Balanced chromosomal rearrangements implicate YIPF5 and SPATC1L in non-obstructive oligoasthenozoospermia and oligozoospermia and of a derivative chromosome 22 in recurrent miscarriage.

Naturally occurring balanced, unbalanced, and complex chromosomal rearrangements have been reported to cause pathogenic genomic or genetic variants leading to infertility and recurrent miscarriage. Therefore, balanced chromosomal rearrangements were used as genomic signposts for identification of candidate genes or genomic loci associated with male infertility due to defects of spermatogenesis, or with recurrent miscarriage. In three male probands, structural chromosomal variants and copy number variants were identified at nucleotide resolution by long-insert genome sequencing approaches and Sanger sequencing.

A Novel Frameshift Variant Leading to Sifrim-Hitz-Weiss Syndrome in a Proband with a Subclinical Familial t(17;19) and a Large dup(2)(q14.3q21.1).

The genetic complexity of neurodevelopmental disorders (NDD), combined with a heterogeneous clinical presentation, makes accurate assessment of their molecular bases and pathogenic mechanisms challenging. Our purpose is to reveal the pathogenic variant underlying a complex NDD through identification of the "full" spectrum of structural genomic and genetic variants. Therefore, clinical phenotyping and identification of variants by genome and exome sequencing, together with comprehensive assessment of these and affected candidate genes, were carried out.

Corrigendum: SVInterpreter: A Comprehensive Topologically Associated Domain Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants.

[This corrects the article DOI: 10.3389/fgene.2021.

SVInterpreter: A Comprehensive Topologically Associated Domain-Based Clinical Outcome Prediction Tool for Balanced and Unbalanced Structural Variants.

With the advent of genomic sequencing, a number of balanced and unbalanced structural variants (SVs) can be detected per individual. Mainly due to incompleteness and the scattered nature of the available annotation data of the human genome, manual interpretation of the SV's clinical significance is laborious and cumbersome. Since bioinformatic tools developed for this task are limited, a comprehensive tool to assist clinical outcome prediction of SVs is warranted.

Comprehensive clinically oriented workflow for nucleotide level resolution and interpretation in prenatal diagnosis of de novo apparently balanced chromosomal translocations in their genomic landscape.

We present a comprehensive clinically oriented workflow for large-insert genome sequencing (liGS)-based nucleotide level resolution and interpretation of de novo (dn) apparently balanced chromosomal abnormalities (BCA) in prenatal diagnosis (PND). Retrospective or concomitant with conventional PND and liGS, molecular and newly developed clinically inspired bioinformatic tools (TAD-GConTool and CNV-ConTool) are applied to analyze and assess the functional and phenotypic outcome of dn structural variants (dnSVs). Retrospective analysis of four phenotype-associated dnSVs identified during conventional PND precisely reveal the genomic elements disrupted by the translocation breakpoints.

Performance Evaluation of a Prototype Architect Antibody Assay for Babesia microti.

The tick-borne protozoan is responsible for more than 200 cases of transfusion-transmitted babesiosis (TTB) infection in the United States that have occurred over the last 30 years. Measures to mitigate the risk of TTB include nucleic acid testing (NAT) and antibody testing. A fully automated prototype antibody test was developed on the Architect instrument.

Identification of OAF and PVRL1 as candidate genes for an ocular anomaly characterized by Peters anomaly type 2 and ectopia lentis.

Keratolenticular dysgenesis (KLD) and ectopia lentis are congenital eye defects. The aim of this study is the identification of molecular genetic alterations responsible for those ocular anomalies with neurologic impairment in an individual with a de novo balanced chromosome translocation t(11;18)(q23.3;q11.

Structure_threader: An improved method for automation and parallelization of programs structure, fastStructure and MavericK on multicore CPU systems.

Structure_threader is a program to parallelize multiple runs of genetic clustering software that does not make use of multithreading technology (structure, fastStructure and MavericK) on multicore computers. Our approach was benchmarked across multiple systems and displayed great speed improvements relative to the single-threaded implementation, scaling very close to linearly with the number of physical cores used. Structure_threader was compared to previous software written for the same task-ParallelStructure and StrAuto and was proven to be the faster (up to 25% faster) wrapper under all tested scenarios.

Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.

RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V.

Brainstem Monitoring in the Neurocritical Care Unit: A Rationale for Real-Time, Automated Neurophysiological Monitoring.

Patients with severe traumatic brain injury or large intracranial space-occupying lesions (spontaneous cerebral hemorrhage, infarction, or tumor) commonly present to the neurocritical care unit with an altered mental status. Many experience progressive stupor and coma from mass effects and transtentorial brain herniation compromising the ascending arousal (reticular activating) system. Yet, little progress has been made in the practicality of bedside, noninvasive, real-time, automated, neurophysiological brainstem, or cerebral hemispheric monitoring.

Comparative Validation of Conventional and RNA-Seq Data-Derived Reference Genes for qPCR Expression Studies of Colletotrichum kahawae.

Colletotrichum kahawae is an emergent fungal pathogen causing severe epidemics of Coffee Berry Disease on Arabica coffee crops in Africa. Currently, the molecular mechanisms underlying the Coffea arabica-C. kahawae interaction are still poorly understood, as well as the differences in pathogen aggressiveness, which makes the development of functional studies for this pathosystem a crucial step.

Shared and divergent pathways for flower abscission are triggered by gibberellic acid and carbon starvation in seedless Vitis vinifera L.

Background: Abscission is a highly coordinated developmental process by which plants control vegetative and reproductive organs load. Aiming at get new insights on flower abscission regulation, changes in the global transcriptome, metabolome and physiology were analyzed in 'Thompson Seedless' grapevine (Vitis vinifera L.) inflorescences, using gibberellic acid (GAc) spraying and shading as abscission stimuli, applied at bloom.

Molecular candidates for early-stage flower-to-fruit transition in stenospermocarpic table grape (Vitis vinifera L.) inflorescences ascribed by differential transcriptome and metabolome profiles.

Flower-to-fruit transition depends of nutrient availability and regulation at the molecular level by sugar and hormone signalling crosstalk. However, in most species, the identities of fruit initiation regulators and their targets are largely unknown. To ascertain the main pathways involved in stenospermocarpic table grape fruit set, comprehensive transcriptional and metabolomic analyses were conducted specifically targeting the early phase of this developmental stage in 'Thompson Seedless'.

Modified brain stem auditory evoked potentials in patients with intracranial mass lesions.

The authors report their experience utilizing a recently described rapid rate, binaural click and 1000-Hz tone burst modification of the brain stem auditory evoked potentials (BAEP), modified (MBP), in 27 symptomatic patients with non-brain stem compressive space-taking cerebral lesions (22), hydrocephalus (4), and pseudotumor cerebri (1).  Many presented with clinical signs suggestive of increased intracranial pressure (ICP) and focal neurological deficits. The cerebral lesions, mostly large tumors with edema, had very substantial radiological signs of mass effect.

Modified brainstem auditory evoked responses in patients with non-brainstem compressive cerebral lesions.

The brainstem auditory evoked response (BAER) is sensitive to pontomesencephalic integrity, transtentorial brain herniation, and at times increased intracranial pressure (ICP). The authors report their experience utilizing a recently described rapid rate, binaural, click and 1,000-Hz tone-burst modification of the BAER (MBAER) in 22 symptomatic non-trauma patients with non-brainstem compressive space-taking cerebral lesions. The majority presented with mild to moderate clinical signs suggestive of increased ICP, and focal neurological deficits.

Brainstem auditory evoked potentials--a review and modified studies in healthy subjects.

The authors review the brainstem auditory evoked potential (BAEP), and present studies on 40 healthy subjects. In addition to the conventional click evoked BAEP, three modified BAEP examinations were performed. The modified BAEP tests include a 1,000 Hz tone-burst BAEP, and more rapid rate binaural click and 1,000 Hz tone-burst BAEPs-each of the last two studies performed at four diminishing moderate intensities.

A newly described ictal pattern: the initial ictal slow shift.

This report deals with a newly described ictal pattern, called the initial ictal slow shift (IS)2. This pattern may be seen in subdural records as the first sign of an ictal event, occurring before the later typical rhythms of a seizure state appear. A positive shift, very similar in appearance from one seizure to another, usually lasted for 1-2 sec, followed by a negativity for 7-9 sec that included the typical rhythmical discharges.

EEG in seizure prognosis: association of slow wave activity and other factors in patients with apparent misleading epileptiform findings.

Our previous study showed that patients with many spikes in their EEGs generally have uncontrolled seizures and those with no or rare spikes have controlled attacks. However, exceptions do exist, and this study was designed to determine what other aspects in the EEG could lead to the proper prognosis with these exceptions, rather than to an incorrect one. Two groups were assembled: 150 patients with 674 EEGs with controlled seizures and 150 patients with 804 EEGs with uncontrolled attacks.

Factors in the interictal record predicting an ictal episode: a case study.

This report deals with a patient with intractable seizures, who had 64 subdural electrodes implanted onto the left frontal and temporal cerebral cortex in anticipation of probable seizure surgery. One specific region on the left frontal lobe proved to be the focus for both the interictal spikes and also for the ictal activity. Our goal was to determine what electrical characteristics in the interictal record predicted the ictal episodes.

The relationship between bilateral spike and wave complexes and focal discharges in patients with partial epilepsy.

The goal of this study was to investigate in patients with partial epilepsy the relationship between bilateral spike and wave (BSW) complexes of a generalized epilepsy and the focal spikes of partial epilepsy. For the study 300 patients were collected, all with focal epilepsy on their last hospital visit: 150 were well controlled (C) and 150 were uncontrolled (U), and the number of EEGs was 674 in the C and 804 in the U groups. BSW were seen at some time in 25% of all patients, more often in the U than C patients, especially the irregular 3/sec form.

The EEG profile of patients with uncontrolled vs. controlled seizures.

The goal of this study was to provide an EEG profile of patients (150) with uncontrolled (U) seizures, in contrast with those (150) with controlled (C) attacks. In the U group 804 EEGs were done and in the C group 674 were performed, all with both waking and sleep recordings; the range of EEG records on a given patient was 2-23. The number of spikes and the amount of abnormal slowing was quantified in each record.

Chemiluminescence quenching of pteroic acid-N-sulfonyl-acridinium-9-carboxamide conjugates by folate binding protein.

N(10)-Trifluoroacetylpteroic acid was conjugated to chemiluminescent N-sulfonylacridinium-9-carboxamide labels at the N(10) or 9-position carboxamide. Upon binding to folate binding protein the light output of the N(10) derivative (9) was quenched up to 62% upon triggering with basic peroxide, while the 9-position carboxamide conjugate (7) was quenched only 12%. The utility of this effect was demonstrated in a model homogeneous chemiluminescent assay for folic acid.

Focal seizures and EEG: prognostic considerations.

The goal of this study was to determine whether the EEG could predict if patients with focal seizures would eventually be uncontrolled (U), more than two seizures per month, or be controlled (C), fewer than two seizures per year. Using these latter criteria, U and C patients were randomly selected from our files, 150 in each of these two groups; 804 EEGs were found in the U and 674 in the C group. Excluded were patients with generalized epilepsy and also the benign epilepsies of childhood.