Test performance and clinical utility of expanded non-invasive prenatal test: Experience on 71,883 unselected routine cases from one single center.

OBJECTIVE: The balance between benefits and risks of discordant outcomes makes the Genome-Wide Non-Invasive Prenatal Test (GW-NIPT) controversial. This study aims to evaluate performance and clinical utility in a wide cohort of unselected clinical cases from a single center when a standardized protocol is applied and integrated with a secondary algorithm for data interpretation. METHOD: In 2 years, over 70,000 pregnant patients underwent GW-NIPT for fetal common trisomies, sex chromosome aneuploidies, rare autosomal aneuploidies, segmental abnormalities (CNVs ≥ 7 Mb) and microdeletions (CNVs < 7 Mb). All samples were uniformly processed with Veriseq NIPT Solution v2 and analyzed using all data metrics along with a home-made algorithm for sequencing data analysis. Results were retrospectively reviewed for clinical outcomes. RESULTS: Among 71,883 eligible cases including twin pregnancies, 1011 (1.4%) received a positive result and 781 were confirmed by invasive prenatal diagnosis. Clinical sensitivity ranged from 99.65% for common trisomy (T21, T18, T13) to 83.33% for microdeletions, while specificity remained high (99.98%) for each class of fetal abnormalities detected. CONCLUSIONS: Integrating a standardized protocol with an internal algorithm allowed discordant results to be reduced, yielding high accuracy. Observed reliability in detecting genome-wide chromosomal conditions reinforced the expanded NIPT utility in clinical practice.

Simultaneous oscillatory encoding of "hot" and "cold" information during social interactions in the monkey medial prefrontal cortex.

Social interactions in primates require social cognition abilities such as anticipating the partner's future choices as well as pure cognitive skills involving processing task-relevant information. The medial prefrontal cortex (mPFC) has been implicated in these cognitive processes. Here, we investigated the neural oscillations underlying the complex social behaviors involving the interplay of social roles (Actor vs. Observer) and interaction types (whether working with a "Good" or "Bad" partner). We found opposite power modulations of the beta and gamma bands by social roles, indicating dedicated processing for task-related information. Concurrently, the interaction type was conveyed by lower frequencies, which are commonly associated with neural circuits linked to performance and reward monitoring. Thus, the mPFC exhibits parallel coding of both "cold" processes (purely cognitive) and "hot" processes (reward and social-related). This allocation of neural resources gives the mPFC a key neural node, flexibly integrating multiple sources of information during social interactions.

Attractor dynamics reflect decision confidence in macaque prefrontal cortex.

Decisions are made with different degrees of consistency, and this consistency can be linked to the confidence that the best choice has been made. Theoretical work suggests that attractor dynamics in networks can account for choice consistency, but how this is implemented in the brain remains unclear. Here we provide evidence that the energy landscape around attractor basins in population neural activity in the prefrontal cortex reflects choice consistency. We trained two rhesus monkeys to make accept/reject decisions based on pretrained visual cues that signaled reward offers with different magnitudes and delays to reward. Monkeys made consistent decisions for very good and very bad offers, but decisions were less consistent for intermediate offers. Analysis of neural data showed that the attractor basins around patterns of activity reflecting decisions had steeper landscapes for offers that led to consistent decisions. Therefore, we provide neural evidence that energy landscapes predict decision consistency, which reflects decision confidence.

Attractor dynamics reflect decision confidence in macaque prefrontal cortex.

Decisions are made with different degrees of consistency, and this consistency can be linked to the confidence that the best choice has been made. Theoretical work suggests that attractor dynamics in networks can account for choice consistency, but how this is implemented in the brain remains unclear. Here, we provide evidence that the energy landscape around attractor basins in population neural activity in prefrontal cortex reflects choice consistency. We trained two rhesus monkeys to make accept/reject decisions based on pretrained visual cues that signaled reward offers with different magnitudes and delays-to-reward. Monkeys made consistent decisions for very good and very bad offers, but decisions were less consistent for intermediate offers. Analysis of neural data showed that the attractor basins around patterns of activity reflecting decisions had steeper landscapes for offers that led to consistent decisions. Therefore, we provide neural evidence that energy landscapes predict decision consistency, which reflects decision confidence.

Neural representation of others during action observation in posterior medial prefrontal cortex.

Making decisions based on the actions of others is critical to daily interpersonal interactions. We investigated the representations of other's actions at single neural level in posterior medial prefrontal cortex (pmPFC) in two monkeys during the observation of actions of another agent, in a social interaction task. Each monkey separately interacted with a human partner. The monkey and the human alternated turns as actor and observer. The actor was required to reach one of two visual targets, avoiding the previously chosen target, while the observer monitored that action. pmPFC neurons decoupled in most cases self from others during both the execution and the observation of explicit actions. pmPFC neurons showed selective directional tuning specific for the agent who was executing the task. Moreover, we assessed the relationship of the response coding between the periods immediately before and after the action, by using a cross-modal decoding analysis. We found neural network stability from the action anticipation period to the observation of other's actions, suggesting a strong relationship between the anticipation and the execution of an action. When the monkey was the actor, the population coding appeared dynamic, possibly reflecting a goal-action transformation unique to the monkey's own action execution.

Dedicated Representation of Others in the Macaque Frontal Cortex: From Action Monitoring and Prediction to Outcome Evaluation.

Social neurophysiology has increasingly addressed how several aspects of self and other are distinctly represented in the brain. In social interactions, the self-other distinction is fundamental for discriminating one's own actions, intentions, and outcomes from those that originate in the external world. In this paper, we review neurophysiological experiments using nonhuman primates that shed light on the importance of the self-other distinction, focusing mainly on the frontal cortex. We start by examining how the findings are impacted by the experimental paradigms that are used, such as the type of social partner or whether a passive or active interaction is required. Next, we describe the 2 sociocognitive systems: mirror and mentalizing. Finally, we discuss how the self-other distinction can occur in different domains to process different aspects of social information: the observation and prediction of others' actions and the monitoring of others' rewards.

RNAi and chemogenetic reporter co-regulation in primate striatal interneurons.

Using genetic tools to study the functional roles of molecularly specified neuronal populations in the primate brain is challenging, primarily because of specificity and verification of virus-mediated targeting. Here, we report a lentivirus-based system that helps improve specificity and verification by (a) targeting a selected molecular mechanism, (b) in vivo reporting of expression, and (c) allowing the option to independently silence all regional neural activity. Specifically, we modulate cholinergic signaling of striatal interneurons by shRNAmir and pair it with hM4Di_CFP, a chemogenetic receptor that can function as an in vivo and in situ reporter. Quantitative analyses by visual and deep-learning assisted methods show an inverse linear relation between hM4Di_CFP and ChAT protein expression for several shRNAmir constructs. This approach successfully applies shRNAmir to modulating gene expression in the primate brain and shows that hM4Di_CFP can act as a readout for this modulation.

Temporal Coding of Reward Value in Monkey Ventral Striatal Tonically Active Neurons.

The rostromedioventral striatum is critical for behavior dependent on evaluating rewards. We asked what contribution tonically active neurons (TANs), the putative striatal cholinergic interneurons, make in coding reward value in this part of the striatum. Two female monkeys were given the option to accept or reject an offered reward in each trial, the value of which was signaled by a visual cue. Forty-five percent of the TANs use temporally modulated activity to encode information about discounted value. These responses were significantly better represented using principal component analysis than by just counting spikes. The temporal coding is straightforward: the spikes are distributed according to a sinusoidal envelope of activity that changes gain, ranging from positive to negative according to discounted value. Our results show that the information about the relative value of an offered reward is temporally encoded in neural spike trains of TANs. This temporal coding may allow well tuned, coordinated behavior to emerge.SIGNIFICANCE STATEMENT Ever since the discovery that neurons use trains of pulses to transmit information, it seemed self-evident that information would be encoded into the pattern of the spikes. However, there is not much evidence that spike patterns encode cognitive information. We find that a set of interneurons, the tonically active neurons (TANs) in monkeys' striatum, use temporal patterns of response to encode information about the discounted value of offered rewards. The code seems straightforward: a sinusoidal envelope that changes gain according to the discounted value of the offer, describes the rate of spiking across time. This temporal modulation may provide a means to synchronize these interneurons and the activity of other neural elements including principal output neurons.

Molecular profiling of lung cancer specimens and liquid biopsies using MALDI-TOF mass spectrometry.

BACKGROUND: Identification of predictive molecular alterations in lung adenocarcinoma is essential for accurate therapeutic decisions. Although several molecular approaches are available, a number of issues, including tumor heterogeneity, frequent material scarcity, and the large number of loci to be investigated, must be taken into account in selecting the most appropriate technique. MALDI-TOF mass spectrometry (MS), which allows multiplexed genotyping, has been adopted in routine diagnostics as a sensitive, reliable, fast, and cost-effective method. Our aim was to test the reliability of this approach in detecting targetable mutations in non-small cell lung cancer (NSCLC). In addition, we also analyzed low-quality samples, such as cytologic specimens, that often, are the unique source of starting material in lung cancer cases, to test the sensitivity of the system. METHODS: We designed a MS-based assay for testing 158 mutations in the EGFR, KRAS, BRAF, ALK, PIK3CA, ERBB2, DDR2, AKT, and MEK1 genes and applied it to 92 NSCLC specimens and 13 liquid biopsies from another subset of NSCLC patients. We also tested the sensitivity of the method to distinguish low represented mutations using serial dilutions of mutated DNA. RESULTS: Our panel is able to detect the most common NSCLC mutations and the frequency of the mutations observed in our cohort was comparable to literature data. The assay identifies mutated alleles at frequencies of 2.5-10%. In addition, we found that the amount of DNA template was irrelevant to efficiently uncover mutated alleles present at high frequency. However, when using less than 10 ng of DNA, the assay can detect mutations present in at least 10% of the alleles. Finally, using MS and a commercial kit for RT-PCR we tested liquid biopsy from 13 patients with identified mutations in cancers and detected the mutations in 4 (MS) and in 5 samples (RT-PCR). CONCLUSIONS: MS is a powerful method for the routine predictive tests of lung cancer also using low quality and scant tissues. Finally, after appropriate validation and improvement, MS could represent a promising and cost-effective strategy for monitoring the presence and percentage of the mutations also in non-invasive sampling.

Neural activity in macaque medial frontal cortex represents others' choices.

Predicting the behavior of others is a fundamental skill in primate social life. We tested the role of medial frontal cortex in the prediction of other agents' behavior in two male macaques, using a monkey-human interactive task in which their actor-observer roles were intermixed. In every trial, the observer monitored the actor's choice to reject it for a different one when he became the actor on the subsequent trial. In the delay period preceding the action, we identified neurons modulated by the agent's identity, as well as a group of neurons encoding the agent's future choice, some of which were neurons that showed differential patterns of activity between agents. The ability of these neurons to flexibly move from 'self-oriented' to 'other-oriented' representations could correspond to the "other side of the coin" of the simulative mirroring activity. Neurons that changed coding scheme, together with neurons exclusively involved in the prediction of the other agent's choice, show a neural substrate for predicting or anticipating others' choices beyond simulation.

MGMT-Methylated Alleles Are Distributed Heterogeneously Within Glioma Samples Irrespective of IDH Status and Chromosome 10q Deletion.

Several molecular markers drive diagnostic classification, prognostic stratification, and/or prediction of response to therapy in patients with gliomas. Among them, IDH gene mutations are valuable markers for defining subtypes and are strongly associated with epigenetic silencing of the methylguanine DNA methyltransferase (MGMT) gene. However, little is known about the percentage of MGMT-methylated alleles in IDH-mutated cells or the potential association between MGMT methylation and deletion of chromosome 10q, which encompasses the MGMT locus. Here, we quantitatively assessed MGMT methylation and IDH1 mutation in 208 primary glioma samples to explore possible differences associated with the IDH genotype. We also explored a potential association between MGMT methylation and loss of chromosome 10q. We observed that MGMT methylation was heterogeneously distributed within glioma samples irrespective of IDH status suggesting an incomplete overlap between IDH1-mutated and MGMT-methylated alleles and indicating a partial association between these two events. Moreover, loss of one MGMT allele did not affect the methylation level of the remaining allele. MGMT was methylated in about half of gliomas harboring a 10q deletion; in those cases, loss of heterozygosity might be considered a second hit leading to complete inactivation of MGMT and further contributing to tumor progression.

Neural Encoding of Self and Another Agent's Goal in the Primate Prefrontal Cortex: Human-Monkey Interactions.

The primate prefrontal cortex represents both past and future goals. To investigate its role in representing the goals of other agents, we designed a nonmatch-to-goal task that involved a human-monkey (H-M) interaction. During each trial, 2 of 4 potential goal objects were presented randomly to the left or right part of a display screen, and the monkey's (or human's) task was to choose the one that did not match the object goal previously chosen. Human and monkey trials were intermixed, and each agent, when acting as observer, was required to monitor the other actor's choice to switch the object goal choice in case it became the actor on the subsequent trial. We found neurons encoding the actor, either the monkey itself or the human, neurons encoding the agent future goal position and neurons encoding the agent previous goal position. In the category of neurons encoding the human future goal, we differentiated between those encoding the future goal of both agents and those encoding only the human agent future goal. While the first one might represent a covert mental simulation in the human trials, the other one could represent a prediction signal of the other's agent choice.

PDGFB hypomethylation is a favourable prognostic biomarker in primary myelofibrosis.

Primary myelofibrosis (PMF) is a myeloproliferative neoplasm characterised by the clonal proliferation of the haematopoietic precursors together with the progressive development of bone marrow fibrosis. This stromal alteration is an important clinical issue and specific prognostic markers are not currently available. In bone marrow biopsies from 58 PMF patients, we explored the methylation pattern of genes encoding cytokines involved in the stromal reaction, namely platelet-derived growth factor-beta (PDGFB), transforming growth factor-beta (TGFB) and basic fibroblast growth factor (FGF2). We also evaluated the methylation profile of the Long Interspersed Nucleotide Element 1 (LINE-1). PDGFB, FGF2 and LINE-1, but not TGFB, were significantly differently methylated in PMF compared to controls. Significantly, PDGFB hypomethylation (<16%) was correlated with a favourable PMF prognosis (grade of marrow fibrosis, p=0.03; International Prognostic Scoring Systems p=0.01 and Dynamic International Prognostic Scoring Systems, p=0.02). Although the basis of the association of PDGFB hypomethylation with favourable prognosis remains to be clarified, we speculate that hypomethylation in PMF could represent the effect of acquired somatic mutations in genes involved in epigenetic regulation of the genome.

ESX1 mRNA expression in seminal fluid is an indicator of residual spermatogenesis in non-obstructive azoospermic men.

STUDY QUESTION: Is the presence of ESX1 mRNA in seminal fluid (SF) an indicator of residual spermatogenesis in men with non-obstructive azoospermic (NOA)? SUMMARY ANSWER: ESX1 mRNA in SF is a suitable molecular marker for predicting the presence of residual spermatogenesis in testis. WHAT IS KNOWN ALREADY: ESX1 is an X-linked homeobox gene whose expression in testis is restricted to germ cells. We previously reported, in the testicular biopsies from azoospermic men, a positive correlation between the presence of ESX1 mRNA and residual spermatogenesis. STUDY DESIGN, SIZE, DURATION: We investigated ESX1 mRNA expression in 70 testicular fragments (TF) and 56 (SF) of 70 NOA men. As controls, we analyzed 8 TF from men with obstructive azoospermic (OA) and 9 SF from normozoospermic men. For all patients we considered the histological classification of testis biopsies and the recovery of spermatozoa by surgical procedures. PARTICIPANTS/MATERIALS, SETTING, METHODS: Relative ESX1 mRNA expression was evaluated by quantitative RT-PCR using the ΔΔCt method. The results were compared with the recovery of spermatozoa at surgery. MAIN RESULTS AND THE ROLE OF CHANCE: In TF from NOA patients we found that: (i) ESX1 mRNA level was significantly decreased as the severity of spermatogenic defects increased (P < 0.0001, one-way analysis of variance); (ii) the presence of ESX1 mRNA can predict the success of sperm retrieval (sensitivity: 80%). In SF from NOA patients we found that: (i) ESX1 mRNA was present in 78.5% of NOA men; (ii) the presence of ESX1 mRNA could predict the success of sperm retrieval (sensitivity: 84%). LIMITATIONS, REASONS FOR CAUTION: Spermatozoa were recovered at surgery in 5 out of 12 patients whose SF was negative for ESX1 mRNA expression. We think that discrepancies between molecular and clinical results could be reduced by analyzing more than one ejaculate from each man. WIDER IMPLICATIONS OF THE FINDINGS: The data confirm that the ESX1 transcript in the semen of men with NOA is a suitable molecular marker for predicting the presence of residual foci of spermatogenesis in the testis. The implication of these results is that some patients 'with azoospermia', although having a severe impairment of spermatogenesis, could still maintain residual foci of spermatogenesis in limited areas of the testes, not always recovered by surgery. STUDY FUNDING/COMPETING INTERESTS: This work was supported by the Fondazione IRCCS Ca' Granda, Ospedale Maggiore Policlinico: Ricerca Corrente [grant number RC2014/519-02] to M.M. and from ASM onlus 2010-2011 to M.M. The authors declare that they have no conflict of interest.

Autonomous encoding of irrelevant goals and outcomes by prefrontal cortex neurons.

Two rhesus monkeys performed a distance discrimination task in which they reported whether a red square or a blue circle had appeared farther from a fixed reference point. Because a new pair of distances was chosen randomly on each trial, and because the monkeys had no opportunity to correct errors, no information from the previous trial was relevant to a current one. Nevertheless, many prefrontal cortex neurons encoded the outcome of the previous trial on current trials. A smaller, intermingled population of cells encoded the spatial goal on the previous trial or the features of the chosen stimuli, such as color or shape. The coding of previous outcomes and goals began at various times during a current trial, and it was selective in that prefrontal cells did not encode other information from the previous trial. The monitoring of previous goals and outcomes often contributes to problem solving, and it can support exploratory behavior. The present results show that such monitoring occurs autonomously and selectively, even when irrelevant to the task at hand.

Macaque monkeys can learn token values from human models through vicarious reward.

Monkeys can learn the symbolic meaning of tokens, and exchange them to get a reward. Monkeys can also learn the symbolic value of a token by observing conspecifics but it is not clear if they can learn passively by observing other actors, e.g., humans. To answer this question, we tested two monkeys in a token exchange paradigm in three experiments. Monkeys learned token values through observation of human models exchanging them. We used, after a phase of object familiarization, different sets of tokens. One token of each set was rewarded with a bit of apple. Other tokens had zero value (neutral tokens). Each token was presented only in one set. During the observation phase, monkeys watched the human model exchange tokens and watched them consume rewards (vicarious rewards). In the test phase, the monkeys were asked to exchange one of the tokens for food reward. Sets of three tokens were used in the first experiment and sets of two tokens were used in the second and third experiments. The valuable token was presented with different probabilities in the observation phase during the first and second experiments in which the monkeys exchanged the valuable token more frequently than any of the neutral tokens. The third experiments examined the effect of unequal probabilities. Our results support the view that monkeys can learn from non-conspecific actors through vicarious reward, even a symbolic task like the token-exchange task.

Transfer of the nonmatch-to-goal rule in monkeys across cognitive domains.

To solve novel problems, it is advantageous to abstract relevant information from past experience to transfer on related problems. To study whether macaque monkeys were able to transfer an abstract rule across cognitive domains, we trained two monkeys on a nonmatch-to-goal (NMTG) task. In the object version of the task (O-NMTG), the monkeys were required to choose between two object-like stimuli, which differed either only in shape or in shape and color. For each choice, they were required to switch from their previously chosen object-goal to a different one. After they reached a performance level of over 90% correct on the O-NMTG task, the monkeys were tested for rule transfer on a spatial version of the task (S-NMTG). To receive a reward, the monkeys had to switch from their previously chosen location to a different one. In both the O-NMTG and S-NMTG tasks, there were four potential choices, presented in pairs from trial-to-trial. We found that both monkeys transferred successfully the NMTG rule within the first testing session, showing effective transfer of the learned rule between two cognitive domains.

Gaze orientation interferes with mental numerical representation.

Number comparison tasks are characterized by distance and size effects. The distance effect reveals that the higher the distance is between two numbers, the easier their magnitude comparison is. Accordingly, people are thought to represent numbers on a spatial dimension, the mental number line, on which any given number corresponds to a location on the line. The size effect, instead, states that at any given distance, comparing two small numbers is easier than comparing two large numbers, thus suggesting that larger numbers are more vaguely represented than smaller ones. In the present work we first tested whether the participants were adopting a spatial strategy to solve a very simple numbers comparison task, by assessing the presence of the distance and the magnitude effect. Secondarily, we focused on the influence of gaze position on their performance. The present results provide evidence that gaze direction interferes with number comparisons, worsening the vague representation of larger numbers and further supporting the hypothesis of the overlapping between physical and mental spaces.

Vicarious learning from human models in monkeys.

We examined whether monkeys can learn by observing a human model, through vicarious learning. Two monkeys observed a human model demonstrating an object-reward association and consuming food found underneath an object. The monkeys observed human models as they solved more than 30 learning problems. For each problem, the human models made a choice between two objects, one of which concealed a piece of apple. In the test phase afterwards, the monkeys made a choice of their own. Learning was apparent from the first trial of the test phase, confirming the ability of monkeys to learn by vicarious observation of human models.

Monkeys monitor human goals in a nonmatch-to-goal interactive task.

We designed a new task, called nonmatch-to-goal, to study the ability of macaque monkeys to interact with humans in a rule-guided paradigm. In this task the monkeys were required to choose one of two targets, from a list of three. For each choice, they were required to switch from their choice on the previous trial to a different one. In a subset of trials the monkeys observed a human partner performing the task. When the human concluded his turn, the monkeys were required to switch to a new goal discarding the human's previous goal. We found that monkeys were very skillful in monitoring goals, not only of their own choice by also those of their human partner. They showed also a surprising ability to coordinate their actions, taking turns with the human partner, starting and stopping their own turn following the decision of the human partner in the task.