10 mM), IL (300 mg/mL), and ATP+IL surrounding Cyt c resulted in 9-to-72-fold higher peroxidase activity than native Cyt c with exceptionally high thermal tolerance (110oC). The polar interactions with the cardiolipin binding site of Cyt c, mediated by hydrotropes, were well correlated with the increased peroxidase activity. Furthermore, higher activity trends were observed in the presence of urea, GuHCl, and trypsin without any protein degradation. Specific binding of hy-drotropes in highly mobile regions of Cyt c (Ω 40-54 residues) and enhanced H-bonding with Lys and Arg offered excel-lent stability under extreme conditions. Additionally, ATP effectively counteracted reactive oxygen species (ROS)-induced denaturation of Cyt c, which was enhanced by the [Sal] counterpart of IL. Overall, this study explored the robustness of nano-structured hydrotropes to have a higher potential for protein packaging with improved stability and activity under extreme conditions. Thus, the present work highlights a novel strategy for real-time industrial bio-catalysis to protect mitochondrial cells from ROS-instigated apoptosis. Summary Suitability of ATP and [Cho][Sal] ionic liquid to form nanostructured hydrotropes and their utility in protein packaging in extreme conditions are discussed. Both ATP and IL form nanostructures in aqueous media and could cage Cyt c via multiple nonspecific soft interactions. The engineered molecular nanocages surrounding Cyt c resulted in 9-to-72-fold higher peroxidase activity than native Cyt c with exceptionally high thermal tolerance (110°C) and stability in the presence of urea, GuHCl, and trypsin without any protein degradation.
Comparative Transcriptomics and Genomics from Continuous Axenic Media Growth Identifies Coxiella burnetii Intracellular Survival Strategies

Coxiella burnetii (Cb) is an obligate intracellular pathogen in nature and the causative agent of acute Q fever as well as chronic diseases. In an effort to identify genes and proteins crucial to their normal intracellular growth lifestyle, we applied a “Reverse evolution” approach where the avirulent Nine Mile Phase II strain of Cb was grown for 67 passages in chemically defined ACCM-D media and gene expression patterns and genome integrity from various passages was compared to passage number one following intracellular growth. Transcriptomic analysis identified a marked downregulation of the structural components of the type 4B secretion system (T4BSS), the general secretory (sec) pathway, as well as 14 out of 118 previously identified genes encoding effector proteins. Additional downregulated pathogenicity determinants genes included several chaperones, LPS, and peptidoglycan biosynthesis. A general marked downregulation of central metabolic pathways was also observed, which was balanced by a marked upregulation of genes encoding transporters. This pattern reflected the richness of the media and diminishing anabolic and ATP-generation needs. Finally, genomic sequencing and comparative genomic analysis demonstrated an extremely low level of mutation across passages, despite the observed Cb gene expression changes following acclimation to axenic media.
Long lifetime and selective accumulation of the A-type lamins accounts for the tissue specificity of Hutchinson-Gilford progeria syndrome

Mutations to the LMNA gene cause laminopathies including Hutchinson-Gilford progeria syndrome (HGPS) that severely affect the cardiovascular system. The origins of tissue specificity in these diseases are unclear, as the A-type Lamins are abundant and broadly expressed proteins. We show that A-type Lamin protein and transcript levels are uncorrelated across tissues. As protein-transcript discordance can be caused by variations in protein lifetime, we applied quantitative proteomics to profile protein turnover rates in healthy and progeroid tissues. We discover that tissue context and disease mutation each influence A-type Lamin protein lifetime. Lamin A/C has a weeks-long lifetime in the aorta, heart, and fat, where progeroid pathology is apparent, but a days-long lifetime in the liver and gastrointestinal tract, which are spared from disease. The A-type Lamins are insoluble and densely bundled in cardiovascular tissues, which may present an energetic barrier to degradation and promote long protein lifetime. Progerin is even more long-lived than Lamin A/C in the cardiovascular system and accumulates there over time. Progerin accumulation interferes broadly with protein homeostasis, as hundreds of abundant proteins turn over more slowly in progeroid tissues. These findings indicate that potential gene therapy interventions for HGPS will have significant latency and limited potency in disrupting the long-lived Progerin protein. Finally, we reveal that human disease alleles are significantly over-represented in the long-lived proteome, indicating that long protein lifetime may influence disease pathology and present a significant barrier to gene therapies for numerous human diseases. Significance statement Many human diseases are caused by mutations to broadly expressed proteins, yet disease mysteriously manifests only in specific tissues. An example of this is Hutchinson-Gilford progeria syndrome (HGPS), which is caused by a mutation to the Lamin A/C protein. We show that this mutation slows the turnover of Lamin A/C proteins in disease-afflicted tissues, causing the mutant “Progerin” protein to accumulate over time and interfere with the normal turnover of hundreds of other proteins. Because Progerin is a long-lived protein, effective therapies for this disease will need to attack the protein and not just the gene that encodes it.
Leveraging type 1 diabetes human genetic and genomic data in the T1D Knowledge Portal

Translating genetic discoveries for type 1 diabetes (T1D) into mechanistic insight can reveal novel biology and therapeutic targets but remains a major challenge. We developed the T1D Knowledge Portal (T1DKP), a disease-specific resource of genetic and functional annotation data that enables users to develop hypotheses for T1D-based research and target discovery. The T1DKP can be used to query genes and genomic regions for genetic associations, identify epigenomic features, access results of bioinformatic analyses, and obtain expert-curated resources. The T1DKP is available at http://t1d.hugeamp. org.
Single-Cell Genomics Reveals the Divergent Mitochondrial Genomes of Retaria (Foraminifera and Radiolaria)

We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. ABSTRACT Mitochondria originated from an ancient bacterial endosymbiont that underwent reductive evolution by gene loss and endosymbiont gene transfer to the nuclear genome. The diversity of mitochondrial genomes published to date has revealed that gene loss and transfer processes are ongoing in many lineages. Most well-studied eukaryotic lineages are represented in mitochondrial genome databases, except for the superphylum Retaria—the lineage comprising Foraminifera and Radiolaria. Using single-cell approaches, we determined two complete mitochondrial genomes of Foraminifera and two nearly complete mitochondrial genomes of radiolarians. We report the complete coding content of an additional 14 foram species. We show that foraminiferan and radiolarian mitochondrial genomes contain a nearly fully overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. In contrast to animals and fungi, many protists encode a diverse set of proteins on their mitochondrial genomes, including several ribosomal genes; however, some aerobic eukaryotic lineages (euglenids, myzozoans, and chlamydomonas-like algae) have reduced mitochondrial gene content and lack all ribosomal genes. Similar to these reduced outliers, we show that retarian mitochondrial genomes lack ribosomal protein and tRNA genes, contain truncated and divergent small and large rRNA genes, and contain only 14 or 15 protein-coding genes, including nad1, -3, -4, -4L, -5, and -7, cob, cox1, -2, and -3, and atp1, -6, and -9, with forams and radiolarians additionally carrying nad2 and nad6, respectively. In radiolarian mitogenomes, a noncanonical genetic code was identified in which all three stop codons encode amino acids. Collectively, these results add to our understanding of mitochondrial genome evolution and fill in one of the last major gaps in mitochondrial sequence databases. IMPORTANCE We present the reduced mitochondrial genomes of Retaria, the rhizarian lineage comprising the phyla Foraminifera and Radiolaria. By applying single-cell genomic approaches, we found that foraminiferan and radiolarian mitochondrial genomes contain an overlapping but reduced mitochondrial gene complement compared to other sequenced rhizarians. An alternative genetic code was identified in radiolarian mitogenomes in which all three stop codons encode amino acids. Collectively, these results shed light on the divergent nature of the mitochondrial genomes from an ecologically important group, warranting further questions into the biological underpinnings of gene content variability and genetic code variation between mitochondrial genomes.
Is NLP Ready for Standardization?

While standardization is a well-established activity in other scientiﬁc ﬁelds such as telecommunications, networks or multimedia, in the ﬁeld of AI and more speciﬁcally NLP it is still at its dawn. In this paper, we explore how various aspects of NLP (evaluation, data, tasks.) lack standards and how that can impact science, but also the society, the industry, and regulations. We argue that the numerous initiatives to rationalize the ﬁeld and establish good practices are only the ﬁrst step, and developing formal standards remains needed to bring further clarity to NLP research and industry, at a time where this community faces various crises regarding ethics or reproducibility. We thus encourage NLP researchers to contribute to existing and upcoming standardization projects, so that they can express their needs and concerns, while sharing their expertise.
MedicalSum: A Guided Clinical Abstractive Summarization Model for Generating Medical Reports from Patient-Doctor Conversations

We introduce MedicalSum , a Transformer-001 based sequence-to-sequence architecture for 002 summarizing medical conversations by integrat-003 ing medical domain knowledge from the Uni-004 fied Medical Language System (UMLS). The 005 novel knowledge augmentation is performed 006 in three ways: (i) introducing a guidance sig-007 nal that consists of the medical words in the 008 input sequence, (ii) leveraging semantic type 009 knowledge in UMLS to create clinically mean-010 ingful input embeddings, and (iii) making use 011 of a novel weighted loss function that provides 012 a stronger incentive for the model to correctly 013 predict words with a medical meaning. 014 By applying these three strategies, Medical-015 Sum takes clinical domain knowledge into con-016 sideration during the summarization process 017 and achieves state-of-the-art ROUGE score im-018 provements of 0.8-2 points (including 6.2% er-019 ror reduction in PE section ROUGE-1) when 020 producing medical summaries of patient-doctor 021 conversations. Furthermore, a qualitative analy-022 sis shows that medical summaries produced by 023 the knowledge augmented model contain more 024 relevant clinical facts from the patient-doctor 025 conversation. 026
MCPG: A Flexible Multi-Level Controllable Framework for Unsupervised Paraphrase Generation

We present MCPG: a simple and effective approach for controllable unsupervised para-phrase generation, which is also flexible to adapt to specific domains without extra training. MCPG is controllable in different levels: local lexicons, global semantics, and universal styles. The unsupervised paradigm of MCPG combines factual keywords and diversified semantic embeddings as local lexical and global semantic constraints. The semantic embeddings are diversified by standard dropout, which is exploited for the first time to increase inference diversity by us. Moreover, MCPG is qualified with good domain adaptability by adding a transfer vector as a universal style constraint, which is refined from the exemplars retrieved from the corpus of the target domain in a training-free way. Extensive experiments show that MCPG outperforms state-of-the-art unsupervised baselines by a margin. Meanwhile, our domain-adapted MCPG also achieves competitive performance with strong supervised baselines even without training.