Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors.

To understand regulatory systems, it would be useful to uniformly determine how different components contribute to the expression of all other genes. We therefore monitored mRNA expression genome-wide, for individual deletions of one-quarter of yeast genes, focusing on (putative) regulators. The resulting genetic perturbation signatures reflect many different properties. These include the architecture of protein complexes and pathways, identification of expression changes compatible with viability, and the varying responsiveness to genetic perturbation. The data are assembled into a genetic perturbation network that shows different connectivities for different classes of regulators. Four feed-forward loop (FFL) types are overrepresented, including incoherent type 2 FFLs that likely represent feedback. Systematic transcription factor classification shows a surprisingly high abundance of gene-specific repressors, suggesting that yeast chromatin is not as generally restrictive to transcription as is often assumed. The data set is useful for studying individual genes and for discovering properties of an entire regulatory system.

Pretransplantation coronavirus disease 2019 vaccination requirements: A matched case-control study of factors associated with waitlist inactivation.

Numerous United States transplant centers require solid organ transplantation candidates to be vaccinated against the coronavirus disease of 2019 to be active on the United Network for Organ Sharing waiting list. This study examined characteristics of adult patients on one center's kidney transplantation waiting list whose status was inactivated due to a lack of coronavirus disease 2019 vaccination by July 1, 2022, and who did not subsequently provide proof of vaccination by August 31, 2022 (cases). Patients in the control group were retrospectively matched to patients in the case group in a 4-to-1 fashion according to age, sex, and "active" status on the waiting list. Multivariable logistic regression was performed, with race/ethnicity, primary language, health insurance, education, and Vaccine Equity Metric (VEM, a measure of health equity at the zip code level) quartile as covariates. Results revealed that patients from zip codes in the lowest VEM quartile (odds ratio [OR] 1.89; P = .02) and those insured by governmental payors (Medicare: OR, 2.00; P < .01 and Medicaid: OR, 2.89; P < .01) had higher odds of being inactivated than those from zip codes that make up the highest VEM quartile and those insured by commercial payors, respectively. These findings serve as a cautionary tale regarding universal pretransplantation vaccination requirements, which may raise equity concerns that should be considered upon policy implementation.

Ultrafast dynamics of fluorene initiated by highly intense laser fields.

We present an investigation of the ultrafast dynamics of the polycyclic aromatic hydrocarbon fluorene initiated by an intense femtosecond near-infrared laser pulse (810 nm) and probed by a weak visible pulse (405 nm). Using a multichannel detection scheme (mass spectra, electron and ion velocity-map imaging), we provide a full disentanglement of the complex dynamics of the vibronically excited parent molecule, its excited ionic states, and fragments. We observed various channels resulting from the strong-field ionization regime. In particular, we observed the formation of the unstable tetracation of fluorene, above-threshold ionization features in the photoelectron spectra, and evidence of ubiquitous secondary fragmentation. We produced a global fit of all observed time-dependent photoelectron and photoion channels. This global fit includes four parent ions extracted from the mass spectra, 15 kinetic-energy-resolved ionic fragments extracted from ion velocity map imaging, and five photoelectron channels obtained from electron velocity map imaging. The fit allowed for the extraction of 60 lifetimes of various metastable photoinduced intermediates.

Can remotely sensed catchment to lake area ratios predict mercury levels in subarctic fishes?

Mercury concentrations ([Hg]) in fish reflect a complex array of interacting biogeochemical and ecological variables. In northern regions where fish are a critical subsistence food, understanding and predicting fish [Hg] can be particularly difficult, largely due to a paucity of comprehensive data associated with the logistical challenges of field sampling. Building on previous work where we elucidated causal relationships between fish [Hg] and a variety of catchment, water quality, and ecological variables in subarctic lakes, we investigated whether using only ratios of catchment area to lake area (CA:LA) can predict [Hg] in northern freshwater fish species. As CA:LA can be sensed remotely, they may be more feasible and practical to obtain than field data in far northern regions. Our study included thirteen remote lakes that represent a CA:LA gradient of 6.2-423.5 within an ∼66,000 km2 subarctic region of Northwest Territories, Canada. We found that size-standardized [Hg] in three widespread fish species, including Lake Whitefish (Coregonus clupeaformis), Walleye (Sander vitreus), and Northern Pike (Esox lucius), were significantly and positively related to CA:LA (p < 0.007, r2 = 67-80%), indicating higher fish [Hg] in smaller lakes surrounded by relatively larger catchments. Our findings provide compelling evidence that remotely sensed CA:LA can be used to predict [Hg] in northern fishes and aid in prioritizing understudied and subsistence fishing lakes of the Canadian subarctic for [Hg] monitoring programs.

X-linked myotubular myopathy is associated with epigenetic alterations and is ameliorated by HDAC inhibition.

X-linked myotubular myopathy (XLMTM) is a fatal neuromuscular disorder caused by loss of function mutations in MTM1. At present, there are no directed therapies for XLMTM, and incomplete understanding of disease pathomechanisms. To address these knowledge gaps, we performed a drug screen in mtm1 mutant zebrafish and identified four positive hits, including valproic acid, which functions as a potent suppressor of the mtm1 zebrafish phenotype via HDAC inhibition. We translated these findings to a mouse XLMTM model, and showed that valproic acid ameliorates the murine phenotype. These observations led us to interrogate the epigenome in Mtm1 knockout mice; we found increased DNA methylation, which is normalized with valproic acid, and likely mediated through aberrant 1-carbon metabolism. Finally, we made the unexpected observation that XLMTM patients share a distinct DNA methylation signature, suggesting that epigenetic alteration is a conserved disease feature amenable to therapeutic intervention.

Topology predicts long-term functional outcome in early psychosis.

Early intervention in psychosis is crucial to improving patient response to treatment and the functional deficits that critically affect their long-term quality of life. Stratification tools are needed to personalize functional deficit prevention strategies at an early stage. In the present study, we applied topological tools to analyze symptoms of early psychosis patients, and detected a clear stratification of the cohort into three groups. One of the groups had a significantly better psychosocial outcome than the others after a 3-year clinical follow-up. This group was characterized by a metabolic profile indicative of an activated antioxidant response, while that of the groups with poorer outcome was indicative of oxidative stress. We replicated in a second cohort the finding that the three distinct clinical profiles at baseline were associated with distinct outcomes at follow-up, thus validating the predictive value of this new stratification. This approach could assist in personalizing treatment strategies.

The kinetic energy of PAH dication and trication dissociation determined by recoil-frame covariance map imaging.

We investigated the dissociation of dications and trications of three polycyclic aromatic hydrocarbons (PAHs), fluorene, phenanthrene, and pyrene. PAHs are a family of molecules ubiquitous in space and involved in much of the chemistry of the interstellar medium. In our experiments, ions are formed by interaction with 30.3 nm extreme ultraviolet (XUV) photons, and their velocity map images are recorded using a PImMS2 multi-mass imaging sensor. Application of recoil-frame covariance analysis allows the total kinetic energy release (TKER) associated with multiple fragmentation channels to be determined to high precision, ranging 1.94-2.60 eV and 2.95-5.29 eV for the dications and trications, respectively. Experimental measurements are supported by Born-Oppenheimer molecular dynamics (BOMD) simulations.

[Pilonidal cyst of the scalp following a single minor trauma]. / Kyste pilonidal du scalp secondaire à un traumatisme inaperçu : à propos d'un cas.

The pilonidal cyst is an inflammatory disease occurring when a hair follicle penetrates inside a surgical wound. Uncommon in the scalp region, the pilonidal sinus is typically encountered in the sacrococcygeal regions. A single minor trauma of the scalp can be an inductor factor. The surgical treatment includes one-piece excision of the cyst followed by direct closure. We report a case of a 4-year-old child presenting a pilonidal sinus of the scalp following a single minor trauma.

Sleeve gastrectomy prior to liver transplantation is superior to medical weight loss in reducing posttransplant metabolic complications.

Strategies to optimize the management of obesity-related metabolic complications after liver transplantation (LT) are needed. We examined the effect of pre-LT sleeve gastrectomy (SG), as compared to medical weight loss (MWL), on post-LT outcomes. This is a cohort study of adults (≥18 years) with medically complicated obesity who were eligible for pre-LT SG and underwent LT from January 1, 2006 to June 1, 2016. Logistic regression models evaluated the association of SG on post-LT diabetes and hypertension, defined as new-onset or progressive disease post-LT. Cox regression models evaluated the association of SG on recurrent and de novo nonalcoholic fatty liver disease (NAFLD). Among 70 LT recipients who were eligible for pre-LT SG, 14 (20%) underwent SG and 56 (80%) underwent MWL only. Mean follow-up was 5.2 years post-LT. The SG cohort sustained higher % total body weight loss at 3 years post-LT (28.9% vs. 5.4%, p < .001). In multivariable analyses, SG was associated with significantly lower risk of post-LT diabetes (OR 0.04, 95% CI 0.00-0.41, p = .01), hypertension (OR 0.15, 95% CI 0.04-0.67, p = .01), and recurrent and de novo NAFLD (HR 0.19, 95% CI 0.04-0.91, p = .04). When compared to MWL, SG resulted in sustained weight loss and significantly lower risk of diabetes, hypertension, and recurrent and de novo NAFLD post-LT.

Brain functional connectivity in individuals with psychogenic nonepileptic seizures (PNES): An application of graph theory.

OBJECTIVE: To determine brain functional connectivity (FC), based on the graph theory, in individuals with psychogenic nonepileptic seizures (PNES), in order to better understand the mechanisms underlying this disease. METHODS: Twenty-three patients with PNES and twenty-five healthy control subjects were examined. Alterations in FC within the whole brain were examined using resting-state functional magnetic resonance imaging (MRI). We calculated measures of the nodal degree, a major feature of the graph theory, for all the cortical and subcortical regions in the brain. Pearson correlation was performed to determine the relationship between nodal degree in abnormal brain regions and patient characteristics. RESULTS: The nodal degrees in the right caudate (CAU), left orbital part of the left inferior frontal gyrus (ORBinf), and right paracentral lobule (PCL) were significantly greater (i.e. hyper-connectivity) in individuals with PNES than in healthy control subjects. On the other hand, a lesser nodal degree (i.e. hypo-connectivity) was detected in several other brain regions including the left and right insula (INS), as well as the right putamen (PUT), and right middle occipital gyrus (MOG). CONCLUSION: Our findings suggest that the FC of several major brain regions can be altered in individuals with PNES. Areas with hypo-connectivity may be involved in emotion processing (e.g., INS) and movement regulation (e.g., PUT), whereas areas with hyper-connectivity may play a role in the inhibition of unwanted movements and cognitive processes (e.g., CAU).

Effective connectivity between emotional and motor brain regions in people with psychogenic nonepileptic seizures (PNES).

OBJECTIVE: To characterize the effective connectivity (EC) between the emotion and motor brain regions in patients with psychogenic nonepileptic seizures (PNES), based on resting-state spectral dynamic causal modeling (spDCM). METHODS: Twenty-three patients with PNES and twenty-five healthy control (HC) subjects underwent resting-state fMRI scanning. The coupling parameters indicating the causal interactions between eight brain regions associated with emotion, executive control, and motion were estimated for both groups, using resting-state fMRI spDCM. RESULTS: Compared to the HC subjects, in patients with PNES: (i) the left insula (INS) and left and right inferior frontal gyri (IFG) are more inhibited by the amygdala (AMYG), anterior cingulate cortex (ACC), and precentral gyrus (PCG); (ii) the left AMYG has greater inhibitory effects on the INS, IFG, dorsolateral prefrontal cortex (DLPFC), PCG, and supplementary motor area (SMA); (iii) the left ACC has more inhibitory effects on the INS and IFG; (iv) the right ACC is more inhibited by the INS and IFG, and has a less inhibitory effect on the SMA and PCG; and (v) the left caudate (CAU) had increased inhibitory effects on the AMYG and IFG and a more excitatory effect on the SMA. CONCLUSION: Our results suggest that in patients with PNES, the emotion-processing regions have inhibitory effects on the executive control areas and motor regions. Our findings may provide further insight into the influence of emotional arousal on functional movements and the underlying mechanisms of involuntary movements during functional seizures. Furthermore, they may suggest that emotion regulation through cognitive behavioral psychotherapies can be a potentially effective treatment modality.

Synthesis, biological evaluation and molecular docking studies of indeno [1, 2-c] pyrazol derivatives as inhibitors of mitochondrial malate dehydrogenase 2 (MDH2).

Hypoxia inducible factor-1 (HIF-1) is a pivotal transcription factor, which is strongly correlated with the induction of angiogenesis, tumor survival, metastasis, and cell proliferation, making it a pivotal therapeutic target for solid tumor therapeutic agents. Herein, a new series of multi-functional chemical probes were designed including principal groups, viz. adamantyl and indene, at various locations of the parent compound LW6. Molecular docking studies were performed on the designed compounds and their relationship with HIF-1α and malate dehydrogenase 2 (MDH2). Inhibition of MDH2 by our compounds was expected to decrease the NADH level. Indeed, treatment of the breast cancer cell line 4T1 led to a strong reduction of the NADH concentration. The greatest reduction in NADH production in mitochondria was observed with (E)-3-(4-((3r, 5r, 7r)-adamantan-1-yl) phenoxy)-N-(5-(piperidine-1-carbonyl)-1, 4-dihydroindeno [1, 2-c] pyrazol-3-yl) acrylamide (18: IC50 = 59 nM), and has the best inhibitory potential under hypoxic conditions (MCF-7: IC50 = 57 nM). This compound also gave one of the highest docking "higher than the score obtained with LW6 in parallel (-31.63 kcal/mol) in the initial docking runs (PDB Code: 4WLO). Other related compounds with good yields were also synthesized from docking results, and all the synthesized compounds (14, 18, 22, 26, 29, 30) were evaluated in vitro on human adenocarcinoma cell lines.

Susceptibility of Colistin-Resistant, Gram-Negative Bacteria to Antimicrobial Peptides and Ceragenins.

The susceptibility of colistin-resistant clinical isolates of Klebsiella pneumoniae to ceragenins and antimicrobial peptides (AMPs) suggests that there is little to no cross-resistance between colistin and ceragenins/AMPs and that lipid A modifications are found in bacteria with modest changes in susceptibility to ceragenins and with high levels of resistance to colistin. These results suggest that there are differences in the resistance mechanisms to colistin and ceragenins/AMPs.

A calcineurin antifungal strategy with analogs of FK506.

A novel antifungal strategy targeting the inhibition of calcineurin is described. To develop a calcineurin based inhibitor of pathogenic fungi, analogs of FK506 were synthesized that were able to permeate mammalian but not fungal cells. Antagonists in combination with FK506 were not immunosuppressive and retained antifungal activity in A. fumigatus. To reduce the dosage burden of the antagonist, murine oral PK was improved an order of magnitude relative to previous FK506 antagonists.

Safety of BTZ retreatment for patients with low-grade peripheral neuropathy during the initial treatment.

OBJECTIVE: Neuropathy is an important complication that may limit treatment options for patients with multiple myeloma. Previous studies have focused on treatment efficacy and have shown that retreatment with bortezomib (BTZ) is an effective treatment option. The goal of this study was to focus on the clinical manifestations of peripheral neuropathy (PN) and to retrospectively compare the incidence and severity of PN between the initial BTZ regimen and upon retreatment. Furthermore, this study evaluated how certain factors affect BIPN, which will help determine what conditions should be considered prior to retreatment. METHODS: Charts were reviewed from 93 patients who were retreated with a BTZ-containing regimen after previously being treated with this drug. RESULTS: Among the patients who developed PN, most patients in the study had low-grade neuropathy during the initial BTZ treatment (n = 52, 68%). The results showed no evidence of cumulative toxicity, and there was no significant difference in the incidence and severity of PN upon retreatment. Factors such as the presence of baseline PN, number of prior treatments, dose of BTZ, and comorbidities did not increase the severity of PN upon retreatment. The lapse of time between the two regimens also did not affect the severity of PN. CONCLUSION: The results suggest that retreatment with BTZ may be a feasible option, without additional risks of PN, for MM patients even with peripheral neuropathy during their initial treatment with this drug.

Total antioxidant status and lipid peroxidation with and without in vitro zinc supplementation in infertile men.

The aim of this study was to assess the total antioxidant capacity (TAC) and malondialdehyde (MDA) level in infertile men with asthenozoospermia and asthenoteratozoospermia compared to fertile donors, and to examine the effect of zinc on sperm lipid peroxidation and antioxidant status in infertile and fertile men. Semen samples provided by infertile men (n = 38) and fertile donors (controls; n = 12) were exposed to 6 mmol/L of zinc for 2 hr at 37°C. After semen analysis, lipid peroxidation was detected by MDA assay and seminal TAC was assessed by colorimetric method using TAS (total antioxidant status) Kit. TAC was significantly lower in infertile group compared to controls (p = .037). However, lipid peroxidation did not alter in infertile patients compared to controls (p > .05). After in vitro incubation of samples with zinc, a significant increase in TAC level was found only in infertile men (p < .001). Meanwhile, zinc had no effect on sperm lipid peroxidation in both fertile and infertile men (p > .05). Our data indicate that antioxidant treatment based on zinc in vitro supplementation may be helpful to enhance the rate of seminal antioxidant status in infertile men; however, it does not prevent sperm lipid peroxidation.

Assessment of human sperm DNA integrity using two cytochemical tests: Acridine orange test and toluidine blue assay.

Primary infertility affects approximately 15% of couples, with male factor infertility accounting for 50% of cases. Semen samples from 41 patients with asthenoteratospermia and 28 men with proven fertility were analysed according to World Health Organization guidelines. Abnormal sperm chromatin structure was assessed by toluidine blue assay (TBA), and DNA denaturation (DD) was detected by the acridine orange test (AOT). The mean (±SEM) rates of DD and abnormal chromatin structure were significantly higher in infertile subjects compared to fertile group respectively p = .003 and p < .001. A significant correlation was established between sperm DD and abnormal chromatin structure (R = .431, p < .001). Sperm DNA damage correlated significantly with abnormal morphology, sperm motility and necrozoospermia. Our study shows that men with increased levels of abnormal sperm chromatin structure have a high incidence of DNA denaturation and altered semen parameters. These findings suggest that male infertility has been linked to sperm DNA damage.

Facilitatory effects of anti-spastic medication on robotic locomotor training in people with chronic incomplete spinal cord injury.

BACKGROUND: The objective of this study was to investigate whether an anti-spasticity medication can facilitate the effects of robotic locomotor treadmill training (LTT) to improve gait function in people with incomplete spinal cord injury (SCI). METHODS: Individuals with chronic incomplete SCI were recruited and carried out a 4 week intervention of either locomotor treadmill training (LTT) alone (n = 26) or LTT combined with Tizanidine (TizLTT), an anti-spasticity medication (n = 22). Gait function was evaluated using clinical outcome measures of gait, speed and endurance. To better understand the underlying mechanisms of the therapeutic effects, maximal strength, active range of motion (AROM) and peak velocity (Vp) of ankle dorsi- and planter-flexor muscles were also measured. Differences were assessed using two-way mixed design analysis of variance. The number of subjects that achieved the minimal important difference (MID) for clinical scores was also measured for each group, and the results of those that did attain the MID were compared with those that did not. RESULTS: Both LTT and TizLTT resulted in significant improvements in walking speed and dorsiflexion maximum strength, with no significant differences between them, using group-averaging analysis. However, using the MID analysis, a higher proportion of subjects in the TizLTT group achieved the MID for walking speed (40%) compared with LTT alone (13%). Those that achieved the MID for walking speed were significantly higher functioning at baseline than those that did not in the TizLTT group, and the change in walking speed was associated with the change in dorsiflexion peak velocity (R(2) = 0.40; P < 0.05). CONCLUSION: Tizanidine appears to facilitate the effects of LTT on gait function in individuals with chronic SCI that are higher functioning at baseline. We speculate that this may be due to restoration of inhibitory mechanisms by Tizanidine, resulting in greater stretch in the planterflexor muscles during the LTT.

Outcome prediction modelling for trauma patients: a German perspective.

Prognostic models may have some clinical advantages when predicting the outcome of individual trauma patients is relevant. The variables that are predicted to have a negative effect on outcome in a model can also guide clinicians in their resuscitation attempt of trauma victims.

Meiotic segregation and sperm DNA fragmentation in Tunisian men with dysplasia of the fibrous sheath (DFS) associated with head abnormalities.

PURPOSE: Dysplasia of the Fibrous Sheath (DFS) is a primitive flagellar pathology for which a broad spectrum of ultrastructural flagellar abnormalities has been described responsible for a severe to total asthenozoospermia. To this phenotype other morphological abnormalities including cephalic and abnormalities in nuclear structure can be associated that could compromise embryonic development in case of use of Assisted Reproductive Technology (ART). The aim of this study was to evaluate the level of DNA fragmentation and aneuploidy rate in ejaculated spermatozoa of Tunisian men presented with DFS sperm defect associated to high percentage of head abnormalities and to compare the results with those from fertile men. METHODS: Sperm DNA fragmentation was evaluated by the terminal desoxynucleotidyl transferase mediated deoxyuridine triphosphate biotin nick-end labelling (TUNEL) assay. The study of meiotic segregation was performed by Fluorescence in situ hybridization (FISH) for chromosomes X, Y and 18. RESULTS: The mean DNA fragmentation index was significantly higher in patients compared to the control group. FISH revealed a significantly higher incidence of sperm aneuploidies compared with controls. All patients showed elevated frequencies of sex chromosomes disomy, disomy 18 and diploidy. CONCLUSIONS: In some cases of syndromic teratozoospermia due to sperm tail structural abnormalities, such as DFS, other morphological cephalic abnormalities may be associated. In these cases we have demonstrated impaired sperm nuclear quality which will affect the results in ICSI. Hence the interest of a thorough study of the sperm nucleus in these forms of infertility in order to predict the chances of success in ART.