G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data

Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. Within the meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in the field of the human microbiome. In this context, we developed G2S, a bioinformatic tool for taxonomic prediction of the human fecal microbiome directly from the oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on paired oral and fecal samples from populations across the globe, which allows inferring the stool microbiome at the family level more accurately than other available approaches. The tool can be used in retrospective studies, where fecal sampling was not performed, and especially in the field of paleomicrobiology, as a unique opportunity to recover data related to ancient gut microbiome configurations. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects

Globigerinoides rublobatus – a new species of Pleistocene planktonic foraminifera

We describe Globigerinoides rublobatus n. sp., a new morphospecies of fossil planktonic foraminifera, from the Pleistocene sediments (∼810 ka) of the Indian Ocean and Pacific Ocean. We use image analysis and morphometry of 860 specimens from International Ocean Discovery Program Site U1483 in the tropical Indian Ocean to document morphological variability in the new morphospecies and related taxa, and we also report it from Pacific Ocean Site U1486 for the first time. The new morphospecies combines characteristics typical of Globigerinoides conglobatus (Brady, 1879) and Globigerinoides ruber (d'Orbigny, 1839), with which it co-occurs, but is distinct from both. Morphometric data indicate that G. rublobatus n. sp. is closer to G. conglobatus, potentially signalling an evolutionary affinity. We find that Globigerinoides rublobatus n. sp. occurs as two variants, a pigmented (pink) form and a non-pigmented (white) form. The non-pigmented forms are on average ∼50 % larger than the pigmented forms. This is so far only the third instance of fossil planktonic foraminifera known to exhibit this pink pigmentation. We regard the pink and white forms as variants of a single morphospecies and suggest the pink form may represent a later evolutionary adaptation

Bridging the extant and fossil record of planktonic foraminifera: implications for the Globigerina lineage

We conducted a morphometric study and wall texture analysis on extant and fossil specimens of the planktonic foraminifera Globigerina falconensis plexus. Our global data reveal morphological inconsistencies between fossil and extant populations. Our results are significant as G. falconensis is widely used in palaeoceanographic studies in conjunction with its sister taxon G. bulloides. Morphologically these two species are similar, with the main difference being the distinctive apertural lip present in G. falconensis. We selected cores covering the entire stratigraphic range of G. falconensis, from the early Miocene to current day, spanning sites from high latitudes in the North Atlantic Ocean and the southern Indian Ocean to sites in equatorial regions. The morphology found in the modern ocean is not consistent with the Miocene holotype of Globigerina falconensis Blow described from lower Miocene sediments in Venezuela. A more lobate morphology evolved in the late Miocene, thus, a new name is required for this morphotype, coexisting in the modern oceans with G. falconensis s.s. We thus describe the new morphospecies, G. neofalconensis for the more lobate forms which evolved in the late Miocene and inhabit the modern oceans. Additionally, we report a pseudocancellate wall texture present in the G. falconensis plexus. We use the molecular sequences from the PR2 database to explore the generic attribution of the G. falconensis lineage, confirming its close relationship with G. bulloides and its retention in the genus Globigerina

Neuronal dynamics of signal selective motor plan cancellation in the macaque dorsal premotor cortex

Primates adopt various strategies to interact with the environment. Yet, no study has examined the effects of behavioural strategies with regard to how movement inhibition is implemented at the neuronal level. We used a modified version of the stop-task by adding an extra signal – termed the Ignore signal – capable of influencing the inhibition of movements only within a specific strategy. We simultaneously recorded multisite neuronal activity from the dorsal premotor (PMd) cortex of macaque monkeys during the task and applied a state-space approach. As a result, we found that movement generation is characterized by neuronal dynamics that evolve between subspaces. When the movement is halted, this evolution is arrested and inverted. Conversely, when the Ignore signal is presented, inversion of the evolution is observed briefly and only when a specific behavioural strategy is adopted. Moreover, neuronal signatures during the inhibitory process were predictive of how PMd processes inhibitory signals, allowing the classification of the resulting behavioural strategy. Our data further corroborate the PMd as a critical node in movement inhibition

Correlation between Quality of Life and severity of Parkinson's Disease by assessing an optimal cut-off point on the Parkinson's Disease questionnaire (PDQ-39) as related to the Hoehn & Yahr (H&Y) scale

Purpose: Strong evidence shows that symptoms in individuals with Parkinson's Disease (PD) restrict both their independence and social participation, leading to a low Quality of Life (QoL). Conversely, a reduced QoL has a negative impact on symptoms. The aim is to evaluate the correlation between QoL and severity of PD by assessing the presence of an optimal cut-off point on the Parkinson's disease questionnaire (PDQ-39) as related to the Hoehn &Yahr (H&Y) scale in a cohort of Italian adults with PD. Methods: A multicenter, cross-sectional study was performed. This study was conducted on a cohort of consecutive individuals. All participants were evaluated with the PDQ-39, and the severity of PD was recorded according to the H&Y scale by a neurologist. Receiver op-erating characteristic (ROC) curves and coordinates, visually inspected, were used to find cut-off points with optimal sensitivity and specificity. These were in turn used to determine the optimal PDQ-39 cut-off score for identifying disease severity according to H&Y stages. Results: 513 individuals were included in the study. The ROC curve analysis showed that QoL worsened with an increase in disease severity and age. Moreover, QoL was worse in females. Conclusions: The results of this study allowed for the correlation of QoL and disease severity in a cohort of individuals with PD. With this cut-off point, it is now possible to make a determination of QoL of an individual with PD at a certain stage of the disease, in a specific age range, and of a particular gender

Acetylcholinesterase Inhibitors (AChEI's) for the treatment of visual hallucinations in schizophrenia: a case report

Background: Visual hallucinations are commonly seen in various neurological and psychiatric disorders including schizophrenia. Current models of visual processing and studies in diseases including Parkinsons Disease and Lewy Body Dementia propose that Acetylcholine (Ach) plays a pivotal role in our ability to accurately interpret visual stimuli. Depletion of Ach is thought to be associated with visual hallucination generation. AchEI’s have been used in the targeted treatment of visual hallucinations in dementia and Parkinson’s Disease patients. In Schizophrenia, it is thought that a similar Ach depletion leads to visual hallucinations and may provide a target for drug treatment Case Presentation: We present a case of a patient with Schizophrenia presenting with treatment resistant and significantly distressing visual hallucinations. After optimising treatment for schizophrenia we used Rivastigmine, an AchEI, as an adjunct to treat her symptoms successfully. Conclusions: This case is the first to illustrate this novel use of an AchEI in the targeted treatment of visual hallucinations in a patient with Schizophrenia. Targeted therapy of this kind can be considered in challenging cases although more evidence is required in this field. Background Visual hallucinations occur in a variety of neurologica

Globigerinoides rublobatus - a new species of Pleistocene planktonic foraminifera

We describe Globigerinoides rublobatus n. sp., a new morphospecies of fossil planktonic foraminifera, from the Pleistocene sediments (∼810 ka) of the Indian Ocean and Pacific Ocean. We use image analysis and morphometry of 860 specimens from International Ocean Discovery Program Site U1483 in the tropical Indian Ocean to document morphological variability in the new morphospecies and related taxa, and we also report it from Pacific Ocean Site U1486 for the first time. The new morphospecies combines characteristics typical of Globigerinoides conglobatus (Brady, 1879) and Globigerinoides ruber (d'Orbigny, 1839), with which it co-occurs, but is distinct from both. Morphometric data indicate that G. rublobatus n. sp. is closer to G. conglobatus, potentially signalling an evolutionary affinity. We find that Globigerinoides rublobatus n. sp. occurs as two variants, a pigmented (pink) form and a non-pigmented (white) form. The non-pigmented forms are on average ∼50 % larger than the pigmented forms. This is so far only the third instance of fossil planktonic foraminifera known to exhibit this pink pigmentation. We regard the pink and white forms as variants of a single morphospecies and suggest the pink form may represent a later evolutionary adaptation

Endoplasmic Reticulum Stress Is Reduced in Tissues of Obese Subjects After Weight Loss

OBJECTIVE—Obesity is associated with insulin resistance and type 2 diabetes, although the mechanisms linking these pathologies remain undetermined. Recent studies in rodent models revealed endoplasmic reticulum (ER) stress in adipose and liver tissues and demonstrated that ER stress could cause insulin resistance. Therefore, we tested whether these stress pathways were also present in obese human subjects and/or regulated by weight loss

The expression of platelet serotonin transporter (SERT) in human obesity

Serotonin (5-HT) is a well-known modulator of eating behavior. However, the molecular mechanisms linking its action to body weight balance have been only partially elucidated. Since platelets are a suitable peripheral model to study 5-HT transport, metabolism and release, we herein evaluated the expression of the platelet 5-HT re-uptake system (SERT) by [3H]-paroxetine binding assay. A cohort of 114 unrelated individuals (34 males, 80 females; age, mean +/- SD: 38.57 +/- 12.47 years) without major psychiatric disorders, was recruited following a naturalistic design regarding age or gender and classified accordingly to their body mass index (BMI). Subjects were divided into 5 groups: normal-weight (NW), overweight (OW) and grade I-III obese (OB) individuals. For gender analyses, data were transformed into [3H]-paroxetine density (Bmax)/BMI ratios to overcome both the disparity of women vs. men number and anthropometric differences between sexes.[3H]-paroxetine Bmax (SERT density, fmol/mg proteins) was reduced in platelet membranes of grade II (p < 0.01) and III (p < 0.001) obese subjects vs. controls and in overweight subjects (p < 0.05) vs. grade III obese individuals. Considering all patients together, a strong negative correlation between Bmax and BMI (r = -0.449; P < 0.0001) was demonstrated. Conversely, [3H]-paroxetine KD (dissociation constant, nM) did not differ among groups. No gender-related variation concerning Bmax/BMI ratios was observed in this cohort of subjects.The down-regulation of SERT in platelet membranes of severe human obesity (BMI > 35 Kg/m2) confirms the involvement of 5-HT system in body weight gain. Moreover, this findings may help to elucidate those monoamine-endocrine networks acting on fat storage, adipocyte signaling and energy balance. Targeting 5-HT/5-HT-related markers will possibly uncover the existence of human obesity subtypes

The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept

The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome’s interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome